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77 Commits

Author SHA1 Message Date
Giancarlo Panichi 5f1fee5ca9 Minor updated 2022-03-15 17:02:12 +01:00
Giancarlo Panichi a308f08c93 Updated bom version for release 2022-03-15 17:01:33 +01:00
Giancarlo Panichi 5e3252ef5b Fixed pom for release 2022-03-15 11:12:16 +01:00
Giancarlo Panichi e76593263b Merge pull request 'feature/22700' (!1) from feature/22700 into master
Reviewed-on: #1
2022-03-15 11:09:05 +01:00
Giancarlo Panichi 6ecfcc9a13 Updated for release 2022-03-15 11:04:40 +01:00
Giancarlo Panichi 71361eb435 Updated gcube-bom to 2.1.0-SNAPSHOT for storagehub 2.0.0 2022-01-27 18:33:07 +01:00
Giancarlo Panichi 5f9681048f ref 22700: DataMiner - Check max computations limit
Updated max computations parameter check.
2022-01-24 18:27:56 +01:00
Roberto Cirillo fbade3e930 Update 'CHANGELOG.md'
snapshot removed from CHANGELOG
2021-10-08 17:30:01 +02:00
Roberto Cirillo 9e26a0680a Update 'pom.xml'
snapshot removed from pom
2021-10-08 17:29:36 +02:00
Roberto Cirillo 106a03dab4 Update 'CHANGELOG.md'
add SNAPSHOT to 1.7.1 version
2021-10-06 12:04:25 +02:00
Roberto Cirillo 403b9c2b2e Update 'pom.xml'
add SNAPSHOT to the version
2021-10-06 12:03:56 +02:00
Giancarlo Panichi 84be7e4fe7 Updated for Release Next 2021-06-15 15:40:52 +02:00
Giancarlo Panichi 193885a1a3 Updated for accounting-lib 2021-06-15 15:31:18 +02:00
Giancarlo Panichi be510cbda0 Updated for Release Next 2021-06-15 15:20:40 +02:00
Giancarlo Panichi 1e0b6b4d02 Rebuild SNAPSHOT 2021-06-15 15:14:36 +02:00
Giancarlo Panichi dbb87e55f7 ref 20971: ShortLink - Check for obsolete short urls
https://support.d4science.org/issues/20971

Fixed ShortLink urls.
2021-05-25 11:14:58 +02:00
Giancarlo Panichi 2d982938ce ref 20971: ShortLink - Check for obsolete short urls
https://support.d4science.org/issues/20971

Fixed ShortLink urls.
2021-05-25 10:50:17 +02:00
Giancarlo Panichi 86f5e9de17 ref 20971: ShortLink - Check for obsolete short urls
https://support.d4science.org/issues/20971

Fixed ShortLink urls.
2021-05-25 10:24:59 +02:00
Giancarlo Panichi 33b08ac966 ref 20971: ShortLink - Check for obsolete short urls
https://support.d4science.org/issues/20971

Fixed ShortLink urls.
2021-05-24 18:45:35 +02:00
Giancarlo Panichi a24383b37e ref 20971: ShortLink - Check for obsolete short urls
https://support.d4science.org/issues/20971

Fixed ShortLink urls.
2021-05-24 18:22:21 +02:00
Giancarlo Panichi e0ad80592d ref 20971: ShortLink - Check for obsolete short urls
https://support.d4science.org/issues/20971

Fixed ShortLink urls.
2021-05-24 18:13:29 +02:00
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
76 changed files with 1679 additions and 912 deletions

3
.classpath Normal file → Executable file
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@ -14,17 +14,20 @@
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"> <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes> <attributes>
<attribute name="maven.pomderived" value="true"/> <attribute name="maven.pomderived" value="true"/>
<attribute name="org.eclipse.jst.component.nondependency" value=""/>
</attributes> </attributes>
</classpathentry> </classpathentry>
<classpathentry kind="src" output="target/test-classes" path="src/test/java"> <classpathentry kind="src" output="target/test-classes" path="src/test/java">
<attributes> <attributes>
<attribute name="optional" value="true"/> <attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/> <attribute name="maven.pomderived" value="true"/>
<attribute name="test" value="true"/>
</attributes> </attributes>
</classpathentry> </classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"> <classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes> <attributes>
<attribute name="maven.pomderived" value="true"/> <attribute name="maven.pomderived" value="true"/>
<attribute name="test" value="true"/>
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</classpathentry> </classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"> <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">

1
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@ -0,0 +1 @@
/target/

13
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@ -5,11 +5,21 @@
<projects> <projects>
</projects> </projects>
<buildSpec> <buildSpec>
<buildCommand>
<name>org.eclipse.wst.common.project.facet.core.builder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand> <buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name> <name>org.eclipse.jdt.core.javabuilder</name>
<arguments> <arguments>
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<buildCommand>
<name>org.eclipse.wst.validation.validationbuilder</name>
<arguments>
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<buildCommand> <buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name> <name>org.eclipse.m2e.core.maven2Builder</name>
<arguments> <arguments>
@ -17,7 +27,10 @@
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<natures> <natures>
<nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature> <nature>org.eclipse.m2e.core.maven2Nature</nature>
<nature>org.eclipse.jdt.core.javanature</nature> <nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures> </natures>
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2
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@ -0,0 +1,2 @@
/org.eclipse.ltk.core.refactoring.prefs
/org.eclipse.wst.xsl.core.prefs

0
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97
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@ -1,12 +1,109 @@
eclipse.preferences.version=1 eclipse.preferences.version=1
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org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
org.eclipse.jdt.core.compiler.annotation.nonnull.secondary=
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org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=ignore
org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=ignore
org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled
org.eclipse.jdt.core.compiler.problem.unusedExceptionParameter=ignore
org.eclipse.jdt.core.compiler.problem.unusedImport=warning
org.eclipse.jdt.core.compiler.problem.unusedLabel=warning
org.eclipse.jdt.core.compiler.problem.unusedLocal=warning
org.eclipse.jdt.core.compiler.problem.unusedObjectAllocation=ignore
org.eclipse.jdt.core.compiler.problem.unusedParameter=ignore
org.eclipse.jdt.core.compiler.problem.unusedParameterIncludeDocCommentReference=enabled
org.eclipse.jdt.core.compiler.problem.unusedParameterWhenImplementingAbstract=disabled
org.eclipse.jdt.core.compiler.problem.unusedParameterWhenOverridingConcrete=disabled
org.eclipse.jdt.core.compiler.problem.unusedPrivateMember=warning
org.eclipse.jdt.core.compiler.problem.unusedTypeParameter=ignore
org.eclipse.jdt.core.compiler.problem.unusedWarningToken=warning
org.eclipse.jdt.core.compiler.problem.varargsArgumentNeedCast=warning
org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.8 org.eclipse.jdt.core.compiler.source=1.8

0
.settings/org.eclipse.m2e.core.prefs Normal file → Executable file
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@ -0,0 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
<wb-module deploy-name="dataminer">
<wb-resource deploy-path="/" source-path="/src/main/java"/>
<wb-resource deploy-path="/" source-path="/src/main/resources"/>
</wb-module>
</project-modules>

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@ -0,0 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<faceted-project>
<installed facet="java" version="1.8"/>
<installed facet="jst.utility" version="1.0"/>
</faceted-project>

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disabled=06target
eclipse.preferences.version=1

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This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
# Changelog for "dataminer"
## [v1.8.0] - 2022-01-24
### Fixes
- Fixed max computations support [#22700]
## [v1.7.1] - 2021-05-24
### Fixes
- Fixed obsolete short urls [#20971]
## [v1.7.0] - 2020-11-20
### Fixes
- 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

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# Acknowledgments
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](https://cordis.europa.eu/project/id/004260) (grant no. 004260).
- the Seventh Framework Programme for research, technological development and demonstration
- [D4Science](https://cordis.europa.eu/project/id/212488) (grant no. 212488);
- [D4Science-II](https://cordis.europa.eu/project/id/239019) (grant no.239019);
- [ENVRI](https://cordis.europa.eu/project/id/283465) (grant no. 283465);
- [iMarine](https://cordis.europa.eu/project/id/283644) (grant no. 283644);
- [EUBrazilOpenBio](https://cordis.europa.eu/project/id/288754) (grant no. 288754).
- the H2020 research and innovation programme
- [SoBigData](https://cordis.europa.eu/project/id/654024) (grant no. 654024);
- [PARTHENOS](https://cordis.europa.eu/project/id/654119) (grant no. 654119);
- [EGI-Engage](https://cordis.europa.eu/project/id/654142) (grant no. 654142);
- [ENVRI PLUS](https://cordis.europa.eu/project/id/654182) (grant no. 654182);
- [BlueBRIDGE](https://cordis.europa.eu/project/id/675680) (grant no. 675680);
- [PerformFISH](https://cordis.europa.eu/project/id/727610) (grant no. 727610);
- [AGINFRA PLUS](https://cordis.europa.eu/project/id/731001) (grant no. 731001);
- [DESIRA](https://cordis.europa.eu/project/id/818194) (grant no. 818194);
- [ARIADNEplus](https://cordis.europa.eu/project/id/823914) (grant no. 823914);
- [RISIS 2](https://cordis.europa.eu/project/id/824091) (grant no. 824091);
- [EOSC-Pillar](https://cordis.europa.eu/project/id/857650) (grant no. 857650);
- [Blue Cloud](https://cordis.europa.eu/project/id/862409) (grant no. 862409);
- [SoBigData-PlusPlus](https://cordis.europa.eu/project/id/871042) (grant no. 871042);

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#European Union Public Licence V.1.1
##*EUPL © the European Community 2007*
This **European Union Public Licence** (the **“EUPL”**) applies to the Work or Software
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Legal Protection: This Licence does not grant permission to use the trade names,
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reasonable and customary use in describing the origin of the Work and
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##6. Chain of Authorship
The original Licensor warrants that the copyright in the Original Work granted
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##7. Disclaimer of Warranty
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##9. Additional agreements
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Distribution and/or Communication by You of the Work or copies thereof.
##11. Information to the public
In case of any Distribution and/or Communication of the Work by means of
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##12. Termination of the Licence
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any breach by the Licensee of the terms of the Licence.
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##13. Miscellaneous
Without prejudice of Article 9 above, the Licence represents the complete
agreement between the Parties as to the Work licensed hereunder.
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law, this will not affect the validity or enforceability of the Licence as a
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The European Commission may publish other linguistic versions and/or new
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Licence will be published with a unique version number.
All linguistic versions of this Licence, approved by the European Commission,
have identical value. Parties can take advantage of the linguistic version of
their choice.
##14. Jurisdiction
Any litigation resulting from the interpretation of this License, arising
between the European Commission, as a Licensor, and any Licensee, will be
subject to the jurisdiction of the Court of Justice of the European Communities,
as laid down in article 238 of the Treaty establishing the European Community.
Any litigation arising between Parties, other than the European Commission, and
resulting from the interpretation of this License, will be subject to the
exclusive jurisdiction of the competent court where the Licensor resides or
conducts its primary business.
##15. Applicable Law
This Licence shall be governed by the law of the European Union country where
the Licensor resides or has his registered office.
This licence shall be governed by the Belgian law if:
- a litigation arises between the European Commission, as a Licensor, and any
- Licensee; the Licensor, other than the European Commission, has no residence
- or registered office inside a European Union country.
---
##Appendix
**“Compatible Licences”** according to article 5 EUPL are:
- GNU General Public License (GNU GPL) v. 2
- Open Software License (OSL) v. 2.1, v. 3.0
- Common Public License v. 1.0
- Eclipse Public License v. 1.0
- Cecill v. 2.0

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# DataMiner
DataMiner is a library for integrate WPS 52North in the D4Science Infrastructure.
## Structure of the project
* The source code is present in the src folder.
## Built With
* [OpenJDK](https://openjdk.java.net/) - The JDK used
* [Maven](https://maven.apache.org/) - Dependency Management
## Documentation
* Use of this library is described on [Wiki](https://wiki.gcube-system.org/gcube/DataMiner_Installation).
## Change log
See [Releases](https://code-repo.d4science.org/gCubeSystem/dataminer/releases).
## Authors
* **Gianpaolo Coro** ([ORCID]()) - [ISTI-CNR Infrascience Group](http://nemis.isti.cnr.it/groups/infrascience)
* **Lucio Lelii** ([ORCID]()) - [ISTI-CNR Infrascience Group](http://nemis.isti.cnr.it/groups/infrascience)
* **Giancarlo Panichi** ([ORCID](http://orcid.org/0000-0001-8375-6644)) - [ISTI-CNR Infrascience Group](http://nemis.isti.cnr.it/groups/infrascience)
## License
This project is licensed under the EUPL V.1.1 License - see the [LICENSE.md](LICENSE.md) file for details.
## About the gCube Framework
This software is part of the [gCubeFramework](https://www.gcube-system.org/ "gCubeFramework"): an
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)

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@ -9,13 +9,13 @@
<baseDirectory>/</baseDirectory> <baseDirectory>/</baseDirectory>
<fileSets> <fileSets>
<fileSet> <fileSet>
<directory>${distroDirectory}</directory>
<outputDirectory>/</outputDirectory> <outputDirectory>/</outputDirectory>
<useDefaultExcludes>true</useDefaultExcludes> <useDefaultExcludes>true</useDefaultExcludes>
<includes> <includes>
<include>README</include> <include>README.md</include>
<include>LICENSE</include> <include>LICENSE.md</include>
<include>changelog.xml</include> <include>CHANGELOG.md</include>
<include>FUNDING.md</include>
<include>profile.xml</include> <include>profile.xml</include>
</includes> </includes>
<fileMode>755</fileMode> <fileMode>755</fileMode>

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@ -1 +0,0 @@
${gcube.license}

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@ -1,69 +0,0 @@
The gCube System - ${name}
--------------------------------------------------
${description}
${gcube.description}
${gcube.funding}
Version
--------------------------------------------------
${version} (${buildDate})
Please see the file named "changelog.xml" in this directory for the release notes.
Authors
--------------------------------------------------
* Gianpaolo Coro (gianpaolo.coro-AT-isti.cnr.it),
Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" CNR, Pisa IT
Maintainers
-----------
* Gianpaolo Coro (gianpaolo.coro-AT-isti.cnr.it),
Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" CNR, Pisa IT
Download information
--------------------------------------------------
Source code is available from SVN:
${scm.url}
Binaries can be downloaded from the gCube website:
${gcube.website}
Installation
--------------------------------------------------
Installation documentation is available on-line in the gCube Wiki:
https://wiki.gcube-system.org/gcube/DataMiner_Installation
Documentation
--------------------------------------------------
Documentation is available on-line in the gCube Wiki:
https://wiki.gcube-system.org/gcube/DataMiner_Installation
Support
--------------------------------------------------
Bugs and support requests can be reported in the gCube issue tracking tool:
${gcube.issueTracking}
Licensing
--------------------------------------------------
This software is licensed under the terms you may find in the file named "LICENSE" in this directory.

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@ -1,15 +0,0 @@
<ReleaseNotes>
<Changeset component="${groupId}.${artifactId}.1-5-2" date="2017-12-13">
<Change>added the right extension on output file</Change>
<Change>lock file created on execution</Change>
</Changeset>
<Changeset component="${groupId}.${artifactId}.1-5-1" date="2017-09-14">
<Change>added accounting on algorithm execution</Change>
</Changeset>
<Changeset component="${groupId}.${artifactId}.1-5-0" date="2017-07-31">
<Change>service interface classes moved to wps project</Change>
</Changeset>
<Changeset component="${groupId}.${artifactId}.1-1-0" date="2016-10-03">
<Change>First Release</Change>
</Changeset>
</ReleaseNotes>

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pom.xml Normal file → Executable file
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@ -4,16 +4,19 @@
<parent> <parent>
<artifactId>maven-parent</artifactId> <artifactId>maven-parent</artifactId>
<groupId>org.gcube.tools</groupId> <groupId>org.gcube.tools</groupId>
<version>1.0.0</version> <version>1.1.0</version>
<relativePath /> <relativePath />
</parent> </parent>
<groupId>org.gcube.dataanalysis</groupId> <groupId>org.gcube.dataanalysis</groupId>
<artifactId>dataminer</artifactId> <artifactId>dataminer</artifactId>
<version>1.5.3-SNAPSHOT</version> <version>1.8.0</version>
<name>dataminer</name> <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> <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> <scm>
<url>https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner</url> <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>
<url>https://code-repo.d4science.org/gCubeSystem/${project.artifactId}</url>
</scm> </scm>
<developers> <developers>
@ -26,13 +29,40 @@
<role>developer</role> <role>developer</role>
</roles> </roles>
</developer> </developer>
<developer>
<name>Lucio Lelii</name>
<email>lucio.lelii@isti.cnr.it</email>
<organization>CNR Pisa, Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo"</organization>
<roles>
<role>architect</role>
<role>developer</role>
</roles>
</developer>
</developers> </developers>
<properties> <properties>
<webappDirectory>${project.build.directory}/${project.build.finalName}</webappDirectory> <webappDirectory>${project.build.directory}/${project.build.finalName}</webappDirectory>
<distroDirectory>distro</distroDirectory> <distroDirectory>distro</distroDirectory>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding> <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
</properties> </properties>
<dependencyManagement>
<!-- Old solution <dependencies> <dependency> <groupId>org.gcube.distribution</groupId>
<artifactId>maven-smartgears-bom</artifactId> <version>2.1.0</version> <type>pom</type>
<scope>import</scope> </dependency> </dependencies> -->
<dependencies>
<dependency>
<groupId>org.gcube.distribution</groupId>
<artifactId>gcube-bom</artifactId>
<version>2.0.2</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies> <dependencies>
<!-- https://mvnrepository.com/artifact/org.reflections/reflections-maven --> <!-- https://mvnrepository.com/artifact/org.reflections/reflections-maven -->
<dependency> <dependency>
@ -61,27 +91,22 @@
<dependency> <dependency>
<groupId>org.gcube.dataanalysis</groupId> <groupId>org.gcube.dataanalysis</groupId>
<artifactId>52n-wps-algorithm-gcube</artifactId> <artifactId>52n-wps-algorithm-gcube</artifactId>
<version>[3.6.1-SNAPSHOT,3.7.0-SNAPSHOT)</version> <version>[3.6.1,3.7.0)</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.gcube.dataanalysis</groupId> <groupId>org.gcube.dataanalysis</groupId>
<artifactId>52n-wps-server-gcube</artifactId> <artifactId>52n-wps-server-gcube</artifactId>
<version>[3.6.1-SNAPSHOT, 3.7.0-SNAPSHOT)</version> <version>[3.6.1, 3.7.0)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine</artifactId>
<version>[1.8.5-SNAPSHOT,2.0.0-SNAPSHOT)</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.gcube.dataanalysis</groupId> <groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-wps-extension</artifactId> <artifactId>ecological-engine-wps-extension</artifactId>
<version>[1.0.2-SNAPSHOT,2.0.0-SNAPSHOT)</version> <version>[1.0.5,2.0.0-SNAPSHOT)</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.gcube.dataanalysis</groupId> <groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-geospatial-extensions</artifactId> <artifactId>ecological-engine-geospatial-extensions</artifactId>
<version>[1.3.2-SNAPSHOT,2.0.0-SNAPSHOT)</version> <version>[1.5.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
<exclusions> <exclusions>
<exclusion> <exclusion>
<artifactId>log4j</artifactId> <artifactId>log4j</artifactId>
@ -92,12 +117,22 @@
<dependency> <dependency>
<groupId>org.gcube.dataanalysis</groupId> <groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-external-algorithms</artifactId> <artifactId>ecological-engine-external-algorithms</artifactId>
<version>[1.1.5-SNAPSHOT,2.0.0-SNAPSHOT)</version> <version>[1.2.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.gcube.dataanalysis</groupId> <groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-smart-executor</artifactId> <artifactId>ecological-engine-smart-executor</artifactId>
<version>[1.0.0-SNAPSHOT,2.0.0-SNAPSHOT)</version> <version>[1.6.5-SNAPSHOT,2.0.0-SNAPSHOT)</version>
<exclusions>
<exclusion>
<groupId>org.glassfish.jersey.core</groupId>
<artifactId>jersey-client</artifactId>
</exclusion>
<exclusion>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-json-jackson</artifactId>
</exclusion>
</exclusions>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.slf4j</groupId> <groupId>org.slf4j</groupId>
@ -116,24 +151,21 @@
<version>4.11</version> <version>4.11</version>
<scope>test</scope> <scope>test</scope>
</dependency> </dependency>
<!-- <dependency> <groupId>org.gcube.common</groupId> <artifactId>common-authorization</artifactId>
</dependency> <dependency> <groupId>org.gcube.core</groupId> <artifactId>common-scope</artifactId>
</dependency> -->
<dependency> <dependency>
<groupId>javassist</groupId> <groupId>javassist</groupId>
<artifactId>javassist</artifactId> <artifactId>javassist</artifactId>
<version>3.12.1.GA</version> <version>3.12.1.GA</version>
</dependency> </dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>home-library-jcr</artifactId>
<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
</dependency>
<dependency> <dependency>
<groupId>org.gcube.common</groupId> <groupId>org.gcube.common</groupId>
<artifactId>home-library</artifactId> <artifactId>storagehub-client-library</artifactId>
<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version> </dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>storagehub-model</artifactId>
</dependency> </dependency>
<dependency> <dependency>
@ -145,7 +177,6 @@
<dependency> <dependency>
<groupId>org.gcube.accounting</groupId> <groupId>org.gcube.accounting</groupId>
<artifactId>accounting-lib</artifactId> <artifactId>accounting-lib</artifactId>
<version>[3.0.0-SNAPSHOT,4.0.0-SNAPSHOT)</version>
<scope>provided</scope> <scope>provided</scope>
</dependency> </dependency>
@ -154,44 +185,14 @@
<build> <build>
<plugins> <plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin> <plugin>
<groupId>org.apache.maven.plugins</groupId> <groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId> <artifactId>maven-surefire-plugin</artifactId>
<version>2.18.1</version>
<configuration> <configuration>
<skipTests>true</skipTests> <skipTests>true</skipTests>
</configuration> </configuration>
</plugin> </plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptors>
<descriptor>${distroDirectory}/descriptor.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>servicearchive</id>
<phase>install</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins> </plugins>
</build> </build>
<repositories> <repositories>

0
distro/profile.xml → profile.xml Normal file → Executable file
View File

View File

@ -30,7 +30,7 @@ public class InfrastructureDialoguer {
public DatabaseInfo getDatabaseInfo(String resourceName) throws Exception{ public DatabaseInfo getDatabaseInfo(String resourceName) throws Exception{
DatabaseInfo dbi = new DatabaseInfo(); DatabaseInfo dbi = new DatabaseInfo();
LOGGER.debug("Searching for Database "+resourceName+" in scope "+scope); LOGGER.debug("Searching for Database {} in scope {}", resourceName, scope);
SimpleQuery query = queryFor(ServiceEndpoint.class); SimpleQuery query = queryFor(ServiceEndpoint.class);
// query.addCondition("$resource/Profile/Category/text() eq 'Database' and $resource/Profile/Name eq 'StatisticalManagerDataBase' "); // query.addCondition("$resource/Profile/Category/text() eq 'Database' and $resource/Profile/Name eq 'StatisticalManagerDataBase' ");
// query.addCondition("$resource/Profile/Category/text() eq 'Database' and $resource/Profile/Name eq '"+resourceName+"' "); // query.addCondition("$resource/Profile/Category/text() eq 'Database' and $resource/Profile/Name eq '"+resourceName+"' ");
@ -51,7 +51,7 @@ public class InfrastructureDialoguer {
dbi.driver = property.value(); dbi.driver = property.value();
} }
LOGGER.debug("Found Database : "+dbi); LOGGER.debug("Found Database : {}",dbi);
} }
if (dbi.url == null) if (dbi.url == null)

View File

@ -50,8 +50,15 @@ import org.slf4j.LoggerFactory;
public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm implements Observable, Cancellable { public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm implements Observable, Cancellable {
private static final int COMPUTATION_WAIT_FOR_RUN_REQUEST = 20000;
/** /**
* 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); private static final Logger LOGGER = LoggerFactory.getLogger(AbstractEcologicalEngineMapper.class);
@ -62,6 +69,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
private TokenManager tokenm = null; private TokenManager tokenm = null;
private EnvironmentVariableManager env = null;
// inputs and outputs // inputs and outputs
public LinkedHashMap<String, Object> inputs = new LinkedHashMap<String, Object>(); public LinkedHashMap<String, Object> inputs = new LinkedHashMap<String, Object>();
public LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>(); public LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>();
@ -78,30 +87,41 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
this.wpsExternalID = wpsExternalID; this.wpsExternalID = wpsExternalID;
} }
public static synchronized void addComputation(String session, String user) { private static synchronized void addComputation(String session, String user) {
runningcomputations.put(session, user); runningcomputations.put(session, user);
} }
public static synchronized void removeComputation(String session) { private static synchronized void removeComputation(String session) {
runningcomputations.remove(session); runningcomputations.remove(session);
} }
public static synchronized int getRuningComputations() { private static synchronized int getRuningComputations() {
return runningcomputations.size(); return runningcomputations.size();
} }
public static synchronized String displayRunningComputations() { private static synchronized String displayRunningComputations() {
return runningcomputations.toString(); return runningcomputations.toString();
} }
public void waitForResources() throws Exception { private void waitForResources(String computationSession, String username, String scope) throws Exception {
while (getRuningComputations() > ConfigurationManager.getMaxComputations()) { while (waitCondition(computationSession, username, scope)) {
Thread.sleep(20000); Thread.sleep(COMPUTATION_WAIT_FOR_RUN_REQUEST);
LOGGER.debug("Waiting for resources to be available: " + displayRunningComputations()); 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 // inner objects
public AlgorithmConfiguration config; public AlgorithmConfiguration config;
public InfrastructureDialoguer infrastructureDialoguer; public InfrastructureDialoguer infrastructureDialoguer;
@ -246,13 +266,15 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
float previousStatus = -3; float previousStatus = -3;
String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname(); String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
public void updateStatus(float status) {
public void updateStatus(float status, boolean canWrite) {
if (agent != null) { if (agent != null) {
if (status != previousStatus) { if (status != previousStatus) {
LOGGER.debug("STATUS update to: {} ", status); LOGGER.debug("STATUS update to: {} ", status);
previousStatus = status; previousStatus = status;
super.update(new Integer((int) status)); super.update(new Integer((int) status));
try { try {
if (canWrite)
updateComputationOnWS(status, null); updateComputationOnWS(status, null);
} catch (Exception e) { } catch (Exception e) {
LOGGER.warn("error updating compution on WS"); LOGGER.warn("error updating compution on WS");
@ -262,6 +284,10 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
} }
public void setEnvironmentVariableManager(EnvironmentVariableManager env) {
this.env = env;
}
public void updateComputationOnWS(float status, String exception) { public void updateComputationOnWS(float status, String exception) {
updateComputationOnWS(status, exception, null, null); updateComputationOnWS(status, exception, null, null);
} }
@ -269,6 +295,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
class RunDataspaceManager implements Runnable { class RunDataspaceManager implements Runnable {
List<StoredData> inputData; List<StoredData> inputData;
List<File> generatedData; List<File> generatedData;
public RunDataspaceManager(List<StoredData> inputData, List<File> generatedData) { public RunDataspaceManager(List<StoredData> inputData, List<File> generatedData) {
this.inputData = inputData; this.inputData = inputData;
this.generatedData = generatedData; this.generatedData = generatedData;
@ -280,23 +307,24 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
LOGGER.debug("Dataspace->Status updater->Writing computational info on the WS asyncronously"); LOGGER.debug("Dataspace->Status updater->Writing computational info on the WS asyncronously");
manager.writeRunningComputationData(); manager.writeRunningComputationData();
} catch (Exception ez) { } 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) { if (currentComputation != null) {
currentComputation.setStatus("" + status); currentComputation.setStatus("" + status);
if (exception != null && exception.length() > 0) if (exception != null && exception.length() > 0)
currentComputation.setException(exception); currentComputation.setException(exception);
LOGGER.debug("RunDataspaceManager: [inputData=" + inputData + ", generatedData=" + generatedData + "]");
RunDataspaceManager rundm = new RunDataspaceManager(inputData, generatedData); RunDataspaceManager rundm = new RunDataspaceManager(inputData, generatedData);
rundm.run(); rundm.run();
/* /*
Thread t = new Thread(rundm); * Thread t = new Thread(rundm); t.start();
t.start();
*/ */
} }
} }
@ -316,7 +344,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
List<String> generatedInputTables = null; List<String> generatedInputTables = null;
List<String> generatedOutputTables = null; List<String> generatedOutputTables = null;
List<File> generatedFiles = 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(); String computationSession = this.getAlgorithmClass().getSimpleName() + "_ID_" + UUID.randomUUID().toString();
if (wpsExternalID != null) { if (wpsExternalID != null) {
LOGGER.info("Using wps External ID " + wpsExternalID); LOGGER.info("Using wps External ID " + wpsExternalID);
@ -324,8 +353,14 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
} else } else
LOGGER.info("Wps External ID not set"); LOGGER.info("Wps External ID not set");
InputsManager inputsManager = null; InputsManager inputsManager = null;
ConfigurationManager configManager = new ConfigurationManager(); // initializes parameters from file ConfigurationManager configManager = new ConfigurationManager(this.env); // initializes
// parameters
// from
// web.xml
manageUserToken(); manageUserToken();
boolean canWriteOnShub = checkWriteAuthorization(tokenm.getUserName());
Path dir = Paths.get(System.getProperty("java.io.tmpdir"), "dmlocks"); Path dir = Paths.get(System.getProperty("java.io.tmpdir"), "dmlocks");
if (!Files.exists(dir)) if (!Files.exists(dir))
dir = Files.createDirectory(dir); dir = Files.createDirectory(dir);
@ -344,17 +379,17 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
config = configManager.getConfig(); config = configManager.getConfig();
LOGGER.info("Configured algorithm with session " + computationSession); LOGGER.info("Configured algorithm with session " + computationSession);
time("Configuration"); time("Configuration");
waitForResources(); waitForResources(computationSession, configManager.getUsername(), configManager.getScope());
LOGGER.info("Running algorithm with session " + computationSession); LOGGER.info("Running algorithm with session " + computationSession);
time("Waiting time for resources to be free"); 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 scope = configManager.getScope();
String username = configManager.getUsername(); String username = configManager.getUsername();
LOGGER.info("1 - Algorithm environment initialized in scope " + scope + " with user name " + username + " and session " + computationSession); LOGGER.info("1 - Algorithm environment initialized in scope " + scope + " with user name " + username
LOGGER.info("Max allowed computations " + ConfigurationManager.getMaxComputations() + " using storage " + ConfigurationManager.useStorage()); + " and session " + computationSession);
LOGGER.info("Max allowed computations " + ConfigurationManager.getMaxComputations() + " using storage "
+ ConfigurationManager.useStorage());
// init the infrastructure dialoguer // init the infrastructure dialoguer
LOGGER.info("2 - Initializing connection to the e-Infrastructure"); LOGGER.info("2 - Initializing connection to the e-Infrastructure");
infrastructureDialoguer = new InfrastructureDialoguer(scope); infrastructureDialoguer = new InfrastructureDialoguer(scope);
@ -380,15 +415,19 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
time("Ecological Engine Algorithm selection"); time("Ecological Engine Algorithm selection");
// adding service parameters to the configuration // adding service parameters to the configuration
LOGGER.info("5 - Adding Service parameters to the configuration"); LOGGER.info("5 - Adding Service parameters to the configuration");
inputsManager.addInputServiceParameters(getInputParameters(algorithm), infrastructureDialoguer); List<StatisticalType> dataminerInputParameters = getInputParameters(algorithm);
LOGGER.debug("Dataminer Algo Default InputParameters: " + dataminerInputParameters);
inputsManager.addInputServiceParameters(dataminerInputParameters, infrastructureDialoguer);
time("Service parameters added to the algorithm"); time("Service parameters added to the algorithm");
// merging wps with ecological engine parameters - modifies the // merging wps with ecological engine parameters - modifies the
// config // config
LOGGER.info("6 - Translating WPS Inputs into Ecological Engine Inputs"); LOGGER.info("6 - Translating WPS Inputs into Ecological Engine Inputs");
LOGGER.debug("Operator class is " + this.getClass().getCanonicalName()); LOGGER.debug("Operator class is " + this.getClass().getCanonicalName());
// build computation Data // 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",
inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo); config.getTaskID(), configManager.getUsername(), config.getGcubeScope(),
this.getClass().getCanonicalName());
inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo, dataminerInputParameters);
generatedInputTables = inputsManager.getGeneratedTables(); generatedInputTables = inputsManager.getGeneratedTables();
generatedFiles = inputsManager.getGeneratedInputFiles(); generatedFiles = inputsManager.getGeneratedInputFiles();
time("Setup and download of input parameters with tables creation"); time("Setup and download of input parameters with tables creation");
@ -412,11 +451,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
LOGGER.info("9 - Running the computation and updater"); LOGGER.info("9 - Running the computation and updater");
LOGGER.info("Initializing the WPS status of the computation"); LOGGER.info("Initializing the WPS status of the computation");
updateStatus(0); updateStatus(0, canWriteOnShub);
LOGGER.info("Initializing the computation"); LOGGER.info("Initializing the computation");
agent.init(); agent.init();
LOGGER.info("Updating status"); LOGGER.info("Updating status");
runStatusUpdater(); runStatusUpdater(canWriteOnShub);
LOGGER.info("Running the computation"); LOGGER.info("Running the computation");
agent.compute(); agent.compute();
LOGGER.info("The computation has finished. Retrieving output"); LOGGER.info("The computation has finished. Retrieving output");
@ -440,13 +479,15 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
outputmanager.shutdown(); outputmanager.shutdown();
// delete all temporary tables LOGGER.debug("12 - Final Computation Output");
LOGGER.info("12 - Deleting possible generated temporary tables"); LOGGER.debug("Outputs: " + outputs);
LOGGER.debug("Final Computation Output: " + outputs);
endTime = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis()); endTime = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
if (!isCancelled()) { if (!isCancelled()) {
saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent, generatedFiles); LOGGER.debug("Save Computation Data");
if (canWriteOnShub)
saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent,
generatedFiles);
} else { } else {
LOGGER.debug("Computation interrupted - no update"); LOGGER.debug("Computation interrupted - no update");
throw new Exception("Computation cancelled"); throw new Exception("Computation cancelled");
@ -461,8 +502,10 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
exitstatus = -1; exitstatus = -1;
if (inputsManager != null) if (inputsManager != null)
updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(), generatedFiles); if (canWriteOnShub)
else updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(),
generatedFiles);
else if (canWriteOnShub)
updateComputationOnWS(exitstatus, e.getMessage()); updateComputationOnWS(exitstatus, e.getMessage());
if (isCancelled()) if (isCancelled())
throw new Exception("Computation cancelled"); throw new Exception("Computation cancelled");
@ -470,6 +513,9 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
throw e; throw e;
} finally { } finally {
LOGGER.debug("accounting algorithm"); LOGGER.debug("accounting algorithm");
if (operationResult == null) {
operationResult = OperationResult.FAILED;
}
accountAlgorithmExecution(startTimeLong, System.currentTimeMillis(), operationResult); accountAlgorithmExecution(startTimeLong, System.currentTimeMillis(), operationResult);
LOGGER.debug("Deleting Input Tables"); LOGGER.debug("Deleting Input Tables");
deleteTemporaryTables(generatedInputTables); deleteTemporaryTables(generatedInputTables);
@ -483,13 +529,26 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
time("Cleaning of resources"); time("Cleaning of resources");
displayTimes(); displayTimes();
cleanResources(); cleanResources();
if (observer!=null) observer.isFinished(this); if (observer != null)
observer.isFinished(this);
LOGGER.debug("All done - Computation Finished"); LOGGER.debug("All done - Computation Finished");
Files.deleteIfExists(lockFile); Files.deleteIfExists(lockFile);
} }
} }
private boolean checkWriteAuthorization(String username) {
if (env != null && env.getShubUsersExcluded() != null) {
if (env.getShubUsersExcluded().isEmpty()) {
return false;
}
if (env.getShubUsersExcluded().contains(username)) {
return false;
}
}
return true;
}
private void accountAlgorithmExecution(long start, long end, OperationResult result) { private void accountAlgorithmExecution(long start, long end, OperationResult result) {
try { try {
JobUsageRecord jobUsageRecord = new JobUsageRecord(); JobUsageRecord jobUsageRecord = new JobUsageRecord();
@ -502,8 +561,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
jobUsageRecord.setHost(WPSConfig.getInstance().getWPSConfig().getServer().getHostname()); jobUsageRecord.setHost(WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
jobUsageRecord.setCallerQualifier(tokenm.getTokenQualifier()); jobUsageRecord.setCallerQualifier(tokenm.getTokenQualifier());
AccountingPersistence accountingPersistence = AccountingPersistence accountingPersistence = AccountingPersistenceFactory.getPersistence();
AccountingPersistenceFactory.getPersistence();
accountingPersistence.account(jobUsageRecord); accountingPersistence.account(jobUsageRecord);
} catch (Throwable e) { } catch (Throwable e) {
LOGGER.error("error accounting algorithm execution", e); LOGGER.error("error accounting algorithm execution", e);
@ -513,30 +571,46 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
public class StatusUpdater implements Runnable { public class StatusUpdater implements Runnable {
private boolean canWrite = true;
public StatusUpdater(boolean canWrite) {
this.canWrite = canWrite;
}
@Override @Override
public void run() { public void run() {
while (agent != null && !isCancelled() && agent.getStatus() < 100) { while (agent != null && !isCancelled() && agent.getStatus() < 100) {
try { try {
updateStatus(agent.getStatus()); updateStatus(agent.getStatus(), canWrite);
Thread.sleep(10000); Thread.sleep(10000);
} catch (InterruptedException e) {} } catch (InterruptedException e) {
}
} }
LOGGER.info("Status updater terminated"); LOGGER.info("Status updater terminated");
} }
} }
private void runStatusUpdater() { private void runStatusUpdater(boolean canWrite) {
StatusUpdater updater = new StatusUpdater(); StatusUpdater updater = new StatusUpdater(canWrite);
Thread t = new Thread(updater); Thread t = new Thread(updater);
t.start(); t.start();
LOGGER.debug("Provenance manager running"); 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("Provenance manager started for operator " + this.getClass().getCanonicalName()); 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 // post on WS
DataspaceManager manager = new DataspaceManager(config, computation, inputData, outputData, generatedFiles); DataspaceManager manager = new DataspaceManager(config, computation, inputData, outputData, generatedFiles);
@ -601,7 +675,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
public static List<String> command(final String cmdline, final String directory) { public static List<String> command(final String cmdline, final String directory) {
try { 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>(); List<String> output = new ArrayList<String>();
BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream())); BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));

View File

@ -29,6 +29,9 @@ public class ConfigurationManager {
private static Boolean useStorage = null; private static Boolean useStorage = null;
static boolean simulationMode = false; static boolean simulationMode = false;
EnvironmentVariableManager env = null;
public static synchronized Integer getMaxComputations(){ public static synchronized Integer getMaxComputations(){
return maxComputations; return maxComputations;
} }
@ -41,7 +44,12 @@ public class ConfigurationManager {
return simulationMode; return simulationMode;
} }
@Deprecated
public void getInitializationProperties() { public void getInitializationProperties() {
}
private void inizializePropertiesUsingTemplateFile() {
try { try {
if (maxComputations == null) { if (maxComputations == null) {
Properties options = new Properties(); Properties options = new Properties();
@ -49,6 +57,7 @@ public class ConfigurationManager {
options.load(is); options.load(is);
is.close(); is.close();
maxComputations = Integer.parseInt(options.getProperty("maxcomputations")); maxComputations = Integer.parseInt(options.getProperty("maxcomputations"));
logger.info("setting max computation to {}",maxComputations);
useStorage = Boolean.parseBoolean(options.getProperty("saveond4sstorage")); useStorage = Boolean.parseBoolean(options.getProperty("saveond4sstorage"));
simulationMode=Boolean.parseBoolean(options.getProperty("simulationMode")); simulationMode=Boolean.parseBoolean(options.getProperty("simulationMode"));
} }
@ -70,8 +79,13 @@ public class ConfigurationManager {
return username; return username;
} }
public ConfigurationManager() { public ConfigurationManager(EnvironmentVariableManager env) {
getInitializationProperties(); if (env == null) inizializePropertiesUsingTemplateFile();
else {
maxComputations = env.getMaxComputation();
useStorage = env.isSaveOnStorage();
simulationMode = env.isSimulationMode();
}
} }
public AlgorithmConfiguration getConfig() { public AlgorithmConfiguration getConfig() {
@ -88,35 +102,33 @@ public class ConfigurationManager {
config.setAlgorithmClassLoader(Thread.currentThread().getContextClassLoader()); config.setAlgorithmClassLoader(Thread.currentThread().getContextClassLoader());
String webperspath = WPSConfig.getConfigDir() + "../persistence/"; String webperspath = WPSConfig.getConfigDir() + "../persistence/";
// selecting persistence path // selecting persistence path
// String persistencePath = File.createTempFile("wpsstatcheck", ".sm").getParent() + "/../cfg/";
//TODO: REMOVE this shit (the persistence must be the persistence dir of the webapp)
String persistencePath = WPSConfig.getConfigDir() + "../ecocfg/"; String persistencePath = WPSConfig.getConfigDir() + "../ecocfg/";
String configPath = persistencePath; String configPath = persistencePath;
if (!new File(configPath).isDirectory()) { if (!new File(configPath).isDirectory()) {
configPath = "./cfg/"; configPath = "./cfg/";
persistencePath = "./"; persistencePath = "./";
} }
logger.debug("Taking configuration from " + (new File(configPath).getAbsolutePath()) + " and persistence in " + persistencePath); logger.debug("Taking configuration from {}", configPath);
//+ " and persistence in " + persistencePath);
// setting configuration and logger // setting configuration and logger
config.setPersistencePath(persistencePath); config.setPersistencePath(configPath);
config.setConfigPath(configPath); config.setConfigPath(configPath);
config.setNumberOfResources(1); config.setNumberOfResources(1);
// setting application paths // setting application paths
String webapp = WPSConfig.getInstance().getWPSConfig().getServer().getWebappPath(); String webapp = WPSConfig.getInstance().getWPSConfig().getServer().getWebappPath();
String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname(); String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
String port = WPSConfig.getInstance().getWPSConfig().getServer().getHostport(); String port = WPSConfig.getInstance().getWPSConfig().getServer().getHostport();
logger.debug("Host: " + host + " Port: " + port + " Webapp: " + webapp + " "); logger.debug("Host: {} Port: {} Webapp: {} ", host, port, webapp );
logger.debug("Web persistence path: " + webperspath); logger.debug("Web persistence path:{} ", webperspath);
String webPath = "http://" + host + ":" + port + "/" + webapp + "/persistence/"; String webPath = "http://" + host + ":" + port + "/" + webapp + "/persistence/";
// logger.debug("Env Vars: \n"+System.getenv()); // logger.debug("Env Vars: \n"+System.getenv());
logger.debug("Web app path: " + webPath); logger.debug("Web app path: {} ", webPath);
// retrieving scope // retrieving scope
scope = (String) inputs.get(scopeParameter); scope = (String) inputs.get(scopeParameter);
logger.debug("Retrieved scope: " + scope); logger.debug("Retrieved scope: {} ", scope);
if (scope == null) 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("/")) if (!scope.startsWith("/"))
@ -125,8 +137,8 @@ public class ConfigurationManager {
username = (String) inputs.get(usernameParameter); username = (String) inputs.get(usernameParameter);
token = (String) inputs.get(tokenParameter); token = (String) inputs.get(tokenParameter);
logger.debug("User name used by the client: " + username); logger.debug("User name used by the client:{} ", username);
logger.debug("User token used by the client: " + token); logger.debug("User token used by the client:{} ", token);
if (username == null || username.trim().length() == 0) 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");
@ -139,7 +151,7 @@ public class ConfigurationManager {
config.setGcubeToken(token); config.setGcubeToken(token);
// DONE get username from request // DONE get username from request
config.setParam(serviceUserNameParameterVariable, username); config.setParam(serviceUserNameParameterVariable, username);
config.setParam(processingSessionVariable, "" + UUID.randomUUID()); config.setParam(processingSessionVariable, UUID.randomUUID().toString());
config.setParam(webpathVariable, webPath); config.setParam(webpathVariable, webPath);
config.setParam(webPersistencePathVariable, webperspath); config.setParam(webPersistencePathVariable, webperspath);

View File

@ -0,0 +1,38 @@
package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping;
import java.util.List;
public class EnvironmentVariableManager {
public EnvironmentVariableManager(int maxComputation, boolean saveOnStorage, boolean simulationMode, List<String> shubUsersExcluded) {
super();
this.maxComputation = maxComputation;
this.saveOnStorage = saveOnStorage;
this.simulationMode = simulationMode;
this.shubUsersExcluded = shubUsersExcluded;
}
private int maxComputation;
private boolean saveOnStorage;
private boolean simulationMode;
//null: all users will write on SHub
//empty: no one will write on Shub
//filled: users reported will not write on Shub
private List<String> shubUsersExcluded;
public int getMaxComputation() {
return maxComputation;
}
public boolean isSaveOnStorage() {
return saveOnStorage;
}
public boolean isSimulationMode() {
return simulationMode;
}
public List<String> getShubUsersExcluded() {
return shubUsersExcluded;
}
}

View File

@ -5,6 +5,7 @@ import java.io.BufferedReader;
import java.io.File; import java.io.File;
import java.io.FileOutputStream; import java.io.FileOutputStream;
import java.io.FileReader; import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.net.HttpURLConnection; import java.net.HttpURLConnection;
import java.net.URL; import java.net.URL;
@ -43,6 +44,8 @@ public class InputsManager {
private static final Logger LOGGER = LoggerFactory.getLogger(InputsManager.class); private static final Logger LOGGER = LoggerFactory.getLogger(InputsManager.class);
private static final long SHUB_RETRY_MILLIS = 2000;
LinkedHashMap<String, Object> inputs; LinkedHashMap<String, Object> inputs;
List<String> generatedTables; List<String> generatedTables;
List<File> generatedFiles; List<File> generatedFiles;
@ -51,11 +54,11 @@ public class InputsManager {
String computationId; String computationId;
List<StoredData> provenanceData = new ArrayList<StoredData>(); List<StoredData> provenanceData = new ArrayList<StoredData>();
public List<StoredData> getProvenanceData() { public List<StoredData> getProvenanceData() {
return provenanceData; return provenanceData;
} }
public static String inputsSeparator = "\\|"; public static String inputsSeparator = "\\|";
public AlgorithmConfiguration getConfig() { public AlgorithmConfiguration getConfig() {
@ -92,7 +95,9 @@ public class InputsManager {
config.setParam("DatabaseURL", supportDatabaseInfo.url); config.setParam("DatabaseURL", supportDatabaseInfo.url);
} }
public void mergeWpsAndEcologicalInputs(DatabaseInfo supportDatabaseInfo) throws Exception { public void mergeWpsAndEcologicalInputs(DatabaseInfo supportDatabaseInfo,
List<StatisticalType> dataminerInputParameters) throws Exception {
LOGGER.debug("Merge WPS And Ecological Inputs");
// browse input parameters from WPS // browse input parameters from WPS
for (String inputName : inputs.keySet()) { for (String inputName : inputs.keySet()) {
Object input = inputs.get(inputName); Object input = inputs.get(inputName);
@ -102,7 +107,8 @@ public class InputsManager {
LOGGER.debug("Simple Input: " + input); LOGGER.debug("Simple Input: " + input);
// manage lists // manage lists
String inputAlgoOrig = ((String) input).trim(); String inputAlgoOrig = ((String) input).trim();
String inputAlgo = ((String) input).trim().replaceAll(inputsSeparator, AlgorithmConfiguration.listSeparator); String inputAlgo = ((String) input).trim().replaceAll(inputsSeparator,
AlgorithmConfiguration.listSeparator);
LOGGER.debug("Simple Input Transformed: " + inputAlgo); LOGGER.debug("Simple Input Transformed: " + inputAlgo);
config.setParam(inputName, inputAlgo); config.setParam(inputName, inputAlgo);
@ -111,11 +117,13 @@ public class InputsManager {
// case of Complex Input // case of Complex Input
else if (input instanceof GenericFileData) { else if (input instanceof GenericFileData) {
LOGGER.debug("Complex Input: " + input); LOGGER.debug("Complex Input");
// retrieve payload // retrieve payload
GenericFileData files = ((GenericFileData) input); GenericFileData files = ((GenericFileData) input);
LOGGER.debug("GenericFileData: [fileExtension=" + files.getFileExtension() + ", mimeType="
+ files.getMimeType() + "]");
List<File> localfiles = getLocalFiles(files,inputName); List<File> localfiles = getLocalFiles(files, inputName, dataminerInputParameters);
String inputtables = ""; String inputtables = "";
int nfiles = localfiles.size(); int nfiles = localfiles.size();
StringBuffer sb = new StringBuffer(); StringBuffer sb = new StringBuffer();
@ -128,7 +136,8 @@ public class InputsManager {
if (inputTableTemplates.get(inputName) != null) { if (inputTableTemplates.get(inputName) != null) {
LOGGER.debug("Creating table: " + tableName); LOGGER.debug("Creating table: " + tableName);
createTable(tableName, tableFile, config, supportDatabaseInfo, inputTableTemplates.get(inputName)); createTable(tableName, tableFile, config, supportDatabaseInfo,
inputTableTemplates.get(inputName));
generatedTables.add(tableName); generatedTables.add(tableName);
} }
// case of non-table input file, e.g. FFANN // case of non-table input file, e.g. FFANN
@ -187,60 +196,81 @@ public class InputsManager {
} }
public String inputNameFromHttpHeader(String url) throws Exception { public String inputNameFromHttpHeader(String url) throws Exception {
LOGGER.debug("Search filename in http header from: " + url);
URL obj = new URL(url); URL obj = new URL(url);
URLConnection conn = obj.openConnection(); URLConnection conn = obj.openConnection();
String filename = null; String filename = null;
// get all headers // get all headers
Map<String, List<String>> map = conn.getHeaderFields(); Map<String, List<String>> map = conn.getHeaderFields();
LOGGER.debug("Getting file name from http header");
for (Map.Entry<String, List<String>> entry : map.entrySet()) { for (Map.Entry<String, List<String>> entry : map.entrySet()) {
String value = entry.getValue().toString(); String value = entry.getValue().toString();
if (value.toLowerCase().contains("filename=")){ LOGGER.debug("Header value: " + value);
LOGGER.debug("Searching in http header: found file name in header value "+value); if (value.toLowerCase().contains("filename")) {
LOGGER.debug("Searching in http header: found file name in header value {}", value);
filename = value.substring(value.indexOf("=") + 1); filename = value.substring(value.indexOf("=") + 1);
filename = filename.replace("\"", "").replace("]", ""); filename = filename.replace("\"", "").replace("]", "");
LOGGER.debug("Searching in http header: retrieved file name "+filename); LOGGER.debug("Searching in http header: retrieved file name {}", filename);
break; break;
} }
} }
LOGGER.debug("Filename retrieved from http header: " + filename);
return filename; return filename;
} }
public List<File> getLocalFiles(GenericFileData files,String inputName) throws Exception { public List<File> getLocalFiles(GenericFileData files, String inputName,
List<StatisticalType> dataminerInputParameters) throws Exception {
LOGGER.debug("GetLocalFiles: [files: " + files + ", inputName: " + inputName + "]");
// download input // download input
List<File> filesList = new ArrayList<File>(); List<File> filesList = new ArrayList<File>();
File f = files.getBaseFile(false); File f = files.getBaseFile(false);
LOGGER.debug("Retrieving file content as a URL link: " + f.getAbsolutePath()); LOGGER.debug("Retrieving local files: " + f.getAbsolutePath());
// TODO DO NOT READ FILE INTO MEMORY // TODO DO NOT READ FILE INTO MEMORY
// read file content // read file content
String fileLink = readOneLine(f.getAbsolutePath()); String fileLink = readOneLine(f.getAbsolutePath());
LOGGER.debug("File link: " + fileLink.substring(0,Math.min(fileLink.length(),10)) + "..."); LOGGER.debug("Check File is link: {} ...", fileLink.substring(0, Math.min(fileLink.length(), 10)));
String fileName = ""; String fileName = "";
// case of a http link // case of a http link
if (fileLink!=null && fileLink.toLowerCase().startsWith("http:") || fileLink.toLowerCase().startsWith("https:")) { if (fileLink != null
&& (fileLink.toLowerCase().startsWith("http:") || fileLink.toLowerCase().startsWith("https:"))) {
// manage the case of multiple files // manage the case of multiple files
LOGGER.debug("Complex Input payload is link");
LOGGER.debug("Retrieving files from url: " + fileLink);
String[] remotefiles = fileLink.split(inputsSeparator); String[] remotefiles = fileLink.split(inputsSeparator);
for (String subfilelink : remotefiles) { for (String subfilelink : remotefiles) {
subfilelink = subfilelink.trim(); subfilelink = subfilelink.trim();
LOGGER.debug("Managing link: " + subfilelink); LOGGER.debug("Managing link: {}", subfilelink);
if (subfilelink.length() == 0) if (subfilelink.length() == 0)
continue; continue;
InputStream is = null; InputStream is = null;
HttpURLConnection urlConnection = null; HttpURLConnection urlConnection = null;
URL url = new URL(subfilelink); URL url = new URL(subfilelink);
try {
urlConnection = (HttpURLConnection) url.openConnection(); urlConnection = (HttpURLConnection) url.openConnection();
is = new BufferedInputStream(urlConnection.getInputStream()); is = new BufferedInputStream(urlConnection.getInputStream());
}catch(IOException e) {
LOGGER.warn("download from storagehub failed. Retry ongoing...");
LOGGER.debug("waiting "+SHUB_RETRY_MILLIS+" millis ");
Thread.sleep(SHUB_RETRY_MILLIS);
urlConnection = (HttpURLConnection) url.openConnection();
is = new BufferedInputStream(urlConnection.getInputStream());
LOGGER.debug(" retry success ");
}
// retrieve payload: for test purpose only // retrieve payload: for test purpose only
String fileNameTemp = inputNameFromHttpHeader(subfilelink); String fileNameTemp = inputNameFromHttpHeader(subfilelink);
if (fileNameTemp==null) LOGGER.debug("the fileNameTemp is {}", fileNameTemp);
fileName = inputName+"_[" + computationId + "]";
else if (fileNameTemp != null && !fileNameTemp.isEmpty()) {
fileName = fileNameTemp+ "_[" + computationId + "]."+FilenameUtils.getExtension(fileNameTemp); fileName = String.format("%s_(%s).%s", inputName, computationId,
FilenameUtils.getExtension(fileNameTemp));
} else {
fileName = String.format("%s_(%s).%s", inputName, computationId,
FilenameUtils.getExtension(inputName));
}
LOGGER.debug("the name of the generated file is {}", fileName);
LOGGER.debug("Retrieving remote input in file: " + fileName);
LOGGER.debug("Creating local temp file: " + fileName);
File of = new File(config.getPersistencePath(), fileName); File of = new File(config.getPersistencePath(), fileName);
FileOutputStream fos = new FileOutputStream(of); FileOutputStream fos = new FileOutputStream(of);
IOUtils.copy(is, fos); IOUtils.copy(is, fos);
@ -249,32 +279,57 @@ public class InputsManager {
fos.close(); fos.close();
urlConnection.disconnect(); urlConnection.disconnect();
filesList.add(of); filesList.add(of);
LOGGER.debug("Created local file: " + of.getAbsolutePath()); LOGGER.debug("Created local file: {}", of.getAbsolutePath());
} }
} else { } else {
LOGGER.debug("Complex Input payload is the filelink"); LOGGER.debug("Complex Input payload is file");
fileName = f.getName(); fileName = f.getName();
LOGGER.debug("Retriving local input from file: " + fileName);
if (isXML(fileLink)) LOGGER.debug("Retrieving local input from file: {}", fileName);
{
String fileExt = null;
if (isXML(fileLink)) {
String xmlFile = f.getAbsolutePath(); String xmlFile = f.getAbsolutePath();
String csvFile = xmlFile + ".csv"; String csvFile = xmlFile + ".csv";
LOGGER.debug("Transforming XML file into a csv: " + csvFile); LOGGER.debug("Transforming XML file into a csv: {} ", csvFile);
GML2CSV.parseGML(xmlFile, csvFile); GML2CSV.parseGML(xmlFile, csvFile);
LOGGER.debug("GML Parsed: " + readOneLine(csvFile)+"[..]"); LOGGER.debug("GML Parsed: {} [..]", readOneLine(csvFile));
f = new File(csvFile); f = new File(csvFile);
fileExt = "csv";
} else {
LOGGER.debug("The file is a csv: {}", f.getAbsolutePath());
fileExt = FilenameUtils.getExtension(fileName);
} }
else{
LOGGER.debug("The file is a csv: " + f.getAbsolutePath()); LOGGER.debug("Retrieve default extension");
String fileDefaultValue = null;
for (StatisticalType defaultInputParameter : dataminerInputParameters) {
if (defaultInputParameter.getName().compareTo(inputName) == 0) {
fileDefaultValue = defaultInputParameter.getDefaultValue();
break;
} }
String absFile = new File(f.getParent(),inputName+ "_[" + computationId + "].csv").getAbsolutePath(); }
LOGGER.debug("Parameter default value retrieved: " + fileDefaultValue);
if (fileDefaultValue != null && !fileDefaultValue.isEmpty()) {
int lastPointIndex = fileDefaultValue.lastIndexOf(".");
if (lastPointIndex > -1 && lastPointIndex < (fileDefaultValue.length() - 1)) {
fileExt = fileDefaultValue.substring(lastPointIndex + 1);
LOGGER.debug("Default Extension retrieved: " + fileExt);
}
}
LOGGER.debug("Use extension: " + fileExt);
String absFile = new File(f.getParent(), String.format("%s_(%s).%s", inputName, computationId, fileExt))
.getAbsolutePath();
LOGGER.debug("Renaming to: " + absFile); LOGGER.debug("Renaming to: " + absFile);
System.gc(); System.gc();
boolean renamed = f.renameTo(new File(absFile)); boolean renamed = f.renameTo(new File(absFile));
if (renamed) if (renamed)
f = new File(absFile); f = new File(absFile);
LOGGER.debug("The file has been renamed as : " + f.getAbsolutePath()+" - "+renamed); LOGGER.debug("The file has been renamed as : {} - {}", f.getAbsolutePath(), renamed);
filesList.add(f); filesList.add(f);
} }
@ -282,7 +337,8 @@ public class InputsManager {
return filesList; return filesList;
} }
public void createTable(String tableName, File tableFile, AlgorithmConfiguration config, DatabaseInfo supportDatabaseInfo, String inputTableTemplate) throws Exception { public void createTable(String tableName, File tableFile, AlgorithmConfiguration config,
DatabaseInfo supportDatabaseInfo, String inputTableTemplate) throws Exception {
// creating table // creating table
LOGGER.debug("Complex Input size after download: " + tableFile.length()); LOGGER.debug("Complex Input size after download: " + tableFile.length());
@ -308,8 +364,10 @@ public class InputsManager {
TableTemplatesMapper mapper = new TableTemplatesMapper(); TableTemplatesMapper mapper = new TableTemplatesMapper();
String createstatement = mapper.generateCreateStatement(tableName, templatename, tableStructure); String createstatement = mapper.generateCreateStatement(tableName, templatename, tableStructure);
LOGGER.debug("Creating table: " + tableName); LOGGER.debug("Creating table: " + tableName);
DatabaseUtils.createBigTable(true, tableName, supportDatabaseInfo.driver, supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url, createstatement, dbConnection); DatabaseUtils.createBigTable(true, tableName, supportDatabaseInfo.driver, supportDatabaseInfo.username,
DatabaseUtils.createRemoteTableFromFile(tableFile.getAbsolutePath(), tableName, ",", true, supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url); supportDatabaseInfo.password, supportDatabaseInfo.url, createstatement, dbConnection);
DatabaseUtils.createRemoteTableFromFile(tableFile.getAbsolutePath(), tableName, ",", true,
supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url);
} catch (Exception e) { } catch (Exception e) {
LOGGER.error("Error in database transaction ", e); LOGGER.error("Error in database transaction ", e);
@ -368,7 +426,8 @@ public class InputsManager {
return structure.toString(); return structure.toString();
} }
public void addInputServiceParameters(List<StatisticalType> agentInputs, InfrastructureDialoguer infrastructureDialoguer) throws Exception { public void addInputServiceParameters(List<StatisticalType> agentInputs,
InfrastructureDialoguer infrastructureDialoguer) throws Exception {
// check and fullfil additional parameters // check and fullfil additional parameters
DatabaseInfo dbinfo = null; DatabaseInfo dbinfo = null;
@ -436,8 +495,8 @@ public class InputsManager {
} }
private void saveInputData(String name, String description, String payload) { private void saveInputData(String name, String description, String payload) {
LOGGER.debug("SaveInputData [name="+name+", description="+description+", payload="+payload+"]");
String id = name; String id = name;
DataProvenance provenance = DataProvenance.IMPORTED; DataProvenance provenance = DataProvenance.IMPORTED;
String creationDate = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis()); String creationDate = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
@ -452,11 +511,10 @@ public class InputsManager {
type = "application/d4science"; type = "application/d4science";
} }
StoredData data = new StoredData(name, description, id, provenance, creationDate, operator, computationId, type,payload,config.getGcubeScope()); StoredData data = new StoredData(name, description, id, provenance, creationDate, operator, computationId, type,
payload, config.getGcubeScope());
provenanceData.add(data); provenanceData.add(data);
} }
} }

View File

@ -51,7 +51,8 @@ public class OutputsManager {
this.computationsession = computationsession; this.computationsession = computationsession;
} }
public LinkedHashMap<String, Object> createOutput(StatisticalType prioroutput, StatisticalType posterioroutput) throws Exception { public LinkedHashMap<String, Object> createOutput(StatisticalType prioroutput, StatisticalType posterioroutput)
throws Exception {
LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>(); LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>();
@ -102,21 +103,23 @@ public class OutputsManager {
if (ConfigurationManager.useStorage()) { if (ConfigurationManager.useStorage()) {
if (postInfo.getLocalMachineContent() != null) { if (postInfo.getLocalMachineContent() != null) {
// return the url from storage manager // return the url from storage manager
String storageurl = uploadFileOnStorage(postInfo.getLocalMachineContent(), postInfo.getMimetype()); String storageurl = uploadFileOnStorage(postInfo.getLocalMachineContent(),
postInfo.getMimetype());
postInfo.setContent(storageurl); postInfo.setContent(storageurl);
} }
} }
/* /*
else if (postInfo.getLocalMachineContent() != null) { * else if (postInfo.getLocalMachineContent() != null) { String
String url = "<wps:Reference mimeType=\""+postInfo.getMimetype()+"\" xlink:href=\""+postInfo.getContent()+"\" method=\"GET\"/>"; * url = "<wps:Reference mimeType=\""+postInfo.getMimetype()
LOGGER.debug("Reference URL: " + url); * +"\" xlink:href=\""+postInfo.getContent()
outputs.put(okey, url); * +"\" method=\"GET\"/>"; LOGGER.debug("Reference URL: " +
} * url); outputs.put(okey, url); } else
else*/ */
if (info != null) { if (info != null) {
LOGGER.debug("Found a corresponding output: " + okey); LOGGER.debug("Found a corresponding output: " + okey);
outputs.put(okey, postInfo.getContent()); outputs.put(okey, postInfo.getContent());
//add link to the file also among the non deterministic output // add link to the file also among the non deterministic
// output
if (postInfo.getLocalMachineContent() != null) { if (postInfo.getLocalMachineContent() != null) {
ndoutput.put(okey, postInfo); ndoutput.put(okey, postInfo);
} }
@ -136,15 +139,15 @@ public class OutputsManager {
// safety check for declared output, i.e. a priori output // safety check for declared output, i.e. a priori output
for (String pkey : priorOutput.keySet()) { for (String pkey : priorOutput.keySet()) {
if (outputs.get(pkey) == null) { if (outputs.get(pkey) == null) {
LOGGER.debug("Safety check: adding empty string for " + pkey+ " of type "+priorOutput.get(pkey).getClassname()); LOGGER.debug("Safety check: adding empty string for " + pkey + " of type "
+ priorOutput.get(pkey).getClassname());
outputs.put(pkey, ""); outputs.put(pkey, "");
} }
} }
LOGGER.debug("OutputsManager outputs " + outputs);
return outputs; return outputs;
} }
private void saveProvenanceData(IOWPSInformation info) { private void saveProvenanceData(IOWPSInformation info) {
String name = info.getName(); String name = info.getName();
String id = info.getName(); String id = info.getName();
@ -153,13 +156,14 @@ public class OutputsManager {
String operator = config.getAgent(); String operator = config.getAgent();
String computationId = computationsession; String computationId = computationsession;
String type = info.getMimetype(); String type = info.getMimetype();
/* if (info.getLocalMachineContent() != null) { /*
type = StoredType.DATA; * if (info.getLocalMachineContent() != null) { type = StoredType.DATA;
} * }
*/ */
String payload = info.getContent(); String payload = info.getContent();
StoredData data = new StoredData(name, info.getAbstractStr(),id, provenance, creationDate, operator, computationId, type,payload,config.getGcubeScope()); StoredData data = new StoredData(name, info.getAbstractStr(), id, provenance, creationDate, operator,
computationId, type, payload, config.getGcubeScope());
provenanceData.add(data); provenanceData.add(data);
} }
@ -171,41 +175,78 @@ public class OutputsManager {
String serviceClass = "WPS"; String serviceClass = "WPS";
String serviceName = "wps.synch"; String serviceName = "wps.synch";
String owner = config.getParam(ConfigurationManager.serviceUserNameParameterVariable); String owner = config.getParam(ConfigurationManager.serviceUserNameParameterVariable);
storageclient = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, MemoryType.VOLATILE).getClient(); storageclient = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, MemoryType.VOLATILE)
.getClient();
LOGGER.debug("Storage client ready"); LOGGER.debug("Storage client ready");
} }
private String uploadFileOnStorage(String localfile, String mimetype) throws Exception { private String uploadFileOnStorage(String localfile, String mimetype) throws Exception {
LOGGER.debug("Storing->Start uploading on storage the following file: " + localfile); LOGGER.debug("Storing->Start uploading on storage the following file: " + localfile);
File localFile = new File(localfile); File localFile = new File(localfile);
String remotef = "/wps_synch_output/" +config.getAgent()+"/"+computationsession+"/"+ localFile.getName(); String remotef = "/wps_synch_output/" + config.getAgent() + "/" + computationsession + "/"
+ localFile.getName();
String contentType=retrieveContentType(localfile);
LOGGER.debug("Retrieved Content-Type: "+contentType);
if(contentType==null||contentType.isEmpty()){
storageclient.put(true).LFile(localfile).RFile(remotef); storageclient.put(true).LFile(localfile).RFile(remotef);
} else {
String url = storageclient.getHttpUrl().RFile(remotef); storageclient.put(true,contentType).LFile(localfile).RFile(remotef);
}
String url = storageclient.getHttpsUrl().RFile(remotef);
/* /*
if (config.getGcubeScope().startsWith("/gcube")) * if (config.getGcubeScope().startsWith("/gcube")) url =
url = "http://data-d.d4science.org/uri-resolver/smp?smp-uri=" + url + "&fileName=" + localFile.getName() + "&contentType=" + mimetype; * "http://data-d.d4science.org/uri-resolver/smp?smp-uri=" + url +
else * "&fileName=" + localFile.getName() + "&contentType=" + mimetype; else
url = "http://data.d4science.org/uri-resolver/smp?smp-uri=" + url+ "&fileName=" + localFile.getName() + "&contentType=" + mimetype; * url = "http://data.d4science.org/uri-resolver/smp?smp-uri=" + url+
* "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
*/ */
LOGGER.info("Storing->Uploading finished - URL: " + url); LOGGER.info("Storing->Uploading finished - URL: " + url);
return url; return url;
} }
private String retrieveContentType(String fileName) {
String contentType=null;
if (fileName != null && !fileName.isEmpty()) {
String fileNameLowerCase = fileName.toLowerCase();
if (fileNameLowerCase.endsWith(".html") || fileNameLowerCase.endsWith(".htm")) {
contentType="text/html";
} else {
if (fileNameLowerCase.endsWith(".pdf")) {
contentType="application/pdf";
} else {
if (fileNameLowerCase.endsWith(".log") || fileNameLowerCase.endsWith(".txt")) {
contentType="text/plain";
} else {
if (fileNameLowerCase.endsWith(".json")) {
contentType="application/json";
} else {
}
}
}
}
}
return contentType;
}
public String cleanTagString(String tag) { public String cleanTagString(String tag) {
return tag.replace(" ", "_").replaceAll("[\\]\\[!\"#$%&'()*+,\\./:;<=>?@\\^`{|}~-]", ""); return tag.replace(" ", "_").replaceAll("[\\]\\[!\"#$%&'()*+,\\./:;<=>?@\\^`{|}~-]", "");
} }
public XmlObject generateNonDeterministicOutputPlain(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception { public XmlObject generateNonDeterministicOutputPlain(LinkedHashMap<String, IOWPSInformation> ndoutput)
String XMLString = "<gml:featureMember xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">\n" + " <d4science:output fid=\"outputcollection\">\n"; throws Exception {
String XMLString = "<gml:featureMember xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">\n"
+ " <d4science:output fid=\"outputcollection\">\n";
for (String key : ndoutput.keySet()) { for (String key : ndoutput.keySet()) {
IOWPSInformation info = ndoutput.get(key); IOWPSInformation info = ndoutput.get(key);
String payload = info.getContent(); String payload = info.getContent();
String mimetype = info.getMimetype(); String mimetype = info.getMimetype();
XMLString += " <d4science:k_" + cleanTagString(key) + ">" + " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </d4science:k_" + cleanTagString(key) + ">\n"; XMLString += " <d4science:k_" + cleanTagString(key) + ">" + " <d4science:Data><![CDATA["
+ payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA["
+ (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n"
+ " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </d4science:k_"
+ cleanTagString(key) + ">\n";
} }
XMLString += " </d4science:output>\n" + "</gml:featureMember>\n"; XMLString += " </d4science:output>\n" + "</gml:featureMember>\n";
@ -219,16 +260,21 @@ public class OutputsManager {
return xmlData; return xmlData;
} }
public XmlObject generateNonDeterministicOutputCollection(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception { public XmlObject generateNonDeterministicOutputCollection(LinkedHashMap<String, IOWPSInformation> ndoutput)
String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">" + throws Exception {
"\n<gml:featureMember>\n" + " <ogr:Result fid=\"F0\">\n" + String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">"
" <d4science:output fid=\"outputcollection\">\n"; + "\n<gml:featureMember>\n" + " <ogr:Result fid=\"F0\">\n"
+ " <d4science:output fid=\"outputcollection\">\n";
for (String key : ndoutput.keySet()) { for (String key : ndoutput.keySet()) {
IOWPSInformation info = ndoutput.get(key); IOWPSInformation info = ndoutput.get(key);
String payload = info.getContent(); String payload = info.getContent();
String mimetype = info.getMimetype(); String mimetype = info.getMimetype();
XMLString += " <d4science:k_" + cleanTagString(key) + ">" + " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </d4science:k_" + cleanTagString(key) + ">\n"; XMLString += " <d4science:k_" + cleanTagString(key) + ">" + " <d4science:Data><![CDATA["
+ payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA["
+ (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n"
+ " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </d4science:k_"
+ cleanTagString(key) + ">\n";
} }
XMLString += " </d4science:output>\n" + " </ogr:Result>\n</gml:featureMember>\n</ogr:FeatureCollection>"; XMLString += " </d4science:output>\n" + " </ogr:Result>\n</gml:featureMember>\n</ogr:FeatureCollection>";
@ -247,8 +293,8 @@ public class OutputsManager {
if (ndoutput.size() == 0) if (ndoutput.size() == 0)
return null; return null;
String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">" + String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">"
"\n<gml:featureMember>\n"; + "\n<gml:featureMember>\n";
int count = 0; int count = 0;
for (String key : ndoutput.keySet()) { for (String key : ndoutput.keySet()) {
IOWPSInformation info = ndoutput.get(key); IOWPSInformation info = ndoutput.get(key);
@ -256,25 +302,31 @@ public class OutputsManager {
String mimetype = info.getMimetype(); String mimetype = info.getMimetype();
String abstractStr = info.getAbstractStr(); String abstractStr = info.getAbstractStr();
LOGGER.debug("IOWPS Information: " + "name "+info.getName()+"," LOGGER.debug("IOWPS Information [name=" + info.getName() + ", abstr=" + info.getAbstractStr() + ", content="
+"abstr "+info.getAbstractStr()+"," + info.getContent() + ", def=" + info.getDefaultVal() + "]");
+"content "+info.getContent()+","
+"def "+info.getDefaultVal()+",");
if ((abstractStr==null || abstractStr.trim().length()==0) && (payload!= null && payload.trim().length()>0)) if ((abstractStr == null || abstractStr.trim().length() == 0)
&& (payload != null && payload.trim().length() > 0))
abstractStr = info.getName(); abstractStr = info.getName();
else if (abstractStr == null) else if (abstractStr == null)
abstractStr = ""; abstractStr = "";
// geospatialized // geospatialized
// XMLString += " <ogr:Result fid=\"F" + count+ "\">" + "<ogr:geometryProperty><gml:Point><gml:coordinates>0,0</gml:coordinates></gml:Point></ogr:geometryProperty>"+ " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </ogr:Result>\n"; // XMLString += " <ogr:Result fid=\"F" + count+ "\">" +
XMLString += " <ogr:Result fid=\"F" + count+ "\">" + " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + abstractStr + "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </ogr:Result>\n"; // "<ogr:geometryProperty><gml:Point><gml:coordinates>0,0</gml:coordinates></gml:Point></ogr:geometryProperty>"+
// " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n"
// + " <d4science:Description><![CDATA[" + (info.getAbstractStr() !=
// null ? info.getAbstractStr() : "") +
// "]]></d4science:Description>\n" + " <d4science:MimeType>" +
// mimetype + "</d4science:MimeType>\n" + " </ogr:Result>\n";
XMLString += " <ogr:Result fid=\"F" + count + "\">" + " <d4science:Data><![CDATA[" + payload
+ "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + abstractStr
+ "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype
+ "</d4science:MimeType>\n" + " </ogr:Result>\n";
count++; count++;
} }
XMLString += " </gml:featureMember>\n</ogr:FeatureCollection>"; XMLString += " </gml:featureMember>\n</ogr:FeatureCollection>";
LOGGER.debug("Non deterministic output: " + XMLString); LOGGER.debug("Non deterministic output: " + XMLString);
XmlObject xmlData = XmlObject.Factory.newInstance(); XmlObject xmlData = XmlObject.Factory.newInstance();

View File

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

View File

@ -13,16 +13,15 @@ import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.UUID; import java.util.UUID;
import org.gcube.common.homelibrary.home.Home; import org.gcube.common.authorization.library.provider.AuthorizationProvider;
import org.gcube.common.homelibrary.home.HomeLibrary; import org.gcube.common.storagehub.client.dsl.FileContainer;
import org.gcube.common.homelibrary.home.HomeManager; import org.gcube.common.storagehub.client.dsl.FolderContainer;
import org.gcube.common.homelibrary.home.HomeManagerFactory; import org.gcube.common.storagehub.client.dsl.ItemContainer;
import org.gcube.common.homelibrary.home.User; import org.gcube.common.storagehub.client.dsl.StorageHubClient;
import org.gcube.common.homelibrary.home.workspace.Workspace; import org.gcube.common.storagehub.model.Metadata;
import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder; import org.gcube.common.storagehub.model.exceptions.ItemLockedException;
import org.gcube.common.homelibrary.home.workspace.WorkspaceItem; import org.gcube.common.storagehub.model.items.GCubeItem;
import org.gcube.common.homelibrary.home.workspace.folder.FolderItem; import org.gcube.common.storagehub.model.items.Item;
import org.gcube.common.homelibrary.util.WorkspaceUtil;
import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools; import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper; import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper;
@ -64,12 +63,20 @@ public class DataspaceManager implements Runnable {
public static String operator = "operator_name"; public static String operator = "operator_name";
public static String payload = "payload"; public static String payload = "payload";
public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, List<File> generatedFiles) { private String statusComputationName;
private static final String STATUS_POSTFIX="-STATUS";
public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData,
List<StoredData> outputData, List<File> generatedFiles) {
this.config = config; this.config = config;
this.computation = computation; this.computation = computation;
this.inputData = inputData; this.inputData = inputData;
this.outputData = outputData; this.outputData = outputData;
this.generatedFiles = generatedFiles; this.generatedFiles = generatedFiles;
this.statusComputationName = this.computation.id+STATUS_POSTFIX;
LOGGER.debug("DataspaceManager [config=" + config + ", computation=" + computation + ", inputData=" + inputData
+ ", outputData=" + outputData + ", generatedFiles=" + generatedFiles + "]");
} }
public void run() { public void run() {
@ -88,57 +95,79 @@ public class DataspaceManager implements Runnable {
} }
public void createFoldersNetwork(Workspace ws, WorkspaceFolder root) throws Exception { public FolderContainer createFoldersNetwork() throws Exception {
LOGGER.debug("Dataspace->Creating folders for DataMiner"); LOGGER.debug("Dataspace->Creating folders for DataMiner");
// manage folders: create the folders network StorageHubClient shc = new StorageHubClient();
if (!ws.exists(dataminerFolder, root.getId())) {
LOGGER.debug("Dataspace->Creating DataMiner main folder");
root.createFolder(dataminerFolder, "A folder collecting DataMiner experiments data and computation information");
((WorkspaceFolder) root.find(dataminerFolder)).setSystemFolder(true);
}
WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
if (!ws.exists(importedDataFolder, dataminerFolderWS.getId())) { FolderContainer root = shc.getWSRoot();
List<ItemContainer<? extends Item>> dataminerItems = root.findByName(dataminerFolder).getContainers();
FolderContainer dataminerFolderContainer;
// manage folders: create the folders network
if (dataminerItems.isEmpty()) {
LOGGER.debug("Dataspace->Creating DataMiner main folder");
dataminerFolderContainer = root.newFolder(dataminerFolder,
"A folder collecting DataMiner experiments data and computation information");
// ((WorkspaceFolder)
// root.find(dataminerFolder)).setSystemFolder(true);
} else if (dataminerItems.size() > 1)
throw new Exception("found more than one dataminer folder (impossible!!!)");
else
dataminerFolderContainer = (FolderContainer) dataminerItems.get(0);
if (dataminerFolderContainer.findByName(importedDataFolder).getContainers().isEmpty()) {
LOGGER.debug("Dataspace->Creating DataMiner imported data folder"); LOGGER.debug("Dataspace->Creating DataMiner imported data folder");
dataminerFolderWS.createFolder(importedDataFolder, "A folder collecting DataMiner imported data"); dataminerFolderContainer.newFolder(importedDataFolder, "A folder collecting DataMiner imported data");
} }
if (!ws.exists(computedDataFolder, dataminerFolderWS.getId())) {
if (dataminerFolderContainer.findByName(computedDataFolder).getContainers().isEmpty()) {
LOGGER.debug("Dataspace->Creating DataMiner computed data folder"); LOGGER.debug("Dataspace->Creating DataMiner computed data folder");
dataminerFolderWS.createFolder(computedDataFolder, "A folder collecting DataMiner computed data"); dataminerFolderContainer.newFolder(computedDataFolder, "A folder collecting DataMiner computed data");
} }
if (!ws.exists(computationsFolder, dataminerFolderWS.getId())) { if (dataminerFolderContainer.findByName(computationsFolder).getContainers().isEmpty()) {
LOGGER.debug("Dataspace->Creating DataMiner computations folder"); LOGGER.debug("Dataspace->Creating DataMiner computations folder");
dataminerFolderWS.createFolder(computationsFolder, "A folder collecting DataMiner computations information"); dataminerFolderContainer.newFolder(computationsFolder,
"A folder collecting DataMiner computations information");
} }
return dataminerFolderContainer;
} }
public String uploadData(StoredData data, WorkspaceFolder wsFolder) throws Exception {
return uploadData(data, wsFolder, true); public String uploadData(StoredData data, FolderContainer destinationFolder) throws Exception {
return uploadData(data, destinationFolder, true);
} }
public String uploadData(StoredData data, WorkspaceFolder wsFolder, boolean changename) throws Exception {
public String uploadData(StoredData data, FolderContainer destinationFolder, boolean changename) throws Exception {
LOGGER.debug("Dataspace->Analysing " + data); LOGGER.debug("Dataspace->Analysing " + data);
// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name, wsFolder); // String filenameonwsString = WorkspaceUtil.getUniqueName(data.name,
// wsFolder);
String filenameonwsString = data.name; String filenameonwsString = data.name;
if (changename) if (changename)
filenameonwsString = data.name + "_[" + data.computationId + "]"+getExtension(data.payload, data.type);// ("_"+UUID.randomUUID()).replace("-", ""); filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId,
getExtension(data.payload));
InputStream in = null; InputStream in = null;
String url = ""; String url = "";
try { try {
long size = 0; //long size = 0;
if (data.type.equals("text/csv")||data.type.equals("application/d4science")||data.type.equals("image/png")) { 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")) { if (new File(data.payload).exists() || !data.payload.startsWith("http")) {
LOGGER.debug("Dataspace->Uploading file " + data.payload); LOGGER.debug("Dataspace->Uploading file {}", data.payload);
in = new FileInputStream(new File(data.payload)); in = new FileInputStream(new File(data.payload));
size = new File(data.payload).length(); //size = new File(data.payload).length();
} else { } else {
LOGGER.debug("Dataspace->Uploading via URL " + data.payload); LOGGER.debug("Dataspace->Uploading via URL {}", data.payload);
int tries = 10; int tries = 10;
for (int i = 0; i < tries; i++) { for (int i = 0; i < tries; i++) {
try { try {
URL urlc = new URL(data.payload); URL urlc = new URL(data.payload);
url = urlc.toString();
HttpURLConnection urlConnection = (HttpURLConnection) urlc.openConnection(); HttpURLConnection urlConnection = (HttpURLConnection) urlc.openConnection();
urlConnection.setConnectTimeout(10000); urlConnection.setConnectTimeout(10000);
urlConnection.setReadTimeout(10000); urlConnection.setReadTimeout(10000);
@ -157,9 +186,10 @@ public class DataspaceManager implements Runnable {
if (in == null) if (in == null)
throw new Exception("Impossible to open stream from " + data.payload); throw new Exception("Impossible to open stream from " + data.payload);
// LOGGER.debug("Dataspace->final file name on ws " + data.name+" description "+data.description); // 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);
LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>(); Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(computation_id, data.computationId); properties.put(computation_id, data.computationId);
properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname()); properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
@ -172,23 +202,24 @@ public class DataspaceManager implements Runnable {
properties.put(data_type, data.type); properties.put(data_type, data.type);
properties.put(payload, url); properties.put(payload, url);
FolderItem fileItem = WorkspaceUtil.createExternalFile(wsFolder, filenameonwsString, data.description, in,properties,data.type,size); FileContainer fileContainer = destinationFolder.uploadFile(in, filenameonwsString, data.description);
//fileItem.getProperties().addProperties(properties); fileContainer.setMetadata(new Metadata(properties));
LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString); LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString);
url = fileItem.getPublicLink(false); url = fileContainer.getPublicLink().toString();
LOGGER.debug("Dataspace->WS OP url produced for the file " + url); LOGGER.debug("Dataspace->WS OP url produced for the file " + url);
data.payload = url; data.payload = url;
try { try {
in.close(); in.close();
} catch (Exception e) { } catch (Exception e) {
LOGGER.debug("Dataspace->Error creating file " + e.getMessage()); LOGGER.debug("Dataspace->Error creating file {}", e.getMessage());
// LOGGER.debug(e); // LOGGER.debug(e);
} }
LOGGER.debug("Dataspace->File created " + filenameonwsString); LOGGER.debug("Dataspace->File created {}", filenameonwsString);
} else { } else {
LOGGER.debug("Dataspace->String parameter " + data.payload); LOGGER.debug("Dataspace->String parameter {}", data.payload);
url = data.payload; url = data.payload;
} }
} catch (Throwable e) { } catch (Throwable e) {
@ -200,75 +231,71 @@ public class DataspaceManager implements Runnable {
return url; return url;
} }
public List<String> uploadInputData(List<StoredData> inputData, WorkspaceFolder dataminerFolder) throws Exception { public List<String> uploadInputData(List<StoredData> inputData, FolderContainer dataminerFolder) throws Exception {
LOGGER.debug("Dataspace->uploading input data; Number of data: " + inputData.size()); LOGGER.debug("Dataspace->uploading input data; Number of data: {}", inputData.size());
WorkspaceItem folderItem = dataminerFolder.find(importedDataFolder); FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(importedDataFolder)
.getContainers().get(0);
List<String> urls = new ArrayList<String>(); List<String> urls = new ArrayList<String>();
if (folderItem != null && folderItem.isFolder()) {
WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem;
for (StoredData input : inputData) { for (StoredData input : inputData) {
WorkspaceItem item = null; List<ItemContainer<? extends Item>> items = null;
if (input.type.equals("text/csv")||input.type.equals("application/d4science")||input.type.equals("image/png")) if (input.type.equals("text/csv") || input.type.equals("application/d4science")
item = destinationFolder.find(input.name); || input.type.equals("image/png"))
items = destinationFolder.findByName(input.name).getContainers();
if (item==null){ if (items == null || items.isEmpty()) {
String url = uploadData(input, destinationFolder, false); String url = uploadData(input, destinationFolder, false);
LOGGER.debug("Dataspace->returning property "+url); LOGGER.debug("Dataspace->returning property {}", url);
urls.add(url); urls.add(url);
} } else {
else{ FileContainer item = (FileContainer) items.get(0);
LOGGER.debug("Dataspace->Input item "+input.name+" is already available in the input folder"); LOGGER.debug("Dataspace->Input item {} is already available in the input folder", input.name);
String url = item.getPublicLink(false); String url = item.getPublicLink().toString();
LOGGER.debug("Dataspace->returning WS url "+url); LOGGER.debug("Dataspace->returning WS url {}", url);
urls.add(url); urls.add(url);
} }
} }
} else
LOGGER.debug("Dataspace->folder is not valid");
LOGGER.debug("Dataspace->finished uploading input data"); LOGGER.debug("Dataspace->finished uploading input data");
return urls; return urls;
} }
public List<String> uploadOutputData(List<StoredData> outputData, WorkspaceFolder dataminerFolder) throws Exception { public List<String> uploadOutputData(List<StoredData> outputData, FolderContainer dataminerFolder)
throws Exception {
LOGGER.debug("Dataspace->uploading output data; Number of data: " + outputData.size()); LOGGER.debug("Dataspace->uploading output data; Number of data: " + outputData.size());
WorkspaceItem folderItem = dataminerFolder.find(computedDataFolder); FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(computedDataFolder)
.getContainers().get(0);
List<String> urls = new ArrayList<String>(); List<String> urls = new ArrayList<String>();
if (folderItem != null && folderItem.isFolder()) {
WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem;
for (StoredData output : outputData) { for (StoredData output : outputData) {
String url = uploadData(output, destinationFolder); String url = uploadData(output, destinationFolder);
urls.add(url); urls.add(url);
} }
} else
LOGGER.debug("Dataspace->folder is not valid");
LOGGER.debug("Dataspace->finished uploading output data"); LOGGER.debug("Dataspace->finished uploading output data");
return urls; return urls;
} }
public void uploadComputationData(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, WorkspaceFolder dataminerFolder, Workspace ws) throws Exception { public void uploadComputationData(ComputationData computation, List<StoredData> inputData,
List<StoredData> outputData, FolderContainer dataminerFolder) throws Exception {
LOGGER.debug("Dataspace->uploading computation data"); LOGGER.debug("Dataspace->uploading computation data");
WorkspaceItem folderItem = dataminerFolder.find(computationsFolder); FolderContainer computationContainer = (FolderContainer) dataminerFolder.findByName(computationsFolder)
if (folderItem != null && folderItem.isFolder()) { .getContainers().get(0);
// create a folder in here // create a folder in here
LOGGER.debug("Dataspace->Creating computation folder " + computation.id); LOGGER.debug("Dataspace->Creating computation folder " + computation.id);
WorkspaceFolder cfolder = ((WorkspaceFolder) folderItem);
String cfoldername = computation.id; String cfoldername = computation.id;
WorkspaceFolder newcomputationFolder = null; FolderContainer newcomputationFolder = null;
try { try {
newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription); newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
} catch (java.lang.ClassCastException e) { } catch (java.lang.ClassCastException e) {
LOGGER.debug("Dataspace->concurrency exception - deleting remaining item"); LOGGER.debug("Dataspace->concurrency exception - deleting remaining item");
deleteRunningComputationData(); deleteRunningComputationData();
newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription); newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
} }
// String itemType = "COMPUTATION"; // String itemType = "COMPUTATION";
// create IO folders // create IO folders
LOGGER.debug("Dataspace->creating IO folders under " + cfoldername); LOGGER.debug("Dataspace->creating IO folders under " + cfoldername);
newcomputationFolder.createFolder(importedDataFolder, importedDataFolder); newcomputationFolder.newFolder(importedDataFolder, importedDataFolder);
newcomputationFolder.createFolder(computedDataFolder, computedDataFolder); newcomputationFolder.newFolder(computedDataFolder, computedDataFolder);
// copy IO in those folders // copy IO in those folders
LOGGER.debug("Dataspace->*****uploading inputs in IO folder*****"); LOGGER.debug("Dataspace->*****uploading inputs in IO folder*****");
@ -281,7 +308,7 @@ public class DataspaceManager implements Runnable {
LOGGER.debug("Dataspace->creating Folder Properties"); LOGGER.debug("Dataspace->creating Folder Properties");
// write a computation item for the computation // write a computation item for the computation
LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>(); Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(computation_id, computation.id); properties.put(computation_id, computation.id);
properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname()); properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
@ -310,7 +337,7 @@ public class DataspaceManager implements Runnable {
StoredData input = inputData.get(i - 1); StoredData input = inputData.get(i - 1);
if (input.payload.contains("|")) { if (input.payload.contains("|")) {
String payload = input.payload; String payload = input.payload;
LOGGER.debug("Dataspace->Managing complex input "+input.name+" : "+payload); LOGGER.debug("Dataspace->Managing complex input {} : {}", input.name, payload);
// delete the names that are not useful // delete the names that are not useful
for (StoredData subinput : inputData) { for (StoredData subinput : inputData) {
@ -335,41 +362,45 @@ public class DataspaceManager implements Runnable {
for (int i = 1; i <= ninput; i++) { for (int i = 1; i <= ninput; i++) {
StoredData input = inputData.get(i - 1); StoredData input = inputData.get(i - 1);
if (input.name != null) { if (input.name != null) {
properties.put("input" + i + "_" + input.name, inputurls.get(i - 1)); properties.put(String.format("input%d_%s", i, input.name), inputurls.get(i - 1));
} }
} }
LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs"); LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs");
for (int i = 1; i <= noutput; i++) { for (int i = 1; i <= noutput; i++) {
properties.put("output" + i + "_" + outputData.get(i - 1).name, outputurls.get(i - 1)); properties.put(String.format("output%d_%s", i, outputData.get(i - 1).name), outputurls.get(i - 1));
} }
LOGGER.debug("Dataspace->Properties of the folder: " + properties); LOGGER.debug("Dataspace->Properties of the folder: {} ", properties);
LOGGER.debug("Dataspace->Saving properties to ProvO XML file " + noutput + " outputs"); LOGGER.debug("Dataspace->Saving properties to ProvO XML file {} outputs", noutput);
/* /*
* XStream xstream = new XStream(); String xmlproperties = xstream.toXML(properties); * XStream xstream = new XStream(); String xmlproperties =
* xstream.toXML(properties);
*/ */
try { try {
String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData); String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData);
File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID()); File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID());
FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8"); FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8");
InputStream sis = new FileInputStream(xmltosave); try (InputStream sis = new FileInputStream(xmltosave)) {
WorkspaceUtil.createExternalFile(newcomputationFolder, computation.id + ".xml", computation.operatorDescription, sis,null,"text/xml",xmltosave.length()); newcomputationFolder.uploadFile(sis, computation.id + ".xml", computation.operatorDescription);
sis.close(); }
xmltosave.delete(); xmltosave.delete();
} catch (Exception e) { } catch (Exception e) {
LOGGER.error("Dataspace->Failed creating ProvO XML file ", e); LOGGER.error("Dataspace->Failed creating ProvO XML file ", e);
} }
//List<String> scopes = new ArrayList<String>(); /*
//scopes.add(config.getGcubeScope()); * List<String> scopes = new ArrayList<String>();
//ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, newcomputationFolder.getId()); * scopes.add(config.getGcubeScope());
newcomputationFolder.getProperties().addProperties(properties); * ws.createGcubeItem(computation.id, computation.operatorDescription,
} * scopes, computation.user, itemType, properties,
* newcomputationFolder.getId());
*/
newcomputationFolder.setMetadata(new Metadata(properties));
LOGGER.debug("Dataspace->finished uploading computation data"); LOGGER.debug("Dataspace->finished uploading computation data");
} }
@ -384,26 +415,17 @@ public class DataspaceManager implements Runnable {
return payload; return payload;
} }
public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData)
public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData) throws Exception { throws Exception {
LOGGER.debug("Dataspace->connecting to Workspace"); LOGGER.debug("Dataspace->connecting to Workspace");
HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
HomeManager manager = factory.getHomeManager();
LOGGER.debug("Dataspace->getting user");
User user = manager.createUser(computation.user);
Home home = manager.getHome(user);
LOGGER.debug("Dataspace->getting root folder");
Workspace ws = home.getWorkspace();
WorkspaceFolder root = ws.getRoot();
LOGGER.debug("Dataspace->create folders network"); LOGGER.debug("Dataspace->create folders network");
createFoldersNetwork(ws, root); FolderContainer dataminerFolder = createFoldersNetwork();
WorkspaceFolder dataminerItem = (WorkspaceFolder) root.find(dataminerFolder);
LOGGER.debug("Dataspace->****uploading input files****"); LOGGER.debug("Dataspace->****uploading input files****");
uploadInputData(inputData, dataminerItem); uploadInputData(inputData, dataminerFolder);
LOGGER.debug("Dataspace->****uploading output files****"); LOGGER.debug("Dataspace->****uploading output files****");
uploadOutputData(outputData, dataminerItem); uploadOutputData(outputData, dataminerFolder);
LOGGER.debug("Dataspace->****uploading computation files****"); LOGGER.debug("Dataspace->****uploading computation files****");
uploadComputationData(computation, inputData, outputData, dataminerItem, ws); uploadComputationData(computation, inputData, outputData, dataminerFolder);
LOGGER.debug("Dataspace->provenance management finished"); LOGGER.debug("Dataspace->provenance management finished");
LOGGER.debug("Dataspace->deleting generated files"); LOGGER.debug("Dataspace->deleting generated files");
AbstractEcologicalEngineMapper.deleteGeneratedFiles(generatedFiles); AbstractEcologicalEngineMapper.deleteGeneratedFiles(generatedFiles);
@ -416,27 +438,18 @@ public class DataspaceManager implements Runnable {
} catch (Exception e) { } catch (Exception e) {
LOGGER.debug("Dataspace->impossible to delete running computation : {} ", e.getMessage()); LOGGER.debug("Dataspace->impossible to delete running computation : {} ", e.getMessage());
} }
// LOGGER.debug("Dataspace->updating computation status");
// LOGGER.debug("Dataspace->connecting to Workspace");
HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
HomeManager manager = factory.getHomeManager();
// LOGGER.debug("Dataspace->getting user");
User user = manager.createUser(computation.user);
Home home = manager.getHome(user);
// LOGGER.debug("Dataspace->getting root folder");
Workspace ws = home.getWorkspace();
WorkspaceFolder root = ws.getRoot();
// LOGGER.debug("Dataspace->create folders network"); // LOGGER.debug("Dataspace->create folders network");
createFoldersNetwork(ws, root); FolderContainer folderContainer = createFoldersNetwork();
WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder); FolderContainer computationsContainer = (FolderContainer) folderContainer.findByName(computationsFolder)
// LOGGER.debug("Dataspace->Creating computation item " + computation.id+" with status"+computation.status); .getContainers().get(0);
// LOGGER.debug("Dataspace->Creating computation item " +
// computation.id+" with status"+computation.status);
String itemType = "COMPUTATION"; String itemType = "COMPUTATION";
// write a computation item for the computation // write a computation item for the computation
LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>(); Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(computation_id, computation.id); properties.put(computation_id, computation.id);
properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname()); properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
properties.put(vre, computation.vre); properties.put(vre, computation.vre);
@ -452,7 +465,17 @@ public class DataspaceManager implements Runnable {
List<String> scopes = new ArrayList<String>(); List<String> scopes = new ArrayList<String>();
scopes.add(config.getGcubeScope()); scopes.add(config.getGcubeScope());
ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, computationsFolderItem.getId());
//TODO: update gcubeItem not recreate it...
GCubeItem gcubeItem = new GCubeItem();
gcubeItem.setName(this.statusComputationName);
gcubeItem.setDescription(computation.operatorDescription);
gcubeItem.setScopes(scopes.toArray(new String[scopes.size()]));
gcubeItem.setItemType(itemType);
gcubeItem.setMetadata(new Metadata(properties));
gcubeItem.setCreator(AuthorizationProvider.instance.get().getClient().getId());
computationsContainer.newGcubeItem(gcubeItem);
LOGGER.debug("Dataspace->finished uploading computation data"); LOGGER.debug("Dataspace->finished uploading computation data");
} }
@ -479,42 +502,50 @@ public class DataspaceManager implements Runnable {
LOGGER.debug("Dataspace->deleting computation item"); LOGGER.debug("Dataspace->deleting computation item");
LOGGER.debug("Dataspace->connecting to Workspace"); LOGGER.debug("Dataspace->connecting to Workspace");
HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory(); StorageHubClient shc = new StorageHubClient();
HomeManager manager = factory.getHomeManager(); FolderContainer dataminerContainer = (FolderContainer) shc.getWSRoot().findByName(dataminerFolder)
LOGGER.debug("Dataspace->getting user"); .getContainers().get(0);
User user = manager.createUser(computation.user); FolderContainer computationContainer = (FolderContainer) dataminerContainer.findByName(computationsFolder)
Home home = manager.getHome(user); .getContainers().get(0);
LOGGER.debug("Dataspace->getting root folder");
Workspace ws = home.getWorkspace();
WorkspaceFolder root = ws.getRoot();
WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder);
LOGGER.debug("Dataspace->removing computation data"); LOGGER.debug("Dataspace->removing computation data");
WorkspaceFolder computationsFolderWs = ((WorkspaceFolder) computationsFolderItem);
WorkspaceItem wi = computationsFolderWs.find(computation.id);
if (wi!=null){
LOGGER.debug("Dataspace->Found "+computation.id+" under "+computationsFolderWs.getName()+" - removing");
wi.remove();
}
else
LOGGER.debug("Dataspace->Warning Could not find "+computation.id+" under "+computationsFolderWs.getName());
int maxtries = 3; List<ItemContainer<? extends Item>> wi = computationContainer.findByName(this.statusComputationName).getContainers();
int i =1; if (!wi.isEmpty()) {
while (ws.exists(computation.id,computationsFolderWs.getId()) && i<maxtries){ for (ItemContainer<? extends Item> container : wi) {
LOGGER.debug("Dataspace->computation data still exist... retrying "+i); boolean retry = false;
do {
try {
container.forceDelete();
retry = false;
}catch (ItemLockedException e) {
LOGGER.warn("item locked, retrying");
Thread.sleep(1000); Thread.sleep(1000);
computationsFolderWs.find(computation.id).remove(); retry = true;
i++; }
}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++; }
*/
LOGGER.debug("Dataspace->finished removing computation data ");
} }
LOGGER.debug("Dataspace->finished removing computation data - success "+!ws.exists(computation.id,computationsFolderWs.getId())); // TODO
} public static String getExtension(String payload) {
LOGGER.debug("DataSpace->Get Extension from: " + payload);
public static String getExtension(String payload, String type){
String extension=""; String extension="";
if (type.toLowerCase().equals("text/plain")){} if (payload.toLowerCase().startsWith("http")) {
else if (payload.toLowerCase().startsWith("http")){
try { try {
URL obj = new URL(payload); URL obj = new URL(payload);
URLConnection conn = obj.openConnection(); URLConnection conn = obj.openConnection();
@ -522,23 +553,25 @@ public class DataspaceManager implements Runnable {
Map<String, List<String>> map = conn.getHeaderFields(); Map<String, List<String>> map = conn.getHeaderFields();
for (Map.Entry<String, List<String>> entry : map.entrySet()) { for (Map.Entry<String, List<String>> entry : map.entrySet()) {
String value = entry.getValue().toString(); String value = entry.getValue().toString();
if (value.toLowerCase().contains("filename=")){ LOGGER.debug("Header value: " + value);
System.out.println("DataSpace->Searching in http header: found "+value); if (value.toLowerCase().contains("filename")) {
LOGGER.debug("DataSpace->Searching in http header: found " + value);
extension = value.substring(value.lastIndexOf("."), value.lastIndexOf("\"")); extension = value.substring(value.lastIndexOf("."), value.lastIndexOf("\""));
break;
} }
} }
conn.getInputStream().close(); conn.getInputStream().close();
} catch (Exception e) { } catch (Exception e) {
System.out.println("DataSpace->Error in the payload http link "+e.getMessage()); LOGGER.warn("DataSpace->Error in the payload http link ", e);
} }
} } else {
else {
File paylFile = new File(payload); File paylFile = new File(payload);
if (paylFile.exists()) { if (paylFile.exists()) {
String paylname = paylFile.getName(); String paylname = paylFile.getName();
extension = paylname.substring(paylname.lastIndexOf(".")); extension = paylname.substring(paylname.lastIndexOf("."));
} }
} }
LOGGER.debug("DataSpace->Extension retrieved: " + extension);
return extension; return extension;
} }

View File

@ -2,7 +2,6 @@ package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.datasp
import java.io.StringReader; import java.io.StringReader;
import java.io.StringWriter; import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List; import java.util.List;
import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilder;

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

2
src/main/resources/templates/setup.cfg Normal file → Executable file
View File

@ -1,3 +1,3 @@
maxcomputations=4 maxcomputations=1
saveond4sstorage=true saveond4sstorage=true
simulationMode=false simulationMode=false

View File

@ -5,7 +5,7 @@
xsi:schemaLocation="http://www.opengis.net/wps/1.0.0 http://schemas.opengis.net/wps/1.0.0/wpsGetCapabilities_response.xsd" xsi:schemaLocation="http://www.opengis.net/wps/1.0.0 http://schemas.opengis.net/wps/1.0.0/wpsGetCapabilities_response.xsd"
updateSequence="1"> updateSequence="1">
<ows:ServiceIdentification> <ows:ServiceIdentification>
<ows:Title>D4Science WPS Service for synchronous executions</ows:Title> <ows:Title>D4Science DataMiner Service</ows:Title>
<ows:Abstract>Service based on the 52°North implementation of WPS 1.0.0</ows:Abstract> <ows:Abstract>Service based on the 52°North implementation of WPS 1.0.0</ows:Abstract>
<ows:Keywords> <ows:Keywords>
<ows:Keyword>WPS</ows:Keyword> <ows:Keyword>WPS</ows:Keyword>
@ -19,8 +19,8 @@
<ows:AccessConstraints>NONE</ows:AccessConstraints> <ows:AccessConstraints>NONE</ows:AccessConstraints>
</ows:ServiceIdentification> </ows:ServiceIdentification>
<ows:ServiceProvider> <ows:ServiceProvider>
<ows:ProviderName>National Research Council of Italy</ows:ProviderName> <ows:ProviderName>D4Science</ows:ProviderName>
<ows:ProviderSite xlink:href="www.d4science.org" /> <ows:ProviderSite xlink:href="https://www.d4science.org" />
<ows:ServiceContact> <ows:ServiceContact>
<ows:IndividualName>Gianpaolo Coro</ows:IndividualName> <ows:IndividualName>Gianpaolo Coro</ows:IndividualName>
<ows:PositionName>Researcher</ows:PositionName> <ows:PositionName>Researcher</ows:PositionName>
@ -34,7 +34,7 @@
<ows:AdministrativeArea>Istituto di Scienza e Tecnologie dell'Informazione A. Faedo</ows:AdministrativeArea> <ows:AdministrativeArea>Istituto di Scienza e Tecnologie dell'Informazione A. Faedo</ows:AdministrativeArea>
<ows:PostalCode>56124</ows:PostalCode> <ows:PostalCode>56124</ows:PostalCode>
<ows:Country>Italy</ows:Country> <ows:Country>Italy</ows:Country>
<ows:ElectronicMailAddress>gianpaolo.coro@isti.cnr.it</ows:ElectronicMailAddress> <ows:ElectronicMailAddress>dataminer-managers@d4science.org</ows:ElectronicMailAddress>
</ows:Address> </ows:Address>
</ows:ContactInfo> </ows:ContactInfo>
</ows:ServiceContact> </ows:ServiceContact>
@ -43,31 +43,29 @@
<ows:Operation name="GetCapabilities"> <ows:Operation name="GetCapabilities">
<ows:DCP> <ows:DCP>
<ows:HTTP> <ows:HTTP>
<ows:Get xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" /> <ows:Get xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Post xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" /> <ows:Post xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
</ows:HTTP> </ows:HTTP>
</ows:DCP> </ows:DCP>
</ows:Operation> </ows:Operation>
<ows:Operation name="DescribeProcess"> <ows:Operation name="DescribeProcess">
<ows:DCP> <ows:DCP>
<ows:HTTP> <ows:HTTP>
<ows:Get xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" /> <ows:Get xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Post xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" /> <ows:Post xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
</ows:HTTP> </ows:HTTP>
</ows:DCP> </ows:DCP>
</ows:Operation> </ows:Operation>
<ows:Operation name="Execute"> <ows:Operation name="Execute">
<ows:DCP> <ows:DCP>
<ows:HTTP> <ows:HTTP>
<ows:Get xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" /> <ows:Get xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Post xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" /> <ows:Post xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
</ows:HTTP> </ows:HTTP>
</ows:DCP> </ows:DCP>
</ows:Operation> </ows:Operation>
</ows:OperationsMetadata> </ows:OperationsMetadata>
<wps:ProcessOfferings> <wps:ProcessOfferings>#PROCESSES#</wps:ProcessOfferings>
#PROCESSES#
</wps:ProcessOfferings>
<wps:Languages> <wps:Languages>
<wps:Default> <wps:Default>
<ows:Language>en-GB</ows:Language> <ows:Language>en-GB</ows:Language>

View File

@ -17,21 +17,21 @@ import org.junit.Test;
public class AlgorithmTest { public class AlgorithmTest {
List<String> executeOnly = Arrays.asList(); List<String> executeOnly = Arrays.asList("#BIONYM", "#AQUAMAPS_SUITABLE", "#AQUAMAPS_SUITABLE 21 sp", "#BIONYM1024","#CMSY2");
@Test @Test
public void executeAlgorithmsFromFile() throws Exception{ public void executeAlgorithmsFromFile() throws Exception{
String env = "dev"; String env = "dev";
Properties prop = new Properties(); /*Properties prop = new Properties();
prop.load(AlgorithmTest.class.getResourceAsStream("/test_params.properties")); prop.load(AlgorithmTest.class.getResourceAsStream("/test_params.properties"));
*/
String protocol = "http"; String protocol = "http";
String hostname = prop.getProperty(env+".host"); String hostname = "dataminer-genericworkers.d4science.org";
String token = prop.getProperty(env+".token"); String token = "257800d8-24bf-4bae-83cd-ea99369e7dd6-843339462";
String layerID = prop.getProperty(env+".layer"); String layerID = "08ee0d70-4d8b-4f42-8b06-d709482bca95";
Iterator<String> uris = getUrisIterator(); Iterator<String> uris = getUrisIterator();
@ -43,7 +43,7 @@ public class AlgorithmTest {
if (nextLine.startsWith("#")) if (nextLine.startsWith("#"))
algorithmName = nextLine; algorithmName = nextLine;
else{ else{
if (!(executeOnly.isEmpty() || executeOnly.contains(algorithmName))) continue; if (executeOnly.contains(algorithmName)) continue;
String callUrl = nextLine.replace("{PROTOCOL}", protocol).replace("{HOST}", hostname).replace("{TOKEN}", token).replace("{LAYERID}", layerID); String callUrl = nextLine.replace("{PROTOCOL}", protocol).replace("{HOST}", hostname).replace("{TOKEN}", token).replace("{LAYERID}", layerID);
try{ try{
long start = System.currentTimeMillis(); long start = System.currentTimeMillis();

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@ -18,13 +18,8 @@ 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 // 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=" + 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")); URLEncoder.encode("DatabaseName=fishbase;Query=select * from food limit 100;Apply Smart Correction=false;Language=POSTGRES;ResourceName=FishBase;Read-Only Query=true;","UTF-8"));

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@ -42,7 +42,6 @@ public class TestMappedEvaluators {
public void testQualityAnalysis() throws Exception{ public void testQualityAnalysis() throws Exception{
HRS algorithm = new HRS(); 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"); // algorithm.setScope("/gcube/devsec");

52
src/test/resources/AlgorithmTestURIs.txt Normal file → Executable file
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@ -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; {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 #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=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}://goo.gl/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}://brokenlink/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;
#KMEANS #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=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}://goo.gl/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}://brokenlink/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;
#LOF #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=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}://goo.gl/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}://brokenlink/VDzpch;minimal_points_upper_bound=10;distance_function=euclidian distance;lof_threshold=2;
#XMEANS #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=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}://goo.gl/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}://brokenlink/VDzpch;FeaturesColumnNames=depthmean|sstmnmax|salinitymean;
#BIONYM #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=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}://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; {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;
#BIONYM_LOCAL #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=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 {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 #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=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}://goo.gl/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}://brokenlink/24XrmE;Take_Randomly=true;Species_Code=Fis-30189;
#HCAF_FILTER #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=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; {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 #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=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://goo.gl/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://brokenlink/5cnKKp;XResolution=0.5;OutputTableLabel=wps_maxent;
#OCCURRENCE_ENRICHMENT #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=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://goo.gl/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://brokenlink/ZfFcfE;LongitudeColumn=decimallongitude;LatitudeColumn=decimallatitude;ScientificNameColumn=scientificname;Layers={LAYERID};TimeColumn=eventdate;Resolution=0.5;
#PRESENCE_CELLS_GENERATION #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=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; {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 #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=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}://goo.gl/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}://brokenlink/sdlD5a;Longitude_Column=decimallongitude;OutputTableName=wps_fao_area_column;
#FAO_OCEAN_AREA_COLUMN_CREATOR_FROM_QUADRANT #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=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}://goo.gl/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}://brokenlink/yJTIBZ;Longitude_Column=centerlong;Quadrant_Column=quadrant;OutputTableName=wps_fao_quadrant;Latitude_Column=centerlat;
#CSQUARE_COLUMN_CREATOR #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=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}://goo.gl/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}://brokenlink/sdlD5a;Longitude_Column=decimallongitude;OutputTableName=wps_csquare_column;
#GENERIC_CHARTS #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=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}://goo.gl/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}://brokenlink/lWTvcw;TopElementsNumber=10;Attributes=x|y
#GEO_CHART #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=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}://goo.gl/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}://brokenlink/lWTvcw
#TIME_GEO_CHART #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=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}://goo.gl/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}://brokenlink/lWTvcw;
#TIME_SERIES_CHARTS #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=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}://goo.gl/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}://brokenlink/lWTvcw;Time=time
#OBIS_SPECIES_OBSERVATIONS_PER_MEOW_AREA #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=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; {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; {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 #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=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}://goo.gl/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}://brokenlink/lWTvcw;Sensitivity=LOW;SSA_Window_in_Samples=12;SSA_EigenvaluesThreshold=0.7;ValueColum=fvalue
#MAPS_COMPARISON #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=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; {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 #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=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}://goo.gl/8zWU7u;DistributionTableKeyColumn=csquarecode;DistributionTable={PROTOCOL}://goo.gl/cXbg2n;NegativeThreshold=0.3;NegativeCasesTable={PROTOCOL}://goo.gl/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}://brokenlink/8zWU7u;DistributionTableKeyColumn=csquarecode;DistributionTable={PROTOCOL}://brokenlink/cXbg2n;NegativeThreshold=0.3;NegativeCasesTable={PROTOCOL}://brokenlink/8zWU7u;
#DISCREPANCY_ANALYSIS #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=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}://goo.gl/cXbg2n;FirstTable={PROTOCOL}://goo.gl/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}://brokenlink/cXbg2n;FirstTable={PROTOCOL}://brokenlink/BBk8iB;KThreshold=0.5;MaxSamples=10000;FirstTableProbabilityColumn=probability;SecondTableProbabilityColumn=probability;FirstTableCsquareColumn=csquarecode;SecondTableCsquareColumn=csquarecode
#XYEXTRACTOR #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=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; {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 {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 #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=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}://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; {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;
#TIMEEXTRACTION_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=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}://goo.gl/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}://brokenlink/VDzpch;valueColumn=centerlong;SamplingFreq=-1;OutputTableLabel=wps_time_extr_table;
#ZEXTRACTION_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=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}://goo.gl/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}://brokenlink/VDzpch;valueColumn=oceanarea;OutputTableLabel=wps_z_table;
#HRS #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=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}://goo.gl/VDzpch;NegativeCasesTable={PROTOCOL}://goo.gl/VDzpch;OptionalCondition= ;ProjectingAreaTable={PROTOCOL}://goo.gl/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}://brokenlink/VDzpch;NegativeCasesTable={PROTOCOL}://brokenlink/VDzpch;OptionalCondition= ;ProjectingAreaTable={PROTOCOL}://brokenlink/VDzpch;FeaturesColumns=depthmin|depthmax;
#SGVM_INTERPOLATION #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=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}://goo.gl/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}://brokenlink/i16kPw;npoints=10;method=cHs;
#BIOCLIMATE_HCAF #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=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}://goo.gl/LTqufC|{PROTOCOL}://goo.gl/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}://brokenlink/LTqufC|{PROTOCOL}://brokenlink/LTqufC;HCAF_Table_Names=h1|h2
#BIOCLIMATE_HSPEN #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=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; {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; {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 #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=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}://goo.gl/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}://brokenlink/ggiPyX;
#OCCURRENCES_DUPLICATES_DELETER #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=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; {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; {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 #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=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}://goo.gl/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}://brokenlink/dYQ089;
#ECOPATH_WITH_ECOSIM #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=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; {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;