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56 Commits

Author SHA1 Message Date
Roberto Cirillo 6334bb4224 Update 'pom.xml'
removed snapshot
2021-01-20 15:59:21 +01:00
Roberto Cirillo d1f61f1693 Update 'pom.xml'
added SNAPSHOT
2021-01-19 17:02:01 +01:00
Roberto Cirillo a1ae32f437 Update 'pom.xml'
update ecological-engine-smart-executor lower bound range
2021-01-19 16:50:15 +01:00
Roberto Cirillo cde6155c81 Update 'pom.xml'
update ecological-engine-external-algorithms lower bound range
2021-01-19 09:46:31 +01:00
lucio.lelii 2b719a7633 pom updated to remove old maven repositories 2021-01-18 20:01:26 +01:00
lucio.lelii d42448591d pom updated 2020-11-30 17:48:03 +01:00
lucio.lelii d9a6eb21be - EnviromentalVariableManager reverted
- import range changed for ecological-engine libraries
2020-11-30 17:39:25 +01:00
user1 279535c13a config Path can be set from EnvManager 2020-11-20 16:25:19 +01:00
Giancarlo Panichi 0a1de08b27 Updated descriptor.xml 2020-06-11 14:30:40 +02:00
Giancarlo Panichi a6e006439e ref 19423: DataMiner - Update DataMiner Service in Dev for support https
https://support.d4science.org/issues/19423

 Updated for support https protocol
2020-06-10 16:53:51 +02:00
Giancarlo Panichi 806effbd6f Renamed CHANGELOG.md 2020-06-10 15:21:32 +02:00
Giancarlo Panichi 6621bb20d9 Renamed CHANGELOG.md 2020-06-10 14:54:38 +02:00
Giancarlo Panichi 45ecff015d Renamed CHANGELOG.md 2020-06-10 14:44:17 +02:00
Giancarlo Panichi a24ecf41cb Renamed CHANGELOG.md 2020-06-10 14:42:03 +02:00
roberto cirillo 577a564b4d update to version 1.6.0:
removed snapshot, edit changelog.md
2020-05-14 17:13:57 +02:00
roberto cirillo cc1cece20e Merge branch 'master' of https://code-repo.d4science.org/gCubeSystem/dataminer.git 2020-05-12 15:23:53 +02:00
roberto cirillo c573360e2a added shub retry on InputManager class, getLocalFile method 2020-05-12 15:23:26 +02:00
roberto cirillo fdffbd6063 reverting retry in order to push another retry feature
Revert "Added Retry in Input Parameter URL retrieve for fix StorageHub sync."

This reverts commit 4d6318df92.
2020-05-12 15:18:23 +02:00
Giancarlo Panichi 4d6318df92 Added Retry in Input Parameter URL retrieve for fix StorageHub sync. 2020-05-12 11:24:31 +02:00
Giancarlo Panichi 34083f1357 ref 18289: the latest wps doesn't work
https://support.d4science.org/issues/18289

Rebuild Snapshot
2020-04-23 11:22:24 +02:00
Giancarlo Panichi a5223ecb43 Updated to Git and Jenkins 2019-11-28 18:50:01 +01:00
Giancarlo Panichi 08a56c02dd Updated to Git and Jenkins 2019-11-28 11:09:46 +01:00
Giancarlo Panichi c2acc48494 Updated to Git and Jenkins 2019-11-26 15:55:00 +01:00
Giancarlo Panichi 9360f1eaa5 Updated to support Git and Jenkins 2019-11-26 15:13:55 +01:00
Giancarlo Panichi a11cb3647f Updated to support Git and Jenkins 2019-11-26 15:11:49 +01:00
Giancarlo Panichi ea88169e41 Updated to Git and Jenkins 2019-11-25 16:15:04 +01:00
Giancarlo Panichi 6b8d28873b Updated to Git and Jenkins 2019-11-25 15:52:32 +01:00
Giancarlo Panichi f16dbd2f71 Updated to Git and Jenkins 2019-11-25 11:58:58 +01:00
Giancarlo Panichi 81ddc263d1 Updated to Git and Jenkins 2019-11-21 17:32:37 +01:00
Giancarlo Panichi 88bc383f3c Updated Pom to build the SNAPSHOT 2019-11-21 14:23:41 +01:00
Giancarlo Panichi 8d0d481e14 Updated to support Git and Jenkins 2019-11-20 17:23:42 +01:00
Giancarlo Panichi 9891b206a5 Updated to support Git and Jenkins 2019-11-20 17:19:23 +01:00
Giancarlo Panichi 790cff989c ref 18096: DataMiner - HTML file does not open in view widget but in a new browser window
https://support.d4science.org/issues/18096

Fixed Content-Type in output files

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@182280 82a268e6-3cf1-43bd-a215-b396298e98cf
2019-11-20 15:43:27 +00:00
Giancarlo Panichi 4d653662ce ref 17659: DataMiner - DataMiner Service - DataMiner service must create https links instead of http links for output parameters to avoid problems with the portal that uses https.
https://support.d4science.org/issues/17659

Fixed https link for output parameter

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@181938 82a268e6-3cf1-43bd-a215-b396298e98cf
2019-10-03 13:26:30 +00:00
Giancarlo Panichi 020c621a34 ref 13024: DataMiner - The service must support the https protocol
https://support.d4science.org/issues/13024

Updated DataMiner now support https

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@181937 82a268e6-3cf1-43bd-a215-b396298e98cf
2019-10-03 13:14:53 +00:00
Lucio Lelii f47693f27a git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@179537 82a268e6-3cf1-43bd-a215-b396298e98cf 2019-05-23 14:48:31 +00:00
Lucio Lelii ed556a9960 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@179518 82a268e6-3cf1-43bd-a215-b396298e98cf 2019-05-22 15:45:21 +00:00
Lucio Lelii 9d6794ffde git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@179069 82a268e6-3cf1-43bd-a215-b396298e98cf 2019-04-17 15:36:38 +00:00
Lucio Lelii 0adfa5b959 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@178855 82a268e6-3cf1-43bd-a215-b396298e98cf 2019-04-04 16:48:29 +00:00
Lucio Lelii fb6c980623 Added possibility to exclude single or all user to write to workspace
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@178710 82a268e6-3cf1-43bd-a215-b396298e98cf
2019-03-27 17:34:46 +00:00
Giancarlo Panichi fc5e616101 Fixed Jersey version in dependencies
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@176633 82a268e6-3cf1-43bd-a215-b396298e98cf
2019-01-17 11:11:46 +00:00
Giancarlo Panichi d3080c4052 ref 13024: DataMiner - The service must support the https protocol
https://support.d4science.org/issues/13024

Updated DataMiner now support https

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@174936 82a268e6-3cf1-43bd-a215-b396298e98cf
2018-12-17 15:07:07 +00:00
Giancarlo Panichi 34d131b900 Aligned Trunk to Branch
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@174213 82a268e6-3cf1-43bd-a215-b396298e98cf
2018-11-19 09:03:18 +00:00
Lucio Lelii 60ccac1784 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@174113 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-11-12 17:16:15 +00:00
Giancarlo Panichi 26ad1e8cc9 ref 12703: Public pages visualised by data miner services and proxies
https://support.d4science.org/issues/12703

Updated DataMiner service metadata info

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173657 82a268e6-3cf1-43bd-a215-b396298e98cf
2018-10-18 15:38:14 +00:00
Lucio Lelii bf7e31697d git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173645 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-10-18 08:00:09 +00:00
Lucio Lelii 3d509ae807 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173523 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-10-16 13:57:23 +00:00
Lucio Lelii 9013721e12 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173518 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-10-16 13:27:01 +00:00
Lucio Lelii 67fbb1f724 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173508 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-10-16 12:35:16 +00:00
Lucio Lelii fdda6ce838 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173507 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-10-16 12:11:26 +00:00
Lucio Lelii f6b3253459 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173502 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-10-16 09:57:30 +00:00
Lucio Lelii 8e7edbb075 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173499 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-10-15 17:41:21 +00:00
Lucio Lelii 30749c37e3 git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173393 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-10-12 14:19:28 +00:00
Lucio Lelii 908e7e57f4 EnvironmentVariableManager added
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173383 82a268e6-3cf1-43bd-a215-b396298e98cf
2018-10-12 13:53:36 +00:00
Lucio Lelii 607f49125c Removed special char "["and "]" from output omputation name
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@173249 82a268e6-3cf1-43bd-a215-b396298e98cf
2018-10-11 16:57:04 +00:00
Lucio Lelii c6676795ce git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@169188 82a268e6-3cf1-43bd-a215-b396298e98cf 2018-06-14 09:29:15 +00:00
75 changed files with 236 additions and 594 deletions

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@ -1,109 +1,15 @@
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@ -1,77 +1,71 @@
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
# Changelog for "dataminer"
## [v1.9.1-SNAPSHOT] - 2022-12-06
- Updated bom to latest version [#24209]
## [v1.9.0] - 2022-04-05
- Added support to new JWT token via URI Resolver [#23107]
## [v1.8.1] - 2022-03-21
- Update wps service to support not writing of the computation status to the user's workspace [#23054]
- Fixed protocol parameter when persistence is disabled
## [v1.8.0] - 2022-01-24
- Fixed max computations support [#22700]
## [v1.7.1] - 2021-05-24
- Fixed obsolete short urls [#20971]
# Changelog
## [v1.7.0] - 2020-11-20
- import range modified to resolve old repositories invalid url
## [v1.6.0] - 2020-05-12
### Fixes
- Added storagehub retry in InputsManager class, getLocalFile method [#19253]
## [v1.5.9] - 2019-11-20
### Fixes
- Fixed Content-Type support for files in the results of computations [#18096]
## [v1.5.8] - 2019-10-01
### Fixes
- Fixed https link for output parameter [#17659]
## [v1.5.7] - 2019-03-01
### Features
- Updated https support [#13024]
## [v1.5.2] - 2017-12-13
### Fixes
- added the right extension on output file
- lock file created on execution
## [v1.5.1] - 2017-09-14
### Features
- added accounting on algorithm execution
## [v1.5.0] - 2017-07-31
### Features
- service interface classes moved to wps project
## [v1.1.0] - 2016-10-03
- First Release
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

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@ -37,4 +37,12 @@ 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 see [FUNDING.md](FUNDING.md)
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);

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<assembly
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
<id>servicearchive</id>
<formats>
<format>tar.gz</format>
</formats>
<baseDirectory>/</baseDirectory>
<fileSets>
<fileSet>
<outputDirectory>/</outputDirectory>
<useDefaultExcludes>true</useDefaultExcludes>
<includes>
<include>README.md</include>
<include>LICENSE.md</include>
<include>CHANGELOG.md</include>
<include>FUNDING.md</include>
<include>profile.xml</include>
</includes>
<fileMode>755</fileMode>
<filtered>true</filtered>
</fileSet>
</fileSets>
<files>
<file>
<source>target/${build.finalName}.${project.packaging}</source>
<outputDirectory>/${artifactId}</outputDirectory>
</file>
</files>
</assembly>

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<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
@ -10,10 +9,10 @@
</parent>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>dataminer</artifactId>
<version>1.9.1-SNAPSHOT</version>
<version>1.7.0</version>
<name>dataminer</name>
<description>An e-Infrastructure service providing state-of-the art DataMining algorithms and ecological modelling approaches under the Web Processing Service (WPS) standard.</description>
<scm>
<connection>scm:git:https://code-repo.d4science.org/gCubeSystem/${project.artifactId}.git</connection>
<developerConnection>scm:git:https://code-repo.d4science.org/gCubeSystem/${project.artifactId}.git</developerConnection>
@ -40,14 +39,14 @@
</roles>
</developer>
</developers>
<properties>
<webappDirectory>${project.build.directory}/${project.build.finalName}</webappDirectory>
<distroDirectory>distro</distroDirectory>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
</properties>
<dependencyManagement>
<!-- Old solution <dependencies> <dependency> <groupId>org.gcube.distribution</groupId>
<artifactId>maven-smartgears-bom</artifactId> <version>2.1.0</version> <type>pom</type>
@ -56,14 +55,14 @@
<dependency>
<groupId>org.gcube.distribution</groupId>
<artifactId>gcube-bom</artifactId>
<version>2.1.0-SNAPSHOT</version>
<version>2.0.0</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<!-- https://mvnrepository.com/artifact/org.reflections/reflections-maven -->
<dependency>
@ -107,7 +106,7 @@
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-geospatial-extensions</artifactId>
<version>[1.5.2,2.0.0-SNAPSHOT)</version>
<version>[1.5.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
<exclusions>
<exclusion>
<artifactId>log4j</artifactId>
@ -118,12 +117,12 @@
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-external-algorithms</artifactId>
<version>[1.2.2,2.0.0-SNAPSHOT)</version>
<version>[1.2.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-smart-executor</artifactId>
<version>[1.6.5,2.0.0-SNAPSHOT)</version>
<version>[1.6.5-SNAPSHOT,2.0.0-SNAPSHOT)</version>
<exclusions>
<exclusion>
<groupId>org.glassfish.jersey.core</groupId>
@ -146,7 +145,6 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
@ -164,10 +162,12 @@
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>storagehub-client-library</artifactId>
<version>[1.0.0, 2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>storagehub-model</artifactId>
<version>[1.0.0, 2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>

View File

@ -1,30 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<Resource>
<ID></ID>
<Type>Service</Type>
<Profile>
<Description>${project.description}</Description>
<Class>DataAnalysis</Class>
<Name>${project.name}</Name>
<Version>1.0.0</Version>
<Packages>
<Software>
<Name>${project.name}</Name>
<Description>${project.description}</Description>
<Version>${version}</Version>
<MavenCoordinates>
<groupId>${project.groupId}</groupId>
<artifactId>${project.artifactId}</artifactId>
<version>${project.version}</version>
</MavenCoordinates>
<Type>Service</Type>
<Files>
<File>${project.build.finalName}.${project.packaging}</File>
</Files>
</Software>
</Packages>
</Profile>
</Resource>

View File

@ -1,67 +0,0 @@
package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.is;
import java.util.List;
import org.gcube.common.resources.gcore.ServiceEndpoint;
import org.gcube.common.resources.gcore.ServiceEndpoint.Runtime;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.resources.discovery.client.api.DiscoveryClient;
import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
import org.gcube.resources.discovery.icclient.ICFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class InformationSystemUtils {
private static final Logger LOGGER = LoggerFactory.getLogger(InformationSystemUtils.class);
private static final String URI_RESOLVER_SERVICE_CATEGORY = "Service";
private static final String URI_RESOLVER_SERVICE_NAME = "HTTP-URI-Resolver";
public static String retrieveUriResolverOat(String scope) throws Exception {
try {
LOGGER.info("Retrieve URI Resolver Oat Service Info");
if (scope == null || scope.length() == 0) {
String error="Invalid request scope: " + scope;
LOGGER.error(error);
throw new Exception(error);
}
ScopeProvider.instance.set(scope);
SimpleQuery query = ICFactory.queryFor(ServiceEndpoint.class);
query.addCondition("$resource/Profile/Category/text() eq '" + URI_RESOLVER_SERVICE_CATEGORY + "'")
.addCondition("$resource/Profile/Name/text() eq '" + URI_RESOLVER_SERVICE_NAME + "'")
.setResult("$resource/Profile/RunTime");
DiscoveryClient<Runtime> client = ICFactory.clientFor(Runtime.class);
List<Runtime> runtimeList = client.submit(query);
String serviceAddress = null;
if (runtimeList != null && !runtimeList.isEmpty()) {
for (int i = 0; i < runtimeList.size(); i++) {
Runtime accessPoint = runtimeList.get(i);
if (accessPoint != null) {
StringBuilder sb=new StringBuilder();
sb.append("https://");
sb.append(accessPoint.hostedOn());
sb.append("/oat/get");
serviceAddress=sb.toString();
break;
}
}
} else {
String error="RuntimeList error: "+runtimeList;
LOGGER.error(error);
throw new Exception(error);
}
LOGGER.info("Uri Resolver Oat Service Info: " + serviceAddress);
return serviceAddress;
} catch (Throwable e) {
LOGGER.error("Error in discovery Uri Resolver Oat Service Endpoint in scope: " + scope);
LOGGER.error(e.getLocalizedMessage(),e);
throw e;
}
}
}

View File

@ -48,16 +48,10 @@ import org.n52.wps.server.AbstractAnnotatedAlgorithm;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm implements Observable, Cancellable {
private static final int COMPUTATION_WAIT_FOR_RUN_REQUEST = 20000;
public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm implements Observable, Cancellable{
/**
* Deploying procedure: 1 - modify configuration files 2 - modify resource file:
* resources/templates/setup.cfg 3 - generate classes with ClassGenerator 4 -
* add new classes in the wps_config.xml on the wps web app config folder 5 -
* produce the Jar file of this project 6 - copy the jar file in the lib folder
* of the wps web app change the server parameters in the wps_config.xml file
* Deploying procedure: 1 - modify configuration files 2 - modify resource file: resources/templates/setup.cfg 3 - generate classes with ClassGenerator 4 - add new classes in the wps_config.xml on the wps web app config folder 5 - produce the Jar file of this project 6 - copy the jar file in the lib folder of the wps web app change the server parameters in the wps_config.xml file
*/
private static final Logger LOGGER = LoggerFactory.getLogger(AbstractEcologicalEngineMapper.class);
@ -65,11 +59,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
private Observer observer = null;
private boolean cancelled = false;
private TokenManager tokenm = null;
private EnvironmentVariableManager env = null;
// inputs and outputs
public LinkedHashMap<String, Object> inputs = new LinkedHashMap<String, Object>();
public LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>();
@ -86,41 +80,30 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
this.wpsExternalID = wpsExternalID;
}
private static synchronized void addComputation(String session, String user) {
public static synchronized void addComputation(String session, String user) {
runningcomputations.put(session, user);
}
private static synchronized void removeComputation(String session) {
public static synchronized void removeComputation(String session) {
runningcomputations.remove(session);
}
private static synchronized int getRuningComputations() {
public static synchronized int getRuningComputations() {
return runningcomputations.size();
}
private static synchronized String displayRunningComputations() {
public static synchronized String displayRunningComputations() {
return runningcomputations.toString();
}
private void waitForResources(String computationSession, String username, String scope) throws Exception {
while (waitCondition(computationSession, username, scope)) {
Thread.sleep(COMPUTATION_WAIT_FOR_RUN_REQUEST);
public void waitForResources() throws Exception {
while (getRuningComputations() > ConfigurationManager.getMaxComputations()) {
Thread.sleep(20000);
LOGGER.debug("Waiting for resources to be available: " + displayRunningComputations());
}
}
private static synchronized boolean waitCondition(String computationSession, String username, String scope) {
if (getRuningComputations() >= ConfigurationManager.getMaxComputations()) {
return true;
} else {
// add the computation to the global list of computations
LOGGER.debug("Add computation to run: {}", computationSession);
addComputation(computationSession, username + ":" + scope);
return false;
}
}
// inner objects
public AlgorithmConfiguration config;
public InfrastructureDialoguer infrastructureDialoguer;
@ -222,7 +205,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
LOGGER.debug("Could not drop Temporary Table: " + table + " table is null");
}
} catch (Exception e) {
LOGGER.error("error deleting temporary table", e);
LOGGER.error("error deleting temporary table",e);
} finally {
DatabaseUtils.closeDBConnection(dbConnection);
}
@ -265,16 +248,14 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
float previousStatus = -3;
String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
public void updateStatus(float status, boolean canWrite) {
if (agent != null) {
if (status != previousStatus) {
LOGGER.debug("STATUS update to: {} ", status);
LOGGER.debug("STATUS update to: {} ", status );
previousStatus = status;
super.update(new Integer((int) status));
try {
if (canWrite)
updateComputationOnWS(status, null);
if (canWrite) updateComputationOnWS(status, null);
} catch (Exception e) {
LOGGER.warn("error updating compution on WS");
}
@ -286,18 +267,17 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
public void setEnvironmentVariableManager(EnvironmentVariableManager env) {
this.env = env;
}
public void updateComputationOnWS(float status, String exception) {
updateComputationOnWS(status, exception, null, null);
}
class RunDataspaceManager implements Runnable {
class RunDataspaceManager implements Runnable{
List<StoredData> inputData;
List<File> generatedData;
public RunDataspaceManager(List<StoredData> inputData, List<File> generatedData) {
this.inputData = inputData;
this.generatedData = generatedData;
public RunDataspaceManager(List<StoredData> inputData, List<File> generatedData){
this.inputData=inputData;
this.generatedData=generatedData;
}
public void run() {
@ -306,35 +286,36 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
LOGGER.debug("Dataspace->Status updater->Writing computational info on the WS asyncronously");
manager.writeRunningComputationData();
} catch (Exception ez) {
LOGGER.error("Dataspace->Status updater->Impossible to write computation information on the Workspace",
ez);
LOGGER.error("Dataspace->Status updater->Impossible to write computation information on the Workspace",ez);
}
}
};
public void updateComputationOnWS(float status, String exception, List<StoredData> inputData,
List<File> generatedData) {
public void updateComputationOnWS(float status, String exception, List<StoredData> inputData, List<File> generatedData) {
if (currentComputation != null) {
currentComputation.setStatus("" + status);
if (exception != null && exception.length() > 0)
currentComputation.setException(exception);
LOGGER.debug("RunDataspaceManager: [inputData=" + inputData + ", generatedData=" + generatedData + "]");
RunDataspaceManager rundm = new RunDataspaceManager(inputData, generatedData);
LOGGER.debug("RunDataspaceManager: [inputData="+inputData+", generatedData="+generatedData+"]");
RunDataspaceManager rundm = new RunDataspaceManager(inputData,generatedData);
rundm.run();
/*
* Thread t = new Thread(rundm); t.start();
Thread t = new Thread(rundm);
t.start();
*/
}
}
@Execute
public void run() throws Exception {
if (observer != null)
if (observer!=null)
observer.isStarted(this);
LOGGER.info("classloader context in this thread is {}", Thread.currentThread().getContextClassLoader());
LOGGER.info("classloader context in this thread is {}",Thread.currentThread().getContextClassLoader());
long startTimeLong = System.currentTimeMillis();
OperationResult operationResult = null;
@ -343,8 +324,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
List<String> generatedInputTables = null;
List<String> generatedOutputTables = null;
List<File> generatedFiles = null;
// String date = new
// java.text.SimpleDateFormat("dd_MM_yyyy_HH:mm:ss").format(System.currentTimeMillis());
//String date = new java.text.SimpleDateFormat("dd_MM_yyyy_HH:mm:ss").format(System.currentTimeMillis());
String computationSession = this.getAlgorithmClass().getSimpleName() + "_ID_" + UUID.randomUUID().toString();
if (wpsExternalID != null) {
LOGGER.info("Using wps External ID " + wpsExternalID);
@ -352,19 +332,16 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
} else
LOGGER.info("Wps External ID not set");
InputsManager inputsManager = null;
ConfigurationManager configManager = new ConfigurationManager(this.env); // initializes
// parameters
// from
// web.xml
ConfigurationManager configManager = new ConfigurationManager(this.env); // initializes parameters from web.xml
manageUserToken();
boolean canWriteOnShub = checkWriteAuthorization(tokenm.getUserName());
Path dir = Paths.get(System.getProperty("java.io.tmpdir"), "dmlocks");
if (!Files.exists(dir))
dir = Files.createDirectory(dir);
Path lockFile = Files.createTempFile(dir, "dm", ".lck");
LOGGER.info("lock file created {}", lockFile.toUri().toURL());
LOGGER.info("lock file created {}",lockFile.toUri().toURL());
try {
// wait for server resources to be available
@ -378,17 +355,17 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
config = configManager.getConfig();
LOGGER.info("Configured algorithm with session " + computationSession);
time("Configuration");
waitForResources(computationSession, configManager.getUsername(), configManager.getScope());
waitForResources();
LOGGER.info("Running algorithm with session " + computationSession);
time("Waiting time for resources to be free");
// add the computation to the global list of computations
addComputation(computationSession, configManager.getUsername() + ":" + configManager.getScope());
String scope = configManager.getScope();
String username = configManager.getUsername();
LOGGER.info("1 - Algorithm environment initialized in scope " + scope + " with user name " + username
+ " and session " + computationSession);
LOGGER.info("Max allowed computations " + ConfigurationManager.getMaxComputations() + " using storage "
+ ConfigurationManager.useStorage());
LOGGER.info("1 - Algorithm environment initialized in scope " + scope + " with user name " + username + " and session " + computationSession);
LOGGER.info("Max allowed computations " + ConfigurationManager.getMaxComputations() + " using storage " + ConfigurationManager.useStorage());
// init the infrastructure dialoguer
LOGGER.info("2 - Initializing connection to the e-Infrastructure");
infrastructureDialoguer = new InfrastructureDialoguer(scope);
@ -415,7 +392,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
// adding service parameters to the configuration
LOGGER.info("5 - Adding Service parameters to the configuration");
List<StatisticalType> dataminerInputParameters = getInputParameters(algorithm);
LOGGER.debug("Dataminer Algo Default InputParameters: " + dataminerInputParameters);
LOGGER.debug("Dataminer Algo Default InputParameters: "+dataminerInputParameters);
inputsManager.addInputServiceParameters(dataminerInputParameters, infrastructureDialoguer);
time("Service parameters added to the algorithm");
// merging wps with ecological engine parameters - modifies the
@ -423,9 +400,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
LOGGER.info("6 - Translating WPS Inputs into Ecological Engine Inputs");
LOGGER.debug("Operator class is " + this.getClass().getCanonicalName());
// build computation Data
currentComputation = new ComputationData(config.getTaskID(), config.getAgent(), "", "", startTime, "-", "0",
config.getTaskID(), configManager.getUsername(), config.getGcubeScope(),
this.getClass().getCanonicalName());
currentComputation = new ComputationData(config.getTaskID(), config.getAgent(), "", "", startTime, "-", "0", config.getTaskID(), configManager.getUsername(), config.getGcubeScope(), this.getClass().getCanonicalName());
inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo, dataminerInputParameters);
generatedInputTables = inputsManager.getGeneratedTables();
generatedFiles = inputsManager.getGeneratedInputFiles();
@ -477,16 +452,14 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
time("Output preparation for WPS document (no storage manager)");
outputmanager.shutdown();
LOGGER.debug("12 - Final Computation Output");
LOGGER.debug("Outputs: " + outputs);
LOGGER.debug("Outputs: "+ outputs);
endTime = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
if (!isCancelled()) {
LOGGER.debug("Save Computation Data");
if (canWriteOnShub)
saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent,
generatedFiles);
if (canWriteOnShub) saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent, generatedFiles);
} else {
LOGGER.debug("Computation interrupted - no update");
throw new Exception("Computation cancelled");
@ -495,26 +468,21 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
operationResult = OperationResult.SUCCESS;
} catch (Exception e) {
operationResult = OperationResult.FAILED;
LOGGER.error("Error execution Algorithm {}", algorithm, e);
LOGGER.error("Error execution Algorithm {}",algorithm,e);
int exitstatus = -2;
if (isCancelled())
exitstatus = -1;
if (inputsManager != null)
if (canWriteOnShub)
updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(),
generatedFiles);
else if (canWriteOnShub)
updateComputationOnWS(exitstatus, e.getMessage());
if (canWriteOnShub) updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(), generatedFiles);
else
if (canWriteOnShub) updateComputationOnWS(exitstatus, e.getMessage());
if (isCancelled())
throw new Exception("Computation cancelled");
else
throw e;
} finally {
LOGGER.debug("accounting algorithm");
if (operationResult == null) {
operationResult = OperationResult.FAILED;
}
accountAlgorithmExecution(startTimeLong, System.currentTimeMillis(), operationResult);
LOGGER.debug("Deleting Input Tables");
deleteTemporaryTables(generatedInputTables);
@ -528,8 +496,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
time("Cleaning of resources");
displayTimes();
cleanResources();
if (observer != null)
observer.isFinished(this);
if (observer!=null) observer.isFinished(this);
LOGGER.debug("All done - Computation Finished");
Files.deleteIfExists(lockFile);
}
@ -537,63 +504,53 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
}
private boolean checkWriteAuthorization(String username) {
if (env != null) {
if (env.getShubUsersExcluded() != null) {
if (env.getShubUsersExcluded().isEmpty()) {
// all users write
return true;
}
if (env.getShubUsersExcluded().contains(username)) {
return false;
} else {
// username write
return true;
}
} else {
//This is the * case, no users write.
if (env!=null && env.getShubUsersExcluded()!=null) {
if (env.getShubUsersExcluded().isEmpty()) {
return false;
}
if (env.getShubUsersExcluded().contains(username)) {
return false;
}
} else {
return false;
}
return true;
}
private void accountAlgorithmExecution(long start, long end, OperationResult result) {
try {
try{
JobUsageRecord jobUsageRecord = new JobUsageRecord();
jobUsageRecord.setJobName(this.getAlgorithmClass().getSimpleName());
jobUsageRecord.setConsumerId(tokenm.getUserName());
jobUsageRecord.setDuration(end - start);
jobUsageRecord.setDuration(end-start);
jobUsageRecord.setOperationResult(result);
jobUsageRecord.setServiceName("DataMiner");
jobUsageRecord.setServiceClass("WPS");
jobUsageRecord.setHost(WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
jobUsageRecord.setCallerQualifier(tokenm.getTokenQualifier());
AccountingPersistence accountingPersistence = AccountingPersistenceFactory.getPersistence();
AccountingPersistence accountingPersistence =
AccountingPersistenceFactory.getPersistence();
accountingPersistence.account(jobUsageRecord);
} catch (Throwable e) {
LOGGER.error("error accounting algorithm execution", e);
}catch(Throwable e){
LOGGER.error("error accounting algorithm execution",e);
}
}
public class StatusUpdater implements Runnable {
private boolean canWrite = true;
public StatusUpdater(boolean canWrite) {
this.canWrite = canWrite;
}
@Override
public void run() {
while (agent != null && !isCancelled() && agent.getStatus() < 100) {
try {
updateStatus(agent.getStatus(), canWrite);
Thread.sleep(10000);
} catch (InterruptedException e) {
}
} catch (InterruptedException e) {}
}
LOGGER.info("Status updater terminated");
}
@ -607,19 +564,15 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
LOGGER.debug("Provenance manager running");
}
private void saveComputationOnWS(List<StoredData> inputData, List<StoredData> outputData, ComputationalAgent agent,
List<File> generatedFiles) {
private void saveComputationOnWS(List<StoredData> inputData, List<StoredData> outputData, ComputationalAgent agent, List<File> generatedFiles) {
LOGGER.debug("Save Computation On WS");
LOGGER.debug("InputData: " + inputData);
LOGGER.debug("OutputData: " + outputData);
LOGGER.debug("Agent: " + agent);
LOGGER.debug("Generated files: " + generatedFiles);
LOGGER.debug("InputData: "+inputData);
LOGGER.debug("OutputData: "+outputData);
LOGGER.debug("Agent: "+agent);
LOGGER.debug("Generated files: "+generatedFiles);
LOGGER.debug("Provenance manager started for operator " + this.getClass().getCanonicalName());
ComputationData computation = new ComputationData(config.getTaskID(), config.getAgent(), agent.getDescription(),
agent.getInfrastructure().name(), startTime, endTime, "100", config.getTaskID(),
config.getParam(ConfigurationManager.serviceUserNameParameterVariable), config.getGcubeScope(),
this.getClass().getCanonicalName());
ComputationData computation = new ComputationData(config.getTaskID(), config.getAgent(), agent.getDescription(), agent.getInfrastructure().name(), startTime, endTime, "100", config.getTaskID(), config.getParam(ConfigurationManager.serviceUserNameParameterVariable), config.getGcubeScope(), this.getClass().getCanonicalName());
// post on WS
DataspaceManager manager = new DataspaceManager(config, computation, inputData, outputData, generatedFiles);
@ -684,8 +637,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
public static List<String> command(final String cmdline, final String directory) {
try {
Process process = new ProcessBuilder(new String[] { "bash", "-c", cmdline }).redirectErrorStream(true)
.directory(new File(directory)).start();
Process process = new ProcessBuilder(new String[] { "bash", "-c", cmdline }).redirectErrorStream(true).directory(new File(directory)).start();
List<String> output = new ArrayList<String>();
BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));
@ -706,16 +658,16 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
@Override
public void setObserver(Observer o) {
LOGGER.debug("setting observer in {} ", wpsExternalID);
this.observer = o;
LOGGER.debug("setting observer in {} ",wpsExternalID);
this.observer = o;
}
@Override
public synchronized boolean cancel() {
if (!cancelled) {
LOGGER.debug("COMPUTATION INTERRUPTED! ({})", wpsExternalID);
try {
if (agent != null) {
if (!cancelled){
LOGGER.debug("COMPUTATION INTERRUPTED! ({})",wpsExternalID);
try{
if (agent!=null){
agent.shutdown();
agent = null;
}
@ -728,12 +680,12 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
}
System.gc();
cancelled = true;
} catch (Exception e) {
LOGGER.warn("error cancelling computation with id {}", wpsExternalID);
}catch(Exception e){
LOGGER.warn("error cancelling computation with id {}",wpsExternalID);
return false;
}
} else {
LOGGER.debug("COMPUTATION ALREADY INTERRUPT! ({})", wpsExternalID);
LOGGER.debug("COMPUTATION ALREADY INTERRUPT! ({})",wpsExternalID);
return false;
}
return true;

View File

@ -22,24 +22,25 @@ public class ConfigurationManager {
public static String usernameParameter = "user.name";
public static String scopeParameter = "scope";
public static String tokenParameter = "usertoken";
public static String defaultScope = "/gcube/devsec";
public static String defaultUsername = "statistical.wps";
public static String defaultScope= "/gcube/devsec";
public static String defaultUsername= "statistical.wps";
private static Integer maxComputations = null;
private static Boolean useStorage = null;
static boolean simulationMode = false;
EnvironmentVariableManager env = null;
public static synchronized Integer getMaxComputations() {
public static synchronized Integer getMaxComputations(){
return maxComputations;
}
public static synchronized Boolean useStorage() {
public static synchronized Boolean useStorage(){
return useStorage;
}
public static synchronized Boolean isSimulationMode() {
public static synchronized Boolean isSimulationMode(){
return simulationMode;
}
@ -56,12 +57,12 @@ public class ConfigurationManager {
options.load(is);
is.close();
maxComputations = Integer.parseInt(options.getProperty("maxcomputations"));
logger.info("setting max computation to {}", maxComputations);
logger.info("setting max computation to {}",maxComputations);
useStorage = Boolean.parseBoolean(options.getProperty("saveond4sstorage"));
simulationMode = Boolean.parseBoolean(options.getProperty("simulationMode"));
simulationMode=Boolean.parseBoolean(options.getProperty("simulationMode"));
}
} catch (Exception e) {
logger.error("error initializing properties", e);
logger.error("error initializing properties",e);
}
}
@ -79,8 +80,7 @@ public class ConfigurationManager {
}
public ConfigurationManager(EnvironmentVariableManager env) {
if (env == null)
inizializePropertiesUsingTemplateFile();
if (env == null) inizializePropertiesUsingTemplateFile();
else {
maxComputations = env.getMaxComputation();
useStorage = env.isSaveOnStorage();
@ -92,7 +92,7 @@ public class ConfigurationManager {
return config;
}
public void setComputationId(String computationId) {
public void setComputationId(String computationId){
config.setTaskID(computationId);
}
@ -108,31 +108,29 @@ public class ConfigurationManager {
configPath = "./cfg/";
persistencePath = "./";
}
logger.debug("Taking configuration from {}", configPath);
// + " and persistence in " + persistencePath);
logger.debug("Taking configuration from {}", configPath);
//+ " and persistence in " + persistencePath);
// setting configuration and logger
config.setPersistencePath(configPath);
config.setConfigPath(configPath);
config.setNumberOfResources(1);
// setting application paths
String protocol = WPSConfig.getInstance().getWPSConfig().getServer().getProtocol();
String webapp = WPSConfig.getInstance().getWPSConfig().getServer().getWebappPath();
String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
String port = WPSConfig.getInstance().getWPSConfig().getServer().getHostport();
logger.debug("Protocol: {} , Host: {} , Port: {} , Webapp: {} ", protocol, host, port, webapp);
logger.info("Web Path Persistence: {}", webperspath);
logger.debug("Host: {} Port: {} Webapp: {} ", host, port, webapp );
logger.debug("Web persistence path:{} ", webperspath);
String webPath = protocol + "://" + host + ":" + port + "/" + webapp + "/persistence/";
String webPath = "http://" + host + ":" + port + "/" + webapp + "/persistence/";
// logger.debug("Env Vars: \n"+System.getenv());
logger.info("Web Path Persistence Url: {}", webPath);
logger.debug("Web app path: {} ", webPath);
// retrieving scope
scope = (String) inputs.get(scopeParameter);
logger.debug("Retrieved scope: {} ", scope);
logger.debug("Retrieved scope: {} ", scope);
if (scope == null)
throw new Exception(
"Error: scope parameter (scope) not set! This violates e-Infrastructure security policies");
throw new Exception("Error: scope parameter (scope) not set! This violates e-Infrastructure security policies");
if (!scope.startsWith("/"))
scope = "/" + scope;
@ -143,8 +141,7 @@ public class ConfigurationManager {
logger.debug("User token used by the client:{} ", token);
if (username == null || username.trim().length() == 0)
throw new Exception(
"Error: user name parameter (user.name) not set! This violates e-Infrastructure security policies");
throw new Exception("Error: user name parameter (user.name) not set! This violates e-Infrastructure security policies");
if (token == null || token.trim().length() == 0)
throw new Exception("Error: token parameter not set! This violates e-Infrastructure security policies");

View File

@ -34,16 +34,16 @@ public class TableTemplatesMapper {
public void linksMapping(){
linksMap = new HashMap<String, String>();
linksMap.put(TableTemplates.HSPEN.name(), "(HSPEN) https://data.d4science.net/kLeQ");
linksMap.put(TableTemplates.HCAF.name(), "(HCAF) https://data.d4science.net/AhwE");
linksMap.put(TableTemplates.HSPEC.name(),"(HSPEC) https://data.d4science.net/TNCR");
linksMap.put(TableTemplates.OCCURRENCE_AQUAMAPS.name(), "(OCCURRENCE_AQUAMAPS) https://data.d4science.net/Un3H");
linksMap.put(TableTemplates.OCCURRENCE_SPECIES.name(), "(OCCURRENCE_SPECIES) https://data.d4science.net/wKRW");
linksMap.put(TableTemplates.MINMAXLAT.name(), "(MINMAXLAT) https://data.d4science.net/fPFQ");
linksMap.put(TableTemplates.TRAININGSET.name(), "(TRAININGSET) https://data.d4science.net/NgvU");
linksMap.put(TableTemplates.TESTSET.name(), "(TESTSET) https://data.d4science.net/EpjE");
linksMap.put(TableTemplates.CLUSTER.name(), "(CLUSTER) https://data.d4science.net/XN7z");
linksMap.put(TableTemplates.TIMESERIES.name(), "(TIMESERIES) https://data.d4science.net/5g4F");
linksMap.put(TableTemplates.HSPEN.name(), "(HSPEN) http://goo.gl/4zDiAK");
linksMap.put(TableTemplates.HCAF.name(), "(HCAF) http://goo.gl/SZG9uM");
linksMap.put(TableTemplates.HSPEC.name(),"(HSPEC) http://goo.gl/OvKa1h");
linksMap.put(TableTemplates.OCCURRENCE_AQUAMAPS.name(), "(OCCURRENCE_AQUAMAPS) http://goo.gl/vHil5T");
linksMap.put(TableTemplates.OCCURRENCE_SPECIES.name(), "(OCCURRENCE_SPECIES) http://goo.gl/4ExuR5");
linksMap.put(TableTemplates.MINMAXLAT.name(), "(MINMAXLAT) http://goo.gl/cRzwgN");
linksMap.put(TableTemplates.TRAININGSET.name(), "(TRAININGSET) http://goo.gl/Br44UQ");
linksMap.put(TableTemplates.TESTSET.name(), "(TESTSET) http://goo.gl/LZHNXt");
linksMap.put(TableTemplates.CLUSTER.name(), "(CLUSTER) http://goo.gl/PnKhhb");
linksMap.put(TableTemplates.TIMESERIES.name(), "(TIMESERIES) http://goo.gl/DoW6fg");
linksMap.put(TableTemplates.GENERIC.name(), "(GENERIC) A generic comma separated csv file in UTF-8 encoding");
}

View File

@ -2,122 +2,59 @@ package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping;
import static org.gcube.common.authorization.client.Constants.authorizationService;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
import javax.ws.rs.core.Response;
import org.gcube.common.authorization.library.AuthorizationEntry;
import org.gcube.common.authorization.library.provider.AccessTokenProvider;
import org.gcube.common.authorization.library.provider.AuthorizationProvider;
import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.is.InformationSystemUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class TokenManager {
private static final Logger LOGGER = LoggerFactory.getLogger(TokenManager.class);
private static final Logger LOGGER= LoggerFactory.getLogger(TokenManager.class);
String username;
String scope;
String token;
String tokenQualifier;
public String getScope() {
public String getScope(){
return scope;
}
public String getUserName() {
public String getUserName(){
return username;
}
public String getToken() {
public String getToken(){
return token;
}
public String getTokenQualifier() {
return tokenQualifier;
}
public void getCredentials() {
try {
LOGGER.info("Retrieving token credentials");
// get username from SmartGears
try{
LOGGER.debug("Retrieving token credentials");
//get username from SmartGears
username = AuthorizationProvider.instance.get().getClient().getId();
token = SecurityTokenProvider.instance.get();
if (token == null || token.isEmpty()) {
String jwtToken = AccessTokenProvider.instance.get();
scope = ScopeProvider.instance.get();
token = getGcubeTokenFromUriResolver(jwtToken, scope);
}
AuthorizationEntry entry = authorizationService().get(token);
scope = entry.getContext();
tokenQualifier = entry.getQualifier();
} catch (Exception e) {
LOGGER.error("Error Retrieving token credentials: "+e.getLocalizedMessage(),e);
}catch(Exception e){
LOGGER.error("Error Retrieving token credentials ",e);
scope = null;
username = null;
username= null;
}
if ((scope == null || username == null) && ConfigurationManager.isSimulationMode()) {
if ((scope==null || username==null) && ConfigurationManager.isSimulationMode()){
scope = ConfigurationManager.defaultScope;
username = ConfigurationManager.defaultUsername;
}
LOGGER.info("Retrieved scope: {} Username: {} Token {} SIMULATION MODE: {} ", scope, username, token,
ConfigurationManager.isSimulationMode());
LOGGER.debug("Retrieved scope: {} Username: {} Token {} SIMULATION MODE: {} ",scope, username, token, ConfigurationManager.isSimulationMode());
}
public String getGcubeTokenFromUriResolver(String jwtToken, String scope) throws Exception {
String gcubeToken = null;
String uriResolverOatURL = InformationSystemUtils.retrieveUriResolverOat(scope);
try {
LOGGER.info("Create Request: "+ uriResolverOatURL);
URL urlObj = new URL(uriResolverOatURL);
HttpURLConnection connection = (HttpURLConnection) urlObj.openConnection();
connection.setRequestMethod("GET");
connection.setRequestProperty("Authorization", "Bearer " + jwtToken);
connection.setDoOutput(true);
try (AutoCloseable conc = () -> connection.disconnect()) {
int responseCode = connection.getResponseCode();
LOGGER.info("Response Code: " + responseCode);
if (Response.Status.fromStatusCode(responseCode).compareTo(Response.Status.OK) == 0) {
try (InputStream ins = connection.getInputStream();
BufferedReader in = new BufferedReader(new InputStreamReader(ins))) {
String inputLine = null;
while ((inputLine = in.readLine()) != null) {
break;
}
gcubeToken = inputLine;
}
} else {
String error = "Invalid Response Code retrieving GCube Token from Uri Resolver: " + responseCode;
LOGGER.error(error);
try (InputStream ins = connection.getErrorStream();
BufferedReader in = new BufferedReader(new InputStreamReader(ins))) {
String inputLine = null;
while ((inputLine = in.readLine()) != null) {
LOGGER.error(inputLine);
}
}
throw new Exception(error);
}
}
} catch (IOException e) {
LOGGER.error("Error retrieving GcubeToken from Uri Resolver: "+e.getLocalizedMessage());
e.printStackTrace();
throw e;
}
LOGGER.info("Retrieved GcubeToken: "+gcubeToken);
return gcubeToken;
}
}

View File

@ -64,7 +64,7 @@ public class DataspaceManager implements Runnable {
public static String payload = "payload";
private String statusComputationName;
private static final String STATUS_POSTFIX = "-STATUS";
private static final String STATUS_POSTFIX="-STATUS";
public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData,
List<StoredData> outputData, List<File> generatedFiles) {
@ -73,7 +73,7 @@ public class DataspaceManager implements Runnable {
this.inputData = inputData;
this.outputData = outputData;
this.generatedFiles = generatedFiles;
this.statusComputationName = this.computation.id + STATUS_POSTFIX;
this.statusComputationName = this.computation.id+STATUS_POSTFIX;
LOGGER.debug("DataspaceManager [config=" + config + ", computation=" + computation + ", inputData=" + inputData
+ ", outputData=" + outputData + ", generatedFiles=" + generatedFiles + "]");
@ -142,26 +142,25 @@ public class DataspaceManager implements Runnable {
}
public String uploadData(StoredData data, FolderContainer destinationFolder, boolean changename) throws Exception {
LOGGER.debug("Dataspace->Uploaddata:"
+ " [data={},destinationFolder={}, changename={}] ", data, destinationFolder,
changename);
LOGGER.debug("Dataspace->Analysing " + data);
// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name,
// wsFolder);
String filenameonwsString = data.name;
if (changename)
filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId, getExtension(data.payload));
filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId,
getExtension(data.payload));
InputStream in = null;
String url = "";
try {
// long size = 0;
//long size = 0;
if (data.type.equals("text/csv") || data.type.equals("application/d4science")
|| data.type.equals("image/png")) {
if (new File(data.payload).exists() || !data.payload.startsWith("http")) {
LOGGER.debug("Dataspace->Uploading file {}", data.payload);
in = new FileInputStream(new File(data.payload));
// size = new File(data.payload).length();
//size = new File(data.payload).length();
} else {
LOGGER.debug("Dataspace->Uploading via URL {}", data.payload);
int tries = 10;
@ -189,7 +188,7 @@ public class DataspaceManager implements Runnable {
// LOGGER.debug("Dataspace->final file name on ws " +
// data.name+" description "+data.description);
LOGGER.debug("Dataspace->WS OP saving the following file on the WS: " + filenameonwsString);
LOGGER.debug("Dataspace->WS OP saving the following file on the WS " + filenameonwsString);
Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(computation_id, data.computationId);
@ -204,11 +203,9 @@ public class DataspaceManager implements Runnable {
properties.put(payload, url);
FileContainer fileContainer = destinationFolder.uploadFile(in, filenameonwsString, data.description);
LOGGER.debug("Dataspace->WS OP file uploaded on WS: " + filenameonwsString);
Metadata metadata = new Metadata(properties);
fileContainer.setMetadata(metadata);
fileContainer.setMetadata(new Metadata(properties));
LOGGER.debug("Dataspace->WS OP file set metadata: " + metadata);
LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString);
url = fileContainer.getPublicLink().toString();
LOGGER.debug("Dataspace->WS OP url produced for the file " + url);
@ -398,9 +395,10 @@ public class DataspaceManager implements Runnable {
}
/*
* List<String> scopes = new ArrayList<String>();
* scopes.add(config.getGcubeScope()); ws.createGcubeItem(computation.id,
* computation.operatorDescription, scopes, computation.user, itemType,
* properties, newcomputationFolder.getId());
* scopes.add(config.getGcubeScope());
* ws.createGcubeItem(computation.id, computation.operatorDescription,
* scopes, computation.user, itemType, properties,
* newcomputationFolder.getId());
*/
newcomputationFolder.setMetadata(new Metadata(properties));
@ -467,8 +465,8 @@ public class DataspaceManager implements Runnable {
List<String> scopes = new ArrayList<String>();
scopes.add(config.getGcubeScope());
// TODO: update gcubeItem not recreate it...
//TODO: update gcubeItem not recreate it...
GCubeItem gcubeItem = new GCubeItem();
gcubeItem.setName(this.statusComputationName);
gcubeItem.setDescription(computation.operatorDescription);
@ -511,8 +509,7 @@ public class DataspaceManager implements Runnable {
.getContainers().get(0);
LOGGER.debug("Dataspace->removing computation data");
List<ItemContainer<? extends Item>> wi = computationContainer.findByName(this.statusComputationName)
.getContainers();
List<ItemContainer<? extends Item>> wi = computationContainer.findByName(this.statusComputationName).getContainers();
if (!wi.isEmpty()) {
for (ItemContainer<? extends Item> container : wi) {
boolean retry = false;
@ -520,23 +517,25 @@ public class DataspaceManager implements Runnable {
try {
container.forceDelete();
retry = false;
} catch (ItemLockedException e) {
}catch (ItemLockedException e) {
LOGGER.warn("item locked, retrying");
Thread.sleep(1000);
retry = true;
}
} while (retry);
}while (retry);
}
} else
LOGGER.debug("Dataspace->Warning Could not find {} under {}", this.statusComputationName,
computationContainer.get().getName());
/*
* TODO: ASK GIANPAOLO int maxtries = 3; int i =1; while
* (ws.exists(computation.id,computationsFolderWs.getId()) && i<maxtries){
* LOGGER.debug("Dataspace->computation data still exist... retrying "+i );
* Thread.sleep(1000); computationsFolderWs.find(computation.id).remove(); i++;
* }
* (ws.exists(computation.id,computationsFolderWs.getId()) &&
* i<maxtries){
* LOGGER.debug("Dataspace->computation data still exist... retrying "+i
* ); Thread.sleep(1000);
* computationsFolderWs.find(computation.id).remove(); i++; }
*/
LOGGER.debug("Dataspace->finished removing computation data ");
@ -545,7 +544,7 @@ public class DataspaceManager implements Runnable {
// TODO
public static String getExtension(String payload) {
LOGGER.debug("DataSpace->Get Extension from: " + payload);
String extension = "";
String extension="";
if (payload.toLowerCase().startsWith("http")) {
try {
URL obj = new URL(payload);

0
src/main/resources/templates/classtemplate.properties Executable file → Normal file
View File

0
src/main/resources/templates/setup.cfg Executable file → Normal file
View File

View File

View File

@ -1,26 +0,0 @@
package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping;
import org.apache.log4j.BasicConfigurator;
import org.junit.Test;
public class TokenManagerTest {
private static final String JWT_TOKEN = "";
private static final String SCOPE = "/gcube/devsec/devVRE";
@Test
public void retrieveTokenFromUriResolver() throws Exception {
try {
BasicConfigurator.configure();
System.out.println("Test Retrieve Token From Uri Resolver");
TokenManager tm = new TokenManager();
String token = tm.getGcubeTokenFromUriResolver(JWT_TOKEN, SCOPE);
System.out.println("GcubeToken retrieved: "+token);
} catch (Exception e) {
System.out.println(e.getLocalizedMessage());
e.getStackTrace();
}
}
}

View File

@ -30,7 +30,7 @@ public class AlgorithmTest {
String protocol = "http";
String hostname = "dataminer-genericworkers.d4science.org";
String token = "xxx-xxx-xxx-xxx";
String token = "257800d8-24bf-4bae-83cd-ea99369e7dd6-843339462";
String layerID = "08ee0d70-4d8b-4f42-8b06-d709482bca95";
Iterator<String> uris = getUrisIterator();

View File

@ -18,8 +18,13 @@ public class MultiThreadingCalls {
// http://statistical-manager-new.d4science.org:8080/wps/WebProcessingService?request=Execute&service=WPS&version=1.0.0&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIONYM_LOCAL&DataInputs=scope=/gcube/devsec/devVRE;user.name=tester;SpeciesAuthorName=Gadus%20morhua;Taxa_Authority_File=ASFIS;Parser_Name=SIMPLE;Activate_Preparsing_Processing=true;Use_Stemmed_Genus_and_Species=false;Accuracy_vs_Speed=MAX_ACCURACY;Matcher_1=GSAy;Threshold_1=0.6;MaxResults_1=10
// final URL urlToCall = new URL("http://"+host+":8080/wps/WebProcessingService?request=Execute&service=WPS&version=1.0.0&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.modellers.FEED_FORWARD_ANN&DataInputs=" +
// URLEncoder.encode("scope=/gcube/devsec;user.name=test.user;LayersNeurons=10|10;LearningThreshold=0.01;MaxIterations=100;ModelName=wps_ann;Reference=1;TargetColumn=depthmean;TrainingColumns=depthmin|depthmax;TrainingDataSet=http://goo.gl/juNsCK@MimeType=text/csv","UTF-8"));
/*
final URL urlToCall = new URL("http://"+host+"/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token=4ccc2c35-60c9-4c9b-9800-616538d5d48b&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.XMEANS&DataInputs=" +
URLEncoder.encode("OccurrencePointsClusterLabel=OccClustersTest;min_points=1;maxIterations=100;minClusters=1;maxClusters=3;OccurrencePointsTable=http://goo.gl/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;","UTF-8"));
*/
final URL urlToCall = new URL("http://dataminer1-devnext.d4science.org/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token=f9d49d76-cd60-48ed-9f8e-036bcc1fc045-98187548&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SUBMITQUERY&DataInputs=" +
URLEncoder.encode("DatabaseName=fishbase;Query=select * from food limit 100;Apply Smart Correction=false;Language=POSTGRES;ResourceName=FishBase;Read-Only Query=true;","UTF-8"));

View File

@ -42,6 +42,7 @@ public class TestMappedEvaluators {
public void testQualityAnalysis() throws Exception{
HRS algorithm = new HRS();
// http://localhost:8080/wps/WebProcessingService?request=Execute&service=WPS&version=1.0.0&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.QUALITY_ANALYSIS&DataInputs=user.name=test.user;scope=/gcube/devsec;NegativeCasesTableKeyColumn=csquarecode;DistributionTableProbabilityColumn=probability;PositiveCasesTableKeyColumn=csquarecode;PositiveThreshold=0.8;PositiveCasesTable=http://goo.gl/DEYAbT;DistributionTableKeyColumn=csquarecode;DistributionTable=http://goo.gl/DEYAbT;NegativeThreshold=0.3;NegativeCasesTable=http://goo.gl/DEYAbT;
// algorithm.setScope("/gcube/devsec");

52
src/test/resources/AlgorithmTestURIs.txt Executable file → Normal file
View File

@ -5,58 +5,58 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ESRI_GRID_EXTRACTION&DataInputs=Layer={LAYERID};YResolution=0.5;XResolution=0.5;BBox_LowerLeftLong=-50;BBox_UpperRightLat=60;BBox_LowerLeftLat=-60;BBox_UpperRightLong=50;Z=0;TimeIndex=0;
#DBSCAN
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.DBSCAN
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.DBSCAN&DataInputs=OccurrencePointsClusterLabel=OccClustersTest;epsilon=10;min_points=1;OccurrencePointsTable={PROTOCOL}://brokenlink/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.DBSCAN&DataInputs=OccurrencePointsClusterLabel=OccClustersTest;epsilon=10;min_points=1;OccurrencePointsTable={PROTOCOL}://goo.gl/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;
#KMEANS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.KMEANS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.KMEANS&DataInputs=OccurrencePointsClusterLabel=OccClustersTest;k=3;max_runs=100;min_points=1;max_optimization_steps=10;OccurrencePointsTable={PROTOCOL}://brokenlink/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.KMEANS&DataInputs=OccurrencePointsClusterLabel=OccClustersTest;k=3;max_runs=100;min_points=1;max_optimization_steps=10;OccurrencePointsTable={PROTOCOL}://goo.gl/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;
#LOF
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.LOF
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.LOF&DataInputs=FeaturesColumnNames=depthmean|sstmnmax|salinitymean;PointsClusterLabel=OccClustersTest;minimal_points_lower_bound=2;PointsTable={PROTOCOL}://brokenlink/VDzpch;minimal_points_upper_bound=10;distance_function=euclidian distance;lof_threshold=2;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.LOF&DataInputs=FeaturesColumnNames=depthmean|sstmnmax|salinitymean;PointsClusterLabel=OccClustersTest;minimal_points_lower_bound=2;PointsTable={PROTOCOL}://goo.gl/VDzpch;minimal_points_upper_bound=10;distance_function=euclidian distance;lof_threshold=2;
#XMEANS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.XMEANS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.XMEANS&DataInputs=OccurrencePointsClusterLabel=OccClustersTest;min_points=1;maxIterations=100;minClusters=1;maxClusters=3;OccurrencePointsTable={PROTOCOL}://brokenlink/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.XMEANS&DataInputs=OccurrencePointsClusterLabel=OccClustersTest;min_points=1;maxIterations=100;minClusters=1;maxClusters=3;OccurrencePointsTable={PROTOCOL}://goo.gl/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;
#BIONYM
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.generators.BIONYM
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.generators.BIONYM&DataInputs=Matcher_1=LEVENSHTEIN;Matcher_4=NONE;Matcher_5=NONE;Matcher_2=NONE;Matcher_3=NONE;Threshold_1=0.6;RawTaxaNamesTable={PROTOCOL}://brokenlink/N9e3pC;Threshold_2=0.6;Accuracy_vs_Speed=MAX_ACCURACY;MaxResults_2=10;MaxResults_1=10;Threshold_3=0.4;RawNamesColumn=species;Taxa_Authority_File=FISHBASE;Parser_Name=SIMPLE;OutputTableLabel=bionymwps;MaxResults_4=0;Threshold_4=0;MaxResults_3=0;MaxResults_5=0;Threshold_5=0;Use_Stemmed_Genus_and_Species=false;Activate_Preparsing_Processing=true;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.generators.BIONYM&DataInputs=Matcher_1=LEVENSHTEIN;Matcher_4=NONE;Matcher_5=NONE;Matcher_2=NONE;Matcher_3=NONE;Threshold_1=0.6;RawTaxaNamesTable={PROTOCOL}://goo.gl/N9e3pC;Threshold_2=0.6;Accuracy_vs_Speed=MAX_ACCURACY;MaxResults_2=10;MaxResults_1=10;Threshold_3=0.4;RawNamesColumn=species;Taxa_Authority_File=FISHBASE;Parser_Name=SIMPLE;OutputTableLabel=bionymwps;MaxResults_4=0;Threshold_4=0;MaxResults_3=0;MaxResults_5=0;Threshold_5=0;Use_Stemmed_Genus_and_Species=false;Activate_Preparsing_Processing=true;
#BIONYM_LOCAL
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIONYM_LOCAL
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIONYM_LOCAL&DataInputs=Matcher_1=LEVENSHTEIN;Matcher_4=NONE;Matcher_5=NONE;Matcher_2=NONE;Matcher_3=NONE;Threshold_1=0.6;Threshold_2=0.6;Accuracy_vs_Speed=MAX_ACCURACY;MaxResults_2=10;MaxResults_1=10;Threshold_3=0.4;Taxa_Authority_File=FISHBASE;Parser_Name=SIMPLE;MaxResults_4=0;Threshold_4=0;MaxResults_3=0;MaxResults_5=0;Threshold_5=0;Use_Stemmed_Genus_and_Species=false;Activate_Preparsing_Processing=true;SpeciesAuthorName=Gadus morhua
#ABSENCE CELLS FROM AQUAMAPS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ABSENCE_CELLS_FROM_AQUAMAPS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ABSENCE_CELLS_FROM_AQUAMAPS&DataInputs=Number_of_Points=20;Table_Label=hcaf_filtered_wps;Aquamaps_HSPEC={PROTOCOL}://brokenlink/24XrmE;Take_Randomly=true;Species_Code=Fis-30189;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ABSENCE_CELLS_FROM_AQUAMAPS&DataInputs=Number_of_Points=20;Table_Label=hcaf_filtered_wps;Aquamaps_HSPEC={PROTOCOL}://goo.gl/24XrmE;Take_Randomly=true;Species_Code=Fis-30189;
#HCAF_FILTER
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.HCAF_FILTER
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.HCAF_FILTER&DataInputs=B_Box_Left_Lower_Lat=-17;B_Box_Right_Upper_Long=147;B_Box_Right_Upper_Lat=25;B_Box_Left_Lower_Long=89;Table_Label=wps_hcaf_filter;
#MAX_ENT_NICHE_MODELLING
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.MAX_ENT_NICHE_MODELLING
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.MAX_ENT_NICHE_MODELLING&DataInputs=LongitudeColumn=decimallongitude;LatitudeColumn=decimallatitude;Z=0;Layers={LAYERID};TimeIndex=0;MaxIterations=100;SpeciesName=Latimeria%20chalumnae;DefaultPrevalence=0.5;YResolution=0.5;OccurrencesTable=http://brokenlink/5cnKKp;XResolution=0.5;OutputTableLabel=wps_maxent;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.MAX_ENT_NICHE_MODELLING&DataInputs=LongitudeColumn=decimallongitude;LatitudeColumn=decimallatitude;Z=0;Layers={LAYERID};TimeIndex=0;MaxIterations=100;SpeciesName=Latimeria%20chalumnae;DefaultPrevalence=0.5;YResolution=0.5;OccurrencesTable=http://goo.gl/5cnKKp;XResolution=0.5;OutputTableLabel=wps_maxent;
#OCCURRENCE_ENRICHMENT
#{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.OCCURRENCE_ENRICHMENT
#{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.OCCURRENCE_ENRICHMENT&DataInputs=OptionalFilter=%20;OutputTableName=wps_enriched;FeaturesNames=temp;OccurrenceTable=http://brokenlink/ZfFcfE;LongitudeColumn=decimallongitude;LatitudeColumn=decimallatitude;ScientificNameColumn=scientificname;Layers={LAYERID};TimeColumn=eventdate;Resolution=0.5;
#{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.OCCURRENCE_ENRICHMENT&DataInputs=OptionalFilter=%20;OutputTableName=wps_enriched;FeaturesNames=temp;OccurrenceTable=http://goo.gl/ZfFcfE;LongitudeColumn=decimallongitude;LatitudeColumn=decimallatitude;ScientificNameColumn=scientificname;Layers={LAYERID};TimeColumn=eventdate;Resolution=0.5;
#PRESENCE_CELLS_GENERATION
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.PRESENCE_CELLS_GENERATION
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.PRESENCE_CELLS_GENERATION&DataInputs=Number_of_Points=20;Table_Label=hcaf_filtered_wps;Species_Code=Fis-30189;
#FAO_OCEAN_AREA_COLUMN_CREATOR
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.FAO_OCEAN_AREA_COLUMN_CREATOR
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.FAO_OCEAN_AREA_COLUMN_CREATOR&DataInputs=Resolution=5;Latitude_Column=decimallatitude;InputTable={PROTOCOL}://brokenlink/sdlD5a;Longitude_Column=decimallongitude;OutputTableName=wps_fao_area_column;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.FAO_OCEAN_AREA_COLUMN_CREATOR&DataInputs=Resolution=5;Latitude_Column=decimallatitude;InputTable={PROTOCOL}://goo.gl/sdlD5a;Longitude_Column=decimallongitude;OutputTableName=wps_fao_area_column;
#FAO_OCEAN_AREA_COLUMN_CREATOR_FROM_QUADRANT
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.FAO_OCEAN_AREA_COLUMN_CREATOR_FROM_QUADRANT
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.FAO_OCEAN_AREA_COLUMN_CREATOR_FROM_QUADRANT&DataInputs=Resolution=5;InputTable={PROTOCOL}://brokenlink/yJTIBZ;Longitude_Column=centerlong;Quadrant_Column=quadrant;OutputTableName=wps_fao_quadrant;Latitude_Column=centerlat;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.FAO_OCEAN_AREA_COLUMN_CREATOR_FROM_QUADRANT&DataInputs=Resolution=5;InputTable={PROTOCOL}://goo.gl/yJTIBZ;Longitude_Column=centerlong;Quadrant_Column=quadrant;OutputTableName=wps_fao_quadrant;Latitude_Column=centerlat;
#CSQUARE_COLUMN_CREATOR
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.CSQUARE_COLUMN_CREATOR
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.CSQUARE_COLUMN_CREATOR&DataInputs=CSquare_Resolution=0.1;Latitude_Column=decimallatitude;InputTable={PROTOCOL}://brokenlink/sdlD5a;Longitude_Column=decimallongitude;OutputTableName=wps_csquare_column;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.CSQUARE_COLUMN_CREATOR&DataInputs=CSquare_Resolution=0.1;Latitude_Column=decimallatitude;InputTable={PROTOCOL}://goo.gl/sdlD5a;Longitude_Column=decimallongitude;OutputTableName=wps_csquare_column;
#GENERIC_CHARTS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GENERIC_CHARTS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GENERIC_CHARTS&DataInputs=Quantities=fvalue;InputTable={PROTOCOL}://brokenlink/lWTvcw;TopElementsNumber=10;Attributes=x|y
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GENERIC_CHARTS&DataInputs=Quantities=fvalue;InputTable={PROTOCOL}://goo.gl/lWTvcw;TopElementsNumber=10;Attributes=x|y
#GEO_CHART
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GEO_CHART
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GEO_CHART&DataInputs=Latitude=y;Quantities=x;Longitude=x;InputTable={PROTOCOL}://brokenlink/lWTvcw
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GEO_CHART&DataInputs=Latitude=y;Quantities=x;Longitude=x;InputTable={PROTOCOL}://goo.gl/lWTvcw
#TIME_GEO_CHART
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_GEO_CHART
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_GEO_CHART&DataInputs=Time=time;Latitude=x;Longitude=y;Quantities=fvalue;InputTable={PROTOCOL}://brokenlink/lWTvcw;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_GEO_CHART&DataInputs=Time=time;Latitude=x;Longitude=y;Quantities=fvalue;InputTable={PROTOCOL}://goo.gl/lWTvcw;
#TIME_SERIES_CHARTS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_SERIES_CHARTS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_SERIES_CHARTS&DataInputs=Attributes=x|y|z;Quantities=fvalue;InputTable={PROTOCOL}://brokenlink/lWTvcw;Time=time
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_SERIES_CHARTS&DataInputs=Attributes=x|y|z;Quantities=fvalue;InputTable={PROTOCOL}://goo.gl/lWTvcw;Time=time
#OBIS_SPECIES_OBSERVATIONS_PER_MEOW_AREA
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SPECIES_OBSERVATION_MEOW_AREA_PER_YEAR
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SPECIES_OBSERVATION_MEOW_AREA_PER_YEAR&DataInputs=Selected species=Gadus morhua;End_year=2015;Start_year=2000;Area_type=NORTH SEA;
@ -80,16 +80,16 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.MOST_OBSERVED_TAXA&DataInputs=Level=GENUS;Taxa_number=10;End_year=2015;Start_year=2000;
#TIME_SERIES_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_SERIES_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_SERIES_ANALYSIS&DataInputs=FFT_Window_Samples=12;SSA_Points_to_Forecast=3;AggregationFunction=SUM;TimeSeriesTable={PROTOCOL}://brokenlink/lWTvcw;Sensitivity=LOW;SSA_Window_in_Samples=12;SSA_EigenvaluesThreshold=0.7;ValueColum=fvalue
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_SERIES_ANALYSIS&DataInputs=FFT_Window_Samples=12;SSA_Points_to_Forecast=3;AggregationFunction=SUM;TimeSeriesTable={PROTOCOL}://goo.gl/lWTvcw;Sensitivity=LOW;SSA_Window_in_Samples=12;SSA_EigenvaluesThreshold=0.7;ValueColum=fvalue
#MAPS_COMPARISON
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.MAPS_COMPARISON
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.MAPS_COMPARISON&DataInputs=TimeIndex_1=0;ValuesComparisonThreshold=0.1;TimeIndex_2=0;Z=0;KThreshold=0.5;Layer_1=483a4a32-729e-422b-b5e4-49f27ba93ec2;Layer_2=483a4a32-729e-422b-b5e4-49f27ba93ec2;
#QUALITY_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.QUALITY_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.QUALITY_ANALYSIS&DataInputs=NegativeCasesTableKeyColumn=csquarecode;DistributionTableProbabilityColumn=probability;PositiveCasesTableKeyColumn=csquarecode;PositiveThreshold=0.8;PositiveCasesTable={PROTOCOL}://brokenlink/8zWU7u;DistributionTableKeyColumn=csquarecode;DistributionTable={PROTOCOL}://brokenlink/cXbg2n;NegativeThreshold=0.3;NegativeCasesTable={PROTOCOL}://brokenlink/8zWU7u;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.QUALITY_ANALYSIS&DataInputs=NegativeCasesTableKeyColumn=csquarecode;DistributionTableProbabilityColumn=probability;PositiveCasesTableKeyColumn=csquarecode;PositiveThreshold=0.8;PositiveCasesTable={PROTOCOL}://goo.gl/8zWU7u;DistributionTableKeyColumn=csquarecode;DistributionTable={PROTOCOL}://goo.gl/cXbg2n;NegativeThreshold=0.3;NegativeCasesTable={PROTOCOL}://goo.gl/8zWU7u;
#DISCREPANCY_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.DISCREPANCY_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.DISCREPANCY_ANALYSIS&DataInputs=ComparisonThreshold=0.1;SecondTable={PROTOCOL}://brokenlink/cXbg2n;FirstTable={PROTOCOL}://brokenlink/BBk8iB;KThreshold=0.5;MaxSamples=10000;FirstTableProbabilityColumn=probability;SecondTableProbabilityColumn=probability;FirstTableCsquareColumn=csquarecode;SecondTableCsquareColumn=csquarecode
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.DISCREPANCY_ANALYSIS&DataInputs=ComparisonThreshold=0.1;SecondTable={PROTOCOL}://goo.gl/cXbg2n;FirstTable={PROTOCOL}://goo.gl/BBk8iB;KThreshold=0.5;MaxSamples=10000;FirstTableProbabilityColumn=probability;SecondTableProbabilityColumn=probability;FirstTableCsquareColumn=csquarecode;SecondTableCsquareColumn=csquarecode
#XYEXTRACTOR
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.XYEXTRACTOR
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.XYEXTRACTOR&DataInputs=OutputTableLabel=wps_xy_extractor;Layer={LAYERID};YResolution=0.5;XResolution=0.5;BBox_LowerLeftLong=-50;BBox_UpperRightLat=60;BBox_LowerLeftLat=-60;BBox_UpperRightLong=50;Z=0;TimeIndex=0;
@ -101,22 +101,22 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ZEXTRACTION&DataInputs=OutputTableLabel=wps_z_extractor;Layer={LAYERID};Resolution=100;Y=38;TimeIndex=0;X=28
#XYEXTRACTOR_TABLE
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.XYEXTRACTOR_TABLE
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.XYEXTRACTOR_TABLE&DataInputs=TimeIndex=0;Z=0;filter= ;zColumn=lme;timeColumn=lme;xColumn=centerlong;yColumn=centerlat;geoReferencedTableName={PROTOCOL}://brokenlink/KjWYQG;valueColumn=oceanarea;XResolution=0.5;YResolution=0.5;BBox_UpperRightLong=50;BBox_LowerLeftLat=-60;BBox_LowerLeftLong=-50;BBox_UpperRightLat=60;OutputTableLabel=wps_xy_extr_table;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.XYEXTRACTOR_TABLE&DataInputs=TimeIndex=0;Z=0;filter= ;zColumn=lme;timeColumn=lme;xColumn=centerlong;yColumn=centerlat;geoReferencedTableName={PROTOCOL}://goo.gl/KjWYQG;valueColumn=oceanarea;XResolution=0.5;YResolution=0.5;BBox_UpperRightLong=50;BBox_LowerLeftLat=-60;BBox_LowerLeftLong=-50;BBox_UpperRightLat=60;OutputTableLabel=wps_xy_extr_table;
#TIMEEXTRACTION_TABLE
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIMEEXTRACTION_TABLE
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIMEEXTRACTION_TABLE&DataInputs=Z=0;Resolution=0.5;filter= ;zColumn=lme;timeColumn=lme;xColumn=centerlong;yColumn=centerlat;Y=3.75;X=102.25;geoReferencedTableName={PROTOCOL}://brokenlink/VDzpch;valueColumn=centerlong;SamplingFreq=-1;OutputTableLabel=wps_time_extr_table;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIMEEXTRACTION_TABLE&DataInputs=Z=0;Resolution=0.5;filter= ;zColumn=lme;timeColumn=lme;xColumn=centerlong;yColumn=centerlat;Y=3.75;X=102.25;geoReferencedTableName={PROTOCOL}://goo.gl/VDzpch;valueColumn=centerlong;SamplingFreq=-1;OutputTableLabel=wps_time_extr_table;
#ZEXTRACTION_TABLE
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ZEXTRACTION_TABLE
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ZEXTRACTION_TABLE&DataInputs=TimeIndex=0;Resolution=1;filter= ;zColumn=centerlong;xColumn=centerlong;yColumn=centerlat;Y=0.25;X=0.25;geoReferencedTableName={PROTOCOL}://brokenlink/VDzpch;valueColumn=oceanarea;OutputTableLabel=wps_z_table;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ZEXTRACTION_TABLE&DataInputs=TimeIndex=0;Resolution=1;filter= ;zColumn=centerlong;xColumn=centerlong;yColumn=centerlat;Y=0.25;X=0.25;geoReferencedTableName={PROTOCOL}://goo.gl/VDzpch;valueColumn=oceanarea;OutputTableLabel=wps_z_table;
#HRS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.HRS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.HRS&DataInputs=PositiveCasesTable={PROTOCOL}://brokenlink/VDzpch;NegativeCasesTable={PROTOCOL}://brokenlink/VDzpch;OptionalCondition= ;ProjectingAreaTable={PROTOCOL}://brokenlink/VDzpch;FeaturesColumns=depthmin|depthmax;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.HRS&DataInputs=PositiveCasesTable={PROTOCOL}://goo.gl/VDzpch;NegativeCasesTable={PROTOCOL}://goo.gl/VDzpch;OptionalCondition= ;ProjectingAreaTable={PROTOCOL}://goo.gl/VDzpch;FeaturesColumns=depthmin|depthmax;
#SGVM_INTERPOLATION
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SGVM_INTERPOLATION
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SGVM_INTERPOLATION&DataInputs=headingAdjustment=0;maxspeedThr=6;minspeedThr=2;fm=0.5;margin=10;distscale=20;res=100;sigline=0.2;interval=120;equalDist=true;InputFile={PROTOCOL}://brokenlink/i16kPw;npoints=10;method=cHs;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SGVM_INTERPOLATION&DataInputs=headingAdjustment=0;maxspeedThr=6;minspeedThr=2;fm=0.5;margin=10;distscale=20;res=100;sigline=0.2;interval=120;equalDist=true;InputFile={PROTOCOL}://goo.gl/i16kPw;npoints=10;method=cHs;
#BIOCLIMATE_HCAF
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIOCLIMATE_HCAF
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIOCLIMATE_HCAF&DataInputs=HCAF_Table_List={PROTOCOL}://brokenlink/LTqufC|{PROTOCOL}://brokenlink/LTqufC;HCAF_Table_Names=h1|h2
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIOCLIMATE_HCAF&DataInputs=HCAF_Table_List={PROTOCOL}://goo.gl/LTqufC|{PROTOCOL}://goo.gl/LTqufC;HCAF_Table_Names=h1|h2
#BIOCLIMATE_HSPEN
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIOCLIMATE_HSPEN
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIOCLIMATE_HSPEN&DataInputs=HSPEN_Table_List={PROTOCOL}://data-d.d4science.org/dDRpendoOEpnUE5nRzM4WHQ3RWVlVUorb3lwa2wzNWJHbWJQNStIS0N6Yz0|{PROTOCOL}://data-d.d4science.org/dDRpendoOEpnUE5nRzM4WHQ3RWVlVUorb3lwa2wzNWJHbWJQNStIS0N6Yz0;HSPEN_Table_Names=h1|h2;
@ -131,7 +131,7 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.modellers.FEED_FORWARD_ANN&DataInputs=TrainingDataSet={PROTOCOL}://data-d.d4science.org/UndsT051bEZwbEpnRzM4WHQ3RWVlVDQ0eHNITWgzRXdHbWJQNStIS0N6Yz0;TrainingColumns=a|b;TargetColumn=t;LayersNeurons=1;Reference=1;LearningThreshold=0.001;MaxIterations=1000;ModelName=neuralnet_t;
#FEED_FORWARD_A_N_N_DISTRIBUTION
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.generators.FEED_FORWARD_A_N_N_DISTRIBUTION
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.generators.FEED_FORWARD_A_N_N_DISTRIBUTION&DataInputs=FeaturesTable={PROTOCOL}://data-d.d4science.org/UndsT051bEZwbEpnRzM4WHQ3RWVlVDQ0eHNITWgzRXdHbWJQNStIS0N6Yz0;FeaturesColumnNames=a|b;FinalTableLabel=Distrib_t;ModelName={PROTOCOL}://brokenlink/ggiPyX;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.generators.FEED_FORWARD_A_N_N_DISTRIBUTION&DataInputs=FeaturesTable={PROTOCOL}://data-d.d4science.org/UndsT051bEZwbEpnRzM4WHQ3RWVlVDQ0eHNITWgzRXdHbWJQNStIS0N6Yz0;FeaturesColumnNames=a|b;FinalTableLabel=Distrib_t;ModelName={PROTOCOL}://goo.gl/ggiPyX;
#OCCURRENCES_DUPLICATES_DELETER
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.OCCURRENCES_DUPLICATES_DELETER
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.OCCURRENCES_DUPLICATES_DELETER&DataInputs=final_Table_Name=DeletedOcc_;OccurrencePointsTableName={PROTOCOL}://data-d.d4science.org/KzI1TmN5TCtJT2hnRzM4WHQ3RWVlZlZLdCttTThpUnRHbWJQNStIS0N6Yz0;longitudeColumn=decimalLongitude;latitudeColumn=decimalLatitude;recordedByColumn=recordedBy;scientificNameColumn=scientificName;eventDateColumn=eventDate;lastModificationColumn=modified;spatialTolerance=0.5;confidence=80;
@ -170,7 +170,7 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.RASTER_DATA_PUBLISHER&DataInputs=PublicationLevel=PUBLIC;DatasetAbstract=Abstract;DatasetTitle=Generic Raster Layer Test3;RasterFile={PROTOCOL}://data.d4science.org/QTVNbXp5cmI0MG52TTE0K2paNzhXZWlCTHhweU8rUCtHbWJQNStIS0N6Yz0;InnerLayerName=analyzed_field;FileNameOnInfra=raster-1465493226242.nc;Topics=analyzed_field;SpatialResolution=-1;
#Web app publisher
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.WEB_APP_PUBLISHER
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.WEB_APP_PUBLISHER&DataInputs=ZipFile={PROTOCOL}://brokenlink/dYQ089;
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.WEB_APP_PUBLISHER&DataInputs=ZipFile={PROTOCOL}://goo.gl/dYQ089;
#ECOPATH_WITH_ECOSIM
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ECOPATH_WITH_ECOSIM
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ECOPATH_WITH_ECOSIM&DataInputs=Model File={PROTOCOL}://data.d4science.org/eHFkNmhoSUwxMVpmcElhcUlmQUpWaWRGSjQzNkFXNElHbWJQNStIS0N6Yz0;Config File={PROTOCOL}://data.d4science.org/ZGFWaGc4NjUrQmRmcElhcUlmQUpWbTNVQjhqdUV3OWdHbWJQNStIS0N6Yz0;