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105 Commits

Author SHA1 Message Date
Giancarlo Panichi c2bf4e3d2c Update pom.xml
Updated for gCubeRelease 6.0.0
2024-10-16 14:26:48 +02:00
Giancarlo Panichi 444efec4ca Update CHANGELOG.md
Updated to gCubeRelease 6.0.0
2024-10-16 14:25:58 +02:00
Giancarlo Panichi 527f98d0a5 Updated to gcube-bom 2.4.1-SNAPSHOT 2024-09-23 17:18:23 +02:00
Giancarlo Panichi e3280c177b Updated pom.xml 2024-09-18 16:43:04 +02:00
Giancarlo Panichi b2da0eec05 Updated nord52 repo url 2024-09-18 12:14:20 +02:00
Giancarlo Panichi 8f44e05c3e Updated maven-parent 2024-09-18 11:01:17 +02:00
Giancarlo Panichi 31e70c462f Updated 52n-wps-io-impl version 2024-09-18 10:57:24 +02:00
Giancarlo Panichi b0ceadb96d Updated 52n-wps-io-impl version 2024-09-18 10:55:18 +02:00
Giancarlo Panichi 819711eee2 Test maven-parent 2024-09-18 10:48:33 +02:00
Giancarlo Panichi fbee16c8f0 Updated gcube-bom to 2.5.0-SNAPSHOT 2024-09-18 10:23:10 +02:00
Giancarlo Panichi d5ae696ed5 Updated sensitive data 2023-01-18 19:09:39 +01:00
Giancarlo Panichi 3102594039 Updated bom to latest version [#24209] 2022-12-06 12:13:15 +01:00
Giancarlo Panichi 86bb6c207f Updated bom to latest version [#24209] 2022-12-06 11:54:51 +01:00
Giancarlo Panichi 01b71e2715 Merge branch 'master' of https://code-repo.d4science.org/gCubeSystem/dataminer.git 2022-04-07 15:27:02 +02:00
Giancarlo Panichi 561e81d244 Fixed dependencies 2022-04-07 15:25:38 +02:00
Giancarlo Panichi 7a64b7c5be Merge pull request 'feature/23107' (!3) from feature/23107 into master
Reviewed-on: #3
2022-04-07 15:23:24 +02:00
Giancarlo Panichi 8d02cd3e83 Update for gCube Release 5.10.1 2022-04-07 15:18:08 +02:00
Giancarlo Panichi d95a4908ba Updated for pre 2022-04-06 16:39:33 +02:00
Giancarlo Panichi 176b4281ed Updated for Dev Env 2022-04-05 18:27:06 +02:00
Giancarlo Panichi 2585b6142d Updated Changelog 2022-04-05 18:23:49 +02:00
Giancarlo Panichi 91caeb280b Added the support to new JWT token via URI Resolver [#23107] 2022-04-05 18:20:49 +02:00
Giancarlo Panichi 69ee033316 Updated bom for release 2022-04-01 11:55:57 +02:00
Giancarlo Panichi c1921a3762 Updated for Next Release 2022-04-01 10:32:55 +02:00
Giancarlo Panichi 5f1e4f9787 Merge pull request 'feature/23054' (!2) from feature/23054 into master
Reviewed-on: #2
2022-04-01 10:27:41 +02:00
Giancarlo Panichi 7899ababdd Updated Changelog 2022-04-01 10:25:36 +02:00
Giancarlo Panichi d2c45d0c8b Changed DatastapaceManager logs 2022-03-31 16:18:26 +02:00
Giancarlo Panichi e093239c7b Updated write exclusion behavior 2022-03-25 12:47:26 +01:00
Giancarlo Panichi 9aed0df4a4 Updated to fix protocol parameters when persistence is disabled 2022-03-21 15:57:29 +01:00
Giancarlo Panichi 1b7de34407 Minor updated 2022-03-15 17:02:12 +01:00
Giancarlo Panichi 62aa6ba5e1 Updated bom version for release 2022-03-15 17:01:33 +01:00
Giancarlo Panichi e2060ff42d Fixed pom for release 2022-03-15 11:12:16 +01:00
Giancarlo Panichi 6937be301c Merge pull request 'feature/22700' (!1) from feature/22700 into master
Reviewed-on: #1
2022-03-15 11:09:05 +01:00
Giancarlo Panichi 69980a374a Updated for release 2022-03-15 11:04:40 +01:00
Giancarlo Panichi c48f391c87 Updated gcube-bom to 2.1.0-SNAPSHOT for storagehub 2.0.0 2022-01-27 18:33:07 +01:00
Giancarlo Panichi 71f0926993 ref 22700: DataMiner - Check max computations limit
Updated max computations parameter check.
2022-01-24 18:27:56 +01:00
Roberto Cirillo 346e0b7748 Update 'CHANGELOG.md'
snapshot removed from CHANGELOG
2021-10-08 17:30:01 +02:00
Roberto Cirillo 2671a67ac1 Update 'pom.xml'
snapshot removed from pom
2021-10-08 17:29:36 +02:00
Roberto Cirillo 4265ae8e70 Update 'CHANGELOG.md'
add SNAPSHOT to 1.7.1 version
2021-10-06 12:04:25 +02:00
Roberto Cirillo 1e49f1d35d Update 'pom.xml'
add SNAPSHOT to the version
2021-10-06 12:03:56 +02:00
Giancarlo Panichi cfdd266838 Updated for Release Next 2021-06-15 15:40:52 +02:00
Giancarlo Panichi 52d41e889d Updated for accounting-lib 2021-06-15 15:31:18 +02:00
Giancarlo Panichi b800556d6f Updated for Release Next 2021-06-15 15:20:40 +02:00
Giancarlo Panichi 5cb240e97a Rebuild SNAPSHOT 2021-06-15 15:14:36 +02:00
Giancarlo Panichi 7bed8b59e9 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 e3c599d292 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 9bd2519bbc 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 e81d732ea1 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 cbea0b56f5 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 cba597494c 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 f513238cd0 Update 'pom.xml'
removed snapshot
2021-01-20 15:59:21 +01:00
Roberto Cirillo cc31ba1de2 Update 'pom.xml'
added SNAPSHOT
2021-01-19 17:02:01 +01:00
Roberto Cirillo 2e57aeb630 Update 'pom.xml'
update ecological-engine-smart-executor lower bound range
2021-01-19 16:50:15 +01:00
Roberto Cirillo ac7e337f3e Update 'pom.xml'
update ecological-engine-external-algorithms lower bound range
2021-01-19 09:46:31 +01:00
lucio.lelii bf3f8cd58c pom updated to remove old maven repositories 2021-01-18 20:01:26 +01:00
lucio.lelii a4dbd0fac2 pom updated 2020-11-30 17:48:03 +01:00
lucio.lelii bdf0b492d5 - EnviromentalVariableManager reverted
- import range changed for ecological-engine libraries
2020-11-30 17:39:25 +01:00
user1 95a92df6de config Path can be set from EnvManager 2020-11-20 16:25:19 +01:00
Giancarlo Panichi 4bff1bd79d Updated descriptor.xml 2020-06-11 14:30:40 +02:00
Giancarlo Panichi df38cb0c46 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 d1251c5b70 Renamed CHANGELOG.md 2020-06-10 15:21:32 +02:00
Giancarlo Panichi c05cce2f82 Renamed CHANGELOG.md 2020-06-10 14:54:38 +02:00
Giancarlo Panichi 0f583d0cc2 Renamed CHANGELOG.md 2020-06-10 14:44:17 +02:00
Giancarlo Panichi 7a4e80f891 Renamed CHANGELOG.md 2020-06-10 14:42:03 +02:00
roberto cirillo 3ab0201546 update to version 1.6.0:
removed snapshot, edit changelog.md
2020-05-14 17:13:57 +02:00
roberto cirillo 089733893e Merge branch 'master' of https://code-repo.d4science.org/gCubeSystem/dataminer.git 2020-05-12 15:23:53 +02:00
roberto cirillo ab13ee6e54 added shub retry on InputManager class, getLocalFile method 2020-05-12 15:23:26 +02:00
roberto cirillo 3a9957d3c5 reverting retry in order to push another retry feature
Revert "Added Retry in Input Parameter URL retrieve for fix StorageHub sync."

This reverts commit 690126d6c0.
2020-05-12 15:18:23 +02:00
Giancarlo Panichi 690126d6c0 Added Retry in Input Parameter URL retrieve for fix StorageHub sync. 2020-05-12 11:24:31 +02:00
Giancarlo Panichi 1dcab757f7 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 45701f4941 Updated to Git and Jenkins 2019-11-28 18:50:01 +01:00
Giancarlo Panichi bbec962117 Updated to Git and Jenkins 2019-11-28 11:09:46 +01:00
Giancarlo Panichi 5cdf891f29 Updated to Git and Jenkins 2019-11-26 15:55:00 +01:00
Giancarlo Panichi 56c5d7af14 Updated to support Git and Jenkins 2019-11-26 15:13:55 +01:00
Giancarlo Panichi 3d05e152ac Updated to support Git and Jenkins 2019-11-26 15:11:49 +01:00
Giancarlo Panichi 7f20c6a0b6 Updated to Git and Jenkins 2019-11-25 16:15:04 +01:00
Giancarlo Panichi 0a6e67b98e Updated to Git and Jenkins 2019-11-25 15:52:32 +01:00
Giancarlo Panichi 12370e08e5 Updated to Git and Jenkins 2019-11-25 11:58:58 +01:00
Giancarlo Panichi d56e3ef04f Updated to Git and Jenkins 2019-11-21 17:32:37 +01:00
Giancarlo Panichi fd6ea10bb9 Updated Pom to build the SNAPSHOT 2019-11-21 14:23:41 +01:00
Giancarlo Panichi ac9b4a19fe Updated to support Git and Jenkins 2019-11-20 17:23:42 +01:00
Giancarlo Panichi 215f1a3d21 Updated to support Git and Jenkins 2019-11-20 17:19:23 +01:00
Giancarlo Panichi 1b1117997e 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 b1fcb7a96f 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 7c9bfbf4bb 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 281476cb0c 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 b84c097408 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 538db67938 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 f89709c5bd 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 2f72667a0c 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 d634499e3c 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 1a4c956c34 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 4e50405169 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 703b6803ee 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 1b4b507cf2 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 13693b56b4 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 195c5e18a9 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 053e90458f 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 2b2d42d120 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 bb05e9b652 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 8447bd6fb5 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 7cb8617529 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 309f6ea62d 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 a2f124a540 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 6d3cab333f 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 c829d56e4d 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
78 changed files with 1869 additions and 940 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">
<attributes>
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<attribute name="org.eclipse.jst.component.nondependency" value=""/>
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<classpathentry kind="src" output="target/test-classes" path="src/test/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
<attribute name="test" value="true"/>
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1
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@ -0,0 +1 @@
/target/

13
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@ -5,11 +5,21 @@
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.wst.common.project.facet.core.builder</name>
<arguments>
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<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
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<name>org.eclipse.wst.validation.validationbuilder</name>
<arguments>
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<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
@ -17,7 +27,10 @@
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<nature>org.eclipse.jdt.core.javanature</nature>
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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 @@
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org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
org.eclipse.jdt.core.compiler.problem.pessimisticNullAnalysisForFreeTypeVariables=warning
org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=ignore
org.eclipse.jdt.core.compiler.problem.potentialNullReference=ignore
org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=ignore
org.eclipse.jdt.core.compiler.problem.rawTypeReference=warning
org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
org.eclipse.jdt.core.compiler.problem.redundantNullCheck=ignore
org.eclipse.jdt.core.compiler.problem.redundantSpecificationOfTypeArguments=ignore
org.eclipse.jdt.core.compiler.problem.redundantSuperinterface=ignore
org.eclipse.jdt.core.compiler.problem.reportMethodCanBePotentiallyStatic=ignore
org.eclipse.jdt.core.compiler.problem.reportMethodCanBeStatic=ignore
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.problem.specialParameterHidingField=disabled
org.eclipse.jdt.core.compiler.problem.staticAccessReceiver=warning
org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=disabled
org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=ignore
org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=ignore
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

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.settings/org.eclipse.m2e.core.prefs Normal file → Executable file
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<?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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<?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"
## [v1.9.1]
- Updated gcube-bom to 2.4.1
## [v1.9.0] - 2022-04-05
- Added support to new JWT token via URI Resolver [#23107]
## [v1.8.1] - 2022-03-21
- Update wps service to support not writing of the computation status to the user's workspace [#23054]
- Fixed protocol parameter when persistence is disabled
## [v1.8.0] - 2022-01-24
- Fixed max computations support [#22700]
## [v1.7.1] - 2021-05-24
- Fixed obsolete short urls [#20971]
## [v1.7.0] - 2020-11-20
- import range modified to resolve old repositories invalid url
## [v1.6.0] - 2020-05-12
- Added storagehub retry in InputsManager class, getLocalFile method [#19253]
## [v1.5.9] - 2019-11-20
- Fixed Content-Type support for files in the results of computations [#18096]
## [v1.5.8] - 2019-10-01
- Fixed https link for output parameter [#17659]
## [v1.5.7] - 2019-03-01
- Updated https support [#13024]
## [v1.5.2] - 2017-12-13
- added the right extension on output file
- lock file created on execution
## [v1.5.1] - 2017-09-14
- added accounting on algorithm execution
## [v1.5.0] - 2017-07-31
- 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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##6. Chain of Authorship
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##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,
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Any litigation arising between Parties, other than the European Commission, and
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exclusive jurisdiction of the competent court where the Licensor resides or
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##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
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- 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>
<fileSets>
<fileSet>
<directory>${distroDirectory}</directory>
<outputDirectory>/</outputDirectory>
<useDefaultExcludes>true</useDefaultExcludes>
<includes>
<include>README</include>
<include>LICENSE</include>
<include>changelog.xml</include>
<include>README.md</include>
<include>LICENSE.md</include>
<include>CHANGELOG.md</include>
<include>FUNDING.md</include>
<include>profile.xml</include>
</includes>
<fileMode>755</fileMode>

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${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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@ -1,210 +1,213 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<artifactId>maven-parent</artifactId>
<groupId>org.gcube.tools</groupId>
<version>1.0.0</version>
<relativePath />
</parent>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>dataminer</artifactId>
<version>1.5.3-SNAPSHOT</version>
<name>dataminer</name>
<description>An e-Infrastructure service providing state-of-the art DataMining algorithms and ecological modelling approaches under the Web Processing Service (WPS) standard.</description>
<scm>
<url>https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner</url>
</scm>
<developers>
<developer>
<name>Gianpaolo Coro</name>
<email>gianpaolo.coro@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>
<properties>
<webappDirectory>${project.build.directory}/${project.build.finalName}</webappDirectory>
<distroDirectory>distro</distroDirectory>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
</properties>
<dependencies>
<!-- https://mvnrepository.com/artifact/org.reflections/reflections-maven -->
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
<version>0.9.10</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
</dependency>
<dependency>
<groupId>org.n52.wps</groupId>
<artifactId>52n-wps-io</artifactId>
<version>3.6.1</version>
</dependency>
<dependency>
<groupId>org.n52.wps</groupId>
<artifactId>52n-wps-io-impl</artifactId>
<version>3.6.1</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>52n-wps-algorithm-gcube</artifactId>
<version>[3.6.1-SNAPSHOT,3.7.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>52n-wps-server-gcube</artifactId>
<version>[3.6.1-SNAPSHOT, 3.7.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine</artifactId>
<version>[1.8.5-SNAPSHOT,2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-wps-extension</artifactId>
<version>[1.0.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-geospatial-extensions</artifactId>
<version>[1.3.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
<exclusions>
<exclusion>
<artifactId>log4j</artifactId>
<groupId>log4j</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-external-algorithms</artifactId>
<version>[1.1.5-SNAPSHOT,2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-smart-executor</artifactId>
<version>[1.0.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-nop</artifactId>
<version>1.7.10</version>
<exclusions>
<exclusion>
<artifactId>slf4j-api</artifactId>
<groupId>org.slf4j</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<!-- <dependency> <groupId>org.gcube.common</groupId> <artifactId>common-authorization</artifactId>
</dependency> <dependency> <groupId>org.gcube.core</groupId> <artifactId>common-scope</artifactId>
</dependency> -->
<dependency>
<groupId>javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.12.1.GA</version>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>home-library-jcr</artifactId>
<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>home-library</artifactId>
<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>2.11.0</version>
</dependency>
<dependency>
<groupId>org.gcube.accounting</groupId>
<artifactId>accounting-lib</artifactId>
<version>[3.0.0-SNAPSHOT,4.0.0-SNAPSHOT)</version>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.18.1</version>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptors>
<descriptor>${distroDirectory}/descriptor.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>servicearchive</id>
<phase>install</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>n52-releases</id>
<name>52n Releases</name>
<url>http://52north.org/maven/repo/releases</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<artifactId>maven-parent</artifactId>
<groupId>org.gcube.tools</groupId>
<version>1.2.0</version>
<relativePath />
</parent>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>dataminer</artifactId>
<version>1.9.1</version>
<name>dataminer</name>
<description>An e-Infrastructure service providing state-of-the art DataMining algorithms and ecological modelling approaches under the Web Processing Service (WPS) standard.</description>
<scm>
<connection>scm:git:https://code-repo.d4science.org/gCubeSystem/${project.artifactId}.git</connection>
<developerConnection>scm:git:https://code-repo.d4science.org/gCubeSystem/${project.artifactId}.git</developerConnection>
<url>https://code-repo.d4science.org/gCubeSystem/${project.artifactId}</url>
</scm>
<developers>
<developer>
<name>Gianpaolo 52n-wps-io-implCoro</name>
<email>gianpaolo.coro@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>
<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>
<properties>
<webappDirectory>${project.build.directory}/${project.build.finalName}</webappDirectory>
<distroDirectory>distro</distroDirectory>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
</properties>
<dependencyManagement>
<!-- Old solution <dependencies> <dependency> <groupId>org.gcube.distribution</groupId>
<artifactId>maven-smartgears-bom</artifactId> <version>2.1.0</version> <type>pom</type>
<scope>import</scope> </dependency> </dependencies> -->
<dependencies>
<dependency>
<groupId>org.gcube.distribution</groupId>
<artifactId>gcube-bom</artifactId>
<version>2.4.1</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<!-- https://mvnrepository.com/artifact/org.reflections/reflections-maven -->
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
<version>0.9.10</version>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>servlet-api</artifactId>
<version>2.5</version>
</dependency>
<dependency>
<groupId>org.n52.wps</groupId>
<artifactId>52n-wps-io</artifactId>
<version>3.6.1</version>
</dependency>
<dependency>
<groupId>org.n52.wps</groupId>
<artifactId>52n-wps-io-impl</artifactId>
<version>3.6.1</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>52n-wps-algorithm-gcube</artifactId>
<version>[3.6.1,3.7.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>52n-wps-server-gcube</artifactId>
<version>[3.6.1, 3.7.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-wps-extension</artifactId>
<version>[1.0.5,2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-geospatial-extensions</artifactId>
<version>[1.5.2,2.0.0-SNAPSHOT)</version>
<exclusions>
<exclusion>
<artifactId>log4j</artifactId>
<groupId>log4j</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-external-algorithms</artifactId>
<version>[1.2.2,2.0.0-SNAPSHOT)</version>
</dependency>
<dependency>
<groupId>org.gcube.dataanalysis</groupId>
<artifactId>ecological-engine-smart-executor</artifactId>
<version>[1.6.5,2.0.0-SNAPSHOT)</version>
<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>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-nop</artifactId>
<version>1.7.10</version>
<exclusions>
<exclusion>
<artifactId>slf4j-api</artifactId>
<groupId>org.slf4j</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>javassist</groupId>
<artifactId>javassist</artifactId>
<version>3.12.1.GA</version>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>storagehub-client-library</artifactId>
</dependency>
<dependency>
<groupId>org.gcube.common</groupId>
<artifactId>storagehub-model</artifactId>
</dependency>
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>2.11.0</version>
</dependency>
<dependency>
<groupId>org.gcube.accounting</groupId>
<artifactId>accounting-lib</artifactId>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>n52-releases</id>
<name>52n Releases</name>
<url>https://52north.org/maven/repo/releases</url>
<releases>
<enabled>true</enabled>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
</project>

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{
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);
// 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+"' ");
@ -51,7 +51,7 @@ public class InfrastructureDialoguer {
dbi.driver = property.value();
}
LOGGER.debug("Found Database : "+dbi);
LOGGER.debug("Found Database : {}",dbi);
}
if (dbi.url == null)

View File

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

View File

@ -48,10 +48,16 @@ import org.n52.wps.server.AbstractAnnotatedAlgorithm;
import org.slf4j.Logger;
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);
@ -59,9 +65,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
private Observer observer = null;
private boolean cancelled = false;
private TokenManager tokenm = null;
private EnvironmentVariableManager env = null;
// inputs and outputs
public LinkedHashMap<String, Object> inputs = new LinkedHashMap<String, Object>();
public LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>();
@ -78,30 +86,41 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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);
}
public static synchronized void removeComputation(String session) {
private static synchronized void removeComputation(String session) {
runningcomputations.remove(session);
}
public static synchronized int getRuningComputations() {
private static synchronized int getRuningComputations() {
return runningcomputations.size();
}
public static synchronized String displayRunningComputations() {
private static synchronized String displayRunningComputations() {
return runningcomputations.toString();
}
public void waitForResources() throws Exception {
while (getRuningComputations() > ConfigurationManager.getMaxComputations()) {
Thread.sleep(20000);
private void waitForResources(String computationSession, String username, String scope) throws Exception {
while (waitCondition(computationSession, username, scope)) {
Thread.sleep(COMPUTATION_WAIT_FOR_RUN_REQUEST);
LOGGER.debug("Waiting for resources to be available: " + displayRunningComputations());
}
}
private static synchronized boolean waitCondition(String computationSession, String username, String scope) {
if (getRuningComputations() >= ConfigurationManager.getMaxComputations()) {
return true;
} else {
// add the computation to the global list of computations
LOGGER.debug("Add computation to run: {}", computationSession);
addComputation(computationSession, username + ":" + scope);
return false;
}
}
// inner objects
public AlgorithmConfiguration config;
public InfrastructureDialoguer infrastructureDialoguer;
@ -203,7 +222,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
LOGGER.debug("Could not drop Temporary Table: " + table + " table is null");
}
} catch (Exception e) {
LOGGER.error("error deleting temporary table",e);
LOGGER.error("error deleting temporary table", e);
} finally {
DatabaseUtils.closeDBConnection(dbConnection);
}
@ -246,14 +265,16 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
float previousStatus = -3;
String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
public void updateStatus(float status) {
public void updateStatus(float status, boolean canWrite) {
if (agent != null) {
if (status != previousStatus) {
LOGGER.debug("STATUS update to: {} ", status );
LOGGER.debug("STATUS update to: {} ", status);
previousStatus = status;
super.update(new Integer((int) status));
try {
updateComputationOnWS(status, null);
if (canWrite)
updateComputationOnWS(status, null);
} catch (Exception e) {
LOGGER.warn("error updating compution on WS");
}
@ -262,16 +283,21 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
}
public void setEnvironmentVariableManager(EnvironmentVariableManager env) {
this.env = env;
}
public void updateComputationOnWS(float status, String exception) {
updateComputationOnWS(status, exception, null, null);
}
class RunDataspaceManager implements Runnable{
class RunDataspaceManager implements Runnable {
List<StoredData> inputData;
List<File> generatedData;
public RunDataspaceManager(List<StoredData> inputData, List<File> generatedData){
this.inputData=inputData;
this.generatedData=generatedData;
public RunDataspaceManager(List<StoredData> inputData, List<File> generatedData) {
this.inputData = inputData;
this.generatedData = generatedData;
}
public void run() {
@ -280,34 +306,35 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
LOGGER.debug("Dataspace->Status updater->Writing computational info on the WS asyncronously");
manager.writeRunningComputationData();
} catch (Exception ez) {
LOGGER.error("Dataspace->Status updater->Impossible to write computation information on the Workspace",ez);
LOGGER.error("Dataspace->Status updater->Impossible to write computation information on the Workspace",
ez);
}
}
};
public void updateComputationOnWS(float status, String exception, List<StoredData> inputData, List<File> generatedData) {
public void updateComputationOnWS(float status, String exception, List<StoredData> inputData,
List<File> generatedData) {
if (currentComputation != null) {
currentComputation.setStatus("" + status);
if (exception != null && exception.length() > 0)
currentComputation.setException(exception);
RunDataspaceManager rundm = new RunDataspaceManager(inputData,generatedData);
LOGGER.debug("RunDataspaceManager: [inputData=" + inputData + ", generatedData=" + generatedData + "]");
RunDataspaceManager rundm = new RunDataspaceManager(inputData, generatedData);
rundm.run();
/*
Thread t = new Thread(rundm);
t.start();
* Thread t = new Thread(rundm); t.start();
*/
}
}
@Execute
public void run() throws Exception {
if (observer!=null)
if (observer != null)
observer.isStarted(this);
LOGGER.info("classloader context in this thread is {}",Thread.currentThread().getContextClassLoader());
LOGGER.info("classloader context in this thread is {}", Thread.currentThread().getContextClassLoader());
long startTimeLong = System.currentTimeMillis();
OperationResult operationResult = null;
@ -316,7 +343,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
List<String> generatedInputTables = null;
List<String> generatedOutputTables = null;
List<File> generatedFiles = null;
//String date = new java.text.SimpleDateFormat("dd_MM_yyyy_HH:mm:ss").format(System.currentTimeMillis());
// String date = new
// java.text.SimpleDateFormat("dd_MM_yyyy_HH:mm:ss").format(System.currentTimeMillis());
String computationSession = this.getAlgorithmClass().getSimpleName() + "_ID_" + UUID.randomUUID().toString();
if (wpsExternalID != null) {
LOGGER.info("Using wps External ID " + wpsExternalID);
@ -324,13 +352,19 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
} else
LOGGER.info("Wps External ID not set");
InputsManager inputsManager = null;
ConfigurationManager configManager = new ConfigurationManager(); // initializes parameters from file
ConfigurationManager configManager = new ConfigurationManager(this.env); // initializes
// parameters
// from
// web.xml
manageUserToken();
boolean canWriteOnShub = checkWriteAuthorization(tokenm.getUserName());
Path dir = Paths.get(System.getProperty("java.io.tmpdir"), "dmlocks");
if (!Files.exists(dir))
dir = Files.createDirectory(dir);
Path lockFile = Files.createTempFile(dir, "dm", ".lck");
LOGGER.info("lock file created {}",lockFile.toUri().toURL());
LOGGER.info("lock file created {}", lockFile.toUri().toURL());
try {
// wait for server resources to be available
@ -344,17 +378,17 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
config = configManager.getConfig();
LOGGER.info("Configured algorithm with session " + computationSession);
time("Configuration");
waitForResources();
waitForResources(computationSession, configManager.getUsername(), configManager.getScope());
LOGGER.info("Running algorithm with session " + computationSession);
time("Waiting time for resources to be free");
// add the computation to the global list of computations
addComputation(computationSession, configManager.getUsername() + ":" + configManager.getScope());
String scope = configManager.getScope();
String username = configManager.getUsername();
LOGGER.info("1 - Algorithm environment initialized in scope " + scope + " with user name " + username + " and session " + computationSession);
LOGGER.info("Max allowed computations " + ConfigurationManager.getMaxComputations() + " using storage " + ConfigurationManager.useStorage());
LOGGER.info("1 - Algorithm environment initialized in scope " + scope + " with user name " + username
+ " and session " + computationSession);
LOGGER.info("Max allowed computations " + ConfigurationManager.getMaxComputations() + " using storage "
+ ConfigurationManager.useStorage());
// init the infrastructure dialoguer
LOGGER.info("2 - Initializing connection to the e-Infrastructure");
infrastructureDialoguer = new InfrastructureDialoguer(scope);
@ -380,15 +414,19 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
time("Ecological Engine Algorithm selection");
// 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");
// merging wps with ecological engine parameters - modifies the
// config
LOGGER.info("6 - Translating WPS Inputs into Ecological Engine Inputs");
LOGGER.debug("Operator class is " + this.getClass().getCanonicalName());
// build computation Data
currentComputation = new ComputationData(config.getTaskID(), config.getAgent(), "", "", startTime, "-", "0", config.getTaskID(), configManager.getUsername(), config.getGcubeScope(), this.getClass().getCanonicalName());
inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo);
currentComputation = new ComputationData(config.getTaskID(), config.getAgent(), "", "", startTime, "-", "0",
config.getTaskID(), configManager.getUsername(), config.getGcubeScope(),
this.getClass().getCanonicalName());
inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo, dataminerInputParameters);
generatedInputTables = inputsManager.getGeneratedTables();
generatedFiles = inputsManager.getGeneratedInputFiles();
time("Setup and download of input parameters with tables creation");
@ -412,11 +450,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
LOGGER.info("9 - Running the computation and updater");
LOGGER.info("Initializing the WPS status of the computation");
updateStatus(0);
updateStatus(0, canWriteOnShub);
LOGGER.info("Initializing the computation");
agent.init();
LOGGER.info("Updating status");
runStatusUpdater();
runStatusUpdater(canWriteOnShub);
LOGGER.info("Running the computation");
agent.compute();
LOGGER.info("The computation has finished. Retrieving output");
@ -440,13 +478,15 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
outputmanager.shutdown();
// delete all temporary tables
LOGGER.info("12 - Deleting possible generated temporary tables");
LOGGER.debug("Final Computation Output: " + outputs);
LOGGER.debug("12 - Final Computation Output");
LOGGER.debug("Outputs: " + outputs);
endTime = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
if (!isCancelled()) {
saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent, generatedFiles);
LOGGER.debug("Save Computation Data");
if (canWriteOnShub)
saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent,
generatedFiles);
} else {
LOGGER.debug("Computation interrupted - no update");
throw new Exception("Computation cancelled");
@ -455,21 +495,26 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
operationResult = OperationResult.SUCCESS;
} catch (Exception e) {
operationResult = OperationResult.FAILED;
LOGGER.error("Error execution Algorithm {}",algorithm,e);
LOGGER.error("Error execution Algorithm {}", algorithm, e);
int exitstatus = -2;
if (isCancelled())
exitstatus = -1;
if (inputsManager != null)
updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(), generatedFiles);
else
updateComputationOnWS(exitstatus, e.getMessage());
if (canWriteOnShub)
updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(),
generatedFiles);
else if (canWriteOnShub)
updateComputationOnWS(exitstatus, e.getMessage());
if (isCancelled())
throw new Exception("Computation cancelled");
else
throw e;
} finally {
LOGGER.debug("accounting algorithm");
if (operationResult == null) {
operationResult = OperationResult.FAILED;
}
accountAlgorithmExecution(startTimeLong, System.currentTimeMillis(), operationResult);
LOGGER.debug("Deleting Input Tables");
deleteTemporaryTables(generatedInputTables);
@ -483,60 +528,98 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
time("Cleaning of resources");
displayTimes();
cleanResources();
if (observer!=null) observer.isFinished(this);
if (observer != null)
observer.isFinished(this);
LOGGER.debug("All done - Computation Finished");
Files.deleteIfExists(lockFile);
}
}
private boolean checkWriteAuthorization(String username) {
if (env != null) {
if (env.getShubUsersExcluded() != null) {
if (env.getShubUsersExcluded().isEmpty()) {
// all users write
return true;
}
if (env.getShubUsersExcluded().contains(username)) {
return false;
} else {
// username write
return true;
}
} else {
//This is the * case, no users write.
return false;
}
} else {
return false;
}
}
private void accountAlgorithmExecution(long start, long end, OperationResult result) {
try{
try {
JobUsageRecord jobUsageRecord = new JobUsageRecord();
jobUsageRecord.setJobName(this.getAlgorithmClass().getSimpleName());
jobUsageRecord.setConsumerId(tokenm.getUserName());
jobUsageRecord.setDuration(end-start);
jobUsageRecord.setDuration(end - start);
jobUsageRecord.setOperationResult(result);
jobUsageRecord.setServiceName("DataMiner");
jobUsageRecord.setServiceClass("WPS");
jobUsageRecord.setHost(WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
jobUsageRecord.setCallerQualifier(tokenm.getTokenQualifier());
AccountingPersistence accountingPersistence =
AccountingPersistenceFactory.getPersistence();
AccountingPersistence accountingPersistence = AccountingPersistenceFactory.getPersistence();
accountingPersistence.account(jobUsageRecord);
}catch(Throwable e){
LOGGER.error("error accounting algorithm execution",e);
} catch (Throwable e) {
LOGGER.error("error accounting algorithm execution", e);
}
}
public class StatusUpdater implements Runnable {
private boolean canWrite = true;
public StatusUpdater(boolean canWrite) {
this.canWrite = canWrite;
}
@Override
public void run() {
while (agent != null && !isCancelled() && agent.getStatus() < 100) {
try {
updateStatus(agent.getStatus());
updateStatus(agent.getStatus(), canWrite);
Thread.sleep(10000);
} catch (InterruptedException e) {}
} catch (InterruptedException e) {
}
}
LOGGER.info("Status updater terminated");
}
}
private void runStatusUpdater() {
StatusUpdater updater = new StatusUpdater();
private void runStatusUpdater(boolean canWrite) {
StatusUpdater updater = new StatusUpdater(canWrite);
Thread t = new Thread(updater);
t.start();
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());
ComputationData computation = new ComputationData(config.getTaskID(), config.getAgent(), agent.getDescription(), agent.getInfrastructure().name(), startTime, endTime, "100", config.getTaskID(), config.getParam(ConfigurationManager.serviceUserNameParameterVariable), config.getGcubeScope(), this.getClass().getCanonicalName());
ComputationData computation = new ComputationData(config.getTaskID(), config.getAgent(), agent.getDescription(),
agent.getInfrastructure().name(), startTime, endTime, "100", config.getTaskID(),
config.getParam(ConfigurationManager.serviceUserNameParameterVariable), config.getGcubeScope(),
this.getClass().getCanonicalName());
// post on WS
DataspaceManager manager = new DataspaceManager(config, computation, inputData, outputData, generatedFiles);
@ -601,7 +684,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
public static List<String> command(final String cmdline, final String directory) {
try {
Process process = new ProcessBuilder(new String[] { "bash", "-c", cmdline }).redirectErrorStream(true).directory(new File(directory)).start();
Process process = new ProcessBuilder(new String[] { "bash", "-c", cmdline }).redirectErrorStream(true)
.directory(new File(directory)).start();
List<String> output = new ArrayList<String>();
BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));
@ -622,16 +706,16 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
@Override
public void setObserver(Observer o) {
LOGGER.debug("setting observer in {} ",wpsExternalID);
this.observer = o;
LOGGER.debug("setting observer in {} ", wpsExternalID);
this.observer = o;
}
@Override
public synchronized boolean cancel() {
if (!cancelled){
LOGGER.debug("COMPUTATION INTERRUPTED! ({})",wpsExternalID);
try{
if (agent!=null){
if (!cancelled) {
LOGGER.debug("COMPUTATION INTERRUPTED! ({})", wpsExternalID);
try {
if (agent != null) {
agent.shutdown();
agent = null;
}
@ -644,12 +728,12 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
}
System.gc();
cancelled = true;
}catch(Exception e){
LOGGER.warn("error cancelling computation with id {}",wpsExternalID);
} catch (Exception e) {
LOGGER.warn("error cancelling computation with id {}", wpsExternalID);
return false;
}
} else {
LOGGER.debug("COMPUTATION ALREADY INTERRUPT! ({})",wpsExternalID);
LOGGER.debug("COMPUTATION ALREADY INTERRUPT! ({})", wpsExternalID);
return false;
}
return true;

View File

@ -14,7 +14,7 @@ import org.slf4j.LoggerFactory;
public class ConfigurationManager {
private static final Logger logger = LoggerFactory.getLogger(ConfigurationManager.class);
public static String serviceUserNameParameterVariable = "ServiceUserName";
public static String processingSessionVariable = "Session";
public static String webpathVariable = "WebPath";
@ -22,26 +22,33 @@ public class ConfigurationManager {
public static String usernameParameter = "user.name";
public static String scopeParameter = "scope";
public static String tokenParameter = "usertoken";
public static String defaultScope= "/gcube/devsec";
public static String defaultUsername= "statistical.wps";
public static String defaultScope = "/gcube/devsec";
public static String defaultUsername = "statistical.wps";
private static Integer maxComputations = null;
private static Boolean useStorage = null;
static boolean simulationMode = false;
public static synchronized Integer getMaxComputations(){
EnvironmentVariableManager env = null;
public static synchronized Integer getMaxComputations() {
return maxComputations;
}
public static synchronized Boolean useStorage(){
public static synchronized Boolean useStorage() {
return useStorage;
}
public static synchronized Boolean isSimulationMode(){
public static synchronized Boolean isSimulationMode() {
return simulationMode;
}
@Deprecated
public void getInitializationProperties() {
}
private void inizializePropertiesUsingTemplateFile() {
try {
if (maxComputations == null) {
Properties options = new Properties();
@ -49,11 +56,12 @@ public class ConfigurationManager {
options.load(is);
is.close();
maxComputations = Integer.parseInt(options.getProperty("maxcomputations"));
logger.info("setting max computation to {}", maxComputations);
useStorage = Boolean.parseBoolean(options.getProperty("saveond4sstorage"));
simulationMode=Boolean.parseBoolean(options.getProperty("simulationMode"));
simulationMode = Boolean.parseBoolean(options.getProperty("simulationMode"));
}
} catch (Exception e) {
logger.error("error initializing properties",e);
logger.error("error initializing properties", e);
}
}
@ -70,67 +78,74 @@ public class ConfigurationManager {
return username;
}
public ConfigurationManager() {
getInitializationProperties();
public ConfigurationManager(EnvironmentVariableManager env) {
if (env == null)
inizializePropertiesUsingTemplateFile();
else {
maxComputations = env.getMaxComputation();
useStorage = env.isSaveOnStorage();
simulationMode = env.isSimulationMode();
}
}
public AlgorithmConfiguration getConfig() {
return config;
}
public void setComputationId(String computationId){
public void setComputationId(String computationId) {
config.setTaskID(computationId);
}
public void configAlgorithmEnvironment(LinkedHashMap<String, Object> inputs) throws Exception {
// set config container
config = new AlgorithmConfiguration();
config.setAlgorithmClassLoader(Thread.currentThread().getContextClassLoader());
String webperspath = WPSConfig.getConfigDir() + "../persistence/";
// 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 configPath = persistencePath;
if (!new File(configPath).isDirectory()) {
configPath = "./cfg/";
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
config.setPersistencePath(persistencePath);
config.setPersistencePath(configPath);
config.setConfigPath(configPath);
config.setNumberOfResources(1);
// setting application paths
String protocol = WPSConfig.getInstance().getWPSConfig().getServer().getProtocol();
String webapp = WPSConfig.getInstance().getWPSConfig().getServer().getWebappPath();
String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
String port = WPSConfig.getInstance().getWPSConfig().getServer().getHostport();
logger.debug("Host: " + host + " Port: " + port + " Webapp: " + webapp + " ");
logger.debug("Web persistence path: " + webperspath);
String webPath = "http://" + host + ":" + port + "/" + webapp + "/persistence/";
logger.debug("Protocol: {} , Host: {} , Port: {} , Webapp: {} ", protocol, host, port, webapp);
logger.info("Web Path Persistence: {}", webperspath);
String webPath = protocol + "://" + host + ":" + port + "/" + webapp + "/persistence/";
// logger.debug("Env Vars: \n"+System.getenv());
logger.debug("Web app path: " + webPath);
logger.info("Web Path Persistence Url: {}", webPath);
// retrieving scope
scope = (String) inputs.get(scopeParameter);
logger.debug("Retrieved scope: " + scope);
logger.debug("Retrieved scope: {} ", scope);
if (scope == null)
throw new Exception("Error: scope parameter (scope) not set! This violates e-Infrastructure security policies");
throw new Exception(
"Error: scope parameter (scope) not set! This violates e-Infrastructure security policies");
if (!scope.startsWith("/"))
scope = "/" + scope;
username = (String) inputs.get(usernameParameter);
token = (String) inputs.get(tokenParameter);
logger.debug("User name used by the client: " + username);
logger.debug("User token used by the client: " + token);
logger.debug("User name used by the client:{} ", username);
logger.debug("User token used by the client:{} ", token);
if (username == null || username.trim().length() == 0)
throw new Exception("Error: user name parameter (user.name) not set! This violates e-Infrastructure security policies");
throw new Exception(
"Error: user name parameter (user.name) not set! This violates e-Infrastructure security policies");
if (token == null || token.trim().length() == 0)
throw new Exception("Error: token parameter not set! This violates e-Infrastructure security policies");
@ -139,7 +154,7 @@ public class ConfigurationManager {
config.setGcubeToken(token);
// DONE get username from request
config.setParam(serviceUserNameParameterVariable, username);
config.setParam(processingSessionVariable, "" + UUID.randomUUID());
config.setParam(processingSessionVariable, UUID.randomUUID().toString());
config.setParam(webpathVariable, webPath);
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.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.net.HttpURLConnection;
import java.net.URL;
@ -41,7 +42,9 @@ import org.slf4j.LoggerFactory;
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;
List<String> generatedTables;
@ -51,11 +54,11 @@ public class InputsManager {
String computationId;
List<StoredData> provenanceData = new ArrayList<StoredData>();
public List<StoredData> getProvenanceData() {
return provenanceData;
}
public static String inputsSeparator = "\\|";
public AlgorithmConfiguration getConfig() {
@ -92,30 +95,35 @@ public class InputsManager {
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
for (String inputName : inputs.keySet()) {
Object input = inputs.get(inputName);
LOGGER.debug("Managing Input Parameter with Name "+ inputName);
LOGGER.debug("Managing Input Parameter with Name " + inputName);
// case of simple input
if (input instanceof String) {
LOGGER.debug("Simple Input: "+ input);
LOGGER.debug("Simple Input: " + input);
// manage lists
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);
config.setParam(inputName, inputAlgo);
saveInputData(inputName,inputName,inputAlgoOrig);
saveInputData(inputName, inputName, inputAlgoOrig);
}
// case of Complex Input
else if (input instanceof GenericFileData) {
LOGGER.debug("Complex Input: " + input);
LOGGER.debug("Complex Input");
// retrieve payload
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 = "";
int nfiles = localfiles.size();
StringBuffer sb = new StringBuffer();
@ -128,10 +136,11 @@ public class InputsManager {
if (inputTableTemplates.get(inputName) != null) {
LOGGER.debug("Creating table: " + tableName);
createTable(tableName, tableFile, config, supportDatabaseInfo, inputTableTemplates.get(inputName));
createTable(tableName, tableFile, config, supportDatabaseInfo,
inputTableTemplates.get(inputName));
generatedTables.add(tableName);
}
//case of non-table input file, e.g. FFANN
// case of non-table input file, e.g. FFANN
else
tableName = tableFile.getAbsolutePath();
if (i > 0)
@ -140,13 +149,13 @@ public class InputsManager {
inputtables += tableName;
saveInputData(tableFile.getName(), inputName, tableFile.getAbsolutePath());
if (i>0)
if (i > 0)
sb.append("|");
sb.append(tableFile.getName());
}
sb.append("|");
if (nfiles>0)
if (nfiles > 0)
saveInputData(inputName, inputName, sb.toString());
// the only possible complex input is a table - check the WPS
@ -157,15 +166,15 @@ public class InputsManager {
}
public boolean isXML(String fileContent){
public boolean isXML(String fileContent) {
if (fileContent.startsWith("&lt;"))
return true;
else
else
return false;
}
public String readOneLine(String filename){
public String readOneLine(String filename) {
try {
BufferedReader in = new BufferedReader(new FileReader(new File(filename)));
@ -173,7 +182,7 @@ public class InputsManager {
String vud = "";
while ((line = in.readLine()) != null) {
if (line.trim().length()>0){
if (line.trim().length() > 0) {
vud = line.trim();
break;
}
@ -183,64 +192,85 @@ public class InputsManager {
} catch (Exception e) {
e.printStackTrace();
return null;
}
}
}
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);
URLConnection conn = obj.openConnection();
String filename=null;
String filename = null;
// get all headers
Map<String, List<String>> map = conn.getHeaderFields();
LOGGER.debug("Getting file name from http header");
for (Map.Entry<String, List<String>> entry : map.entrySet()) {
String value = entry.getValue().toString();
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=filename.replace("\"", "").replace("]", "");
LOGGER.debug("Searching in http header: retrieved file name "+filename);
LOGGER.debug("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 = filename.replace("\"", "").replace("]", "");
LOGGER.debug("Searching in http header: retrieved file name {}", filename);
break;
}
}
LOGGER.debug("Filename retrieved from http header: " + 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
List<File> filesList = new ArrayList<File>();
File f = files.getBaseFile(false);
LOGGER.debug("Retrieving file content as a URL link: " + f.getAbsolutePath());
//TODO DO NOT READ FILE INTO MEMORY
LOGGER.debug("Retrieving local files: " + f.getAbsolutePath());
// TODO DO NOT READ FILE INTO MEMORY
// read file content
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 = "";
// 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
LOGGER.debug("Complex Input payload is link");
LOGGER.debug("Retrieving files from url: " + fileLink);
String[] remotefiles = fileLink.split(inputsSeparator);
for (String subfilelink : remotefiles) {
subfilelink = subfilelink.trim();
LOGGER.debug("Managing link: " + subfilelink);
LOGGER.debug("Managing link: {}", subfilelink);
if (subfilelink.length() == 0)
continue;
InputStream is = null;
HttpURLConnection urlConnection = null;
URL url = new URL(subfilelink);
urlConnection = (HttpURLConnection) url.openConnection();
is = new BufferedInputStream(urlConnection.getInputStream());
try {
urlConnection = (HttpURLConnection) url.openConnection();
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
String fileNameTemp = inputNameFromHttpHeader(subfilelink);
if (fileNameTemp==null)
fileName = inputName+"_[" + computationId + "]";
else
fileName = fileNameTemp+ "_[" + computationId + "]."+FilenameUtils.getExtension(fileNameTemp);
LOGGER.debug("the fileNameTemp is {}", fileNameTemp);
if (fileNameTemp != null && !fileNameTemp.isEmpty()) {
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);
FileOutputStream fos = new FileOutputStream(of);
IOUtils.copy(is, fos);
@ -249,32 +279,57 @@ public class InputsManager {
fos.close();
urlConnection.disconnect();
filesList.add(of);
LOGGER.debug("Created local file: " + of.getAbsolutePath());
LOGGER.debug("Created local file: {}", of.getAbsolutePath());
}
} else {
LOGGER.debug("Complex Input payload is the filelink");
LOGGER.debug("Complex Input payload is file");
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 csvFile = xmlFile+".csv";
LOGGER.debug("Transforming XML file into a csv: " + csvFile);
String csvFile = xmlFile + ".csv";
LOGGER.debug("Transforming XML file into a csv: {} ", csvFile);
GML2CSV.parseGML(xmlFile, csvFile);
LOGGER.debug("GML Parsed: " + readOneLine(csvFile)+"[..]");
LOGGER.debug("GML Parsed: {} [..]", readOneLine(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("Renaming to: "+absFile);
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);
System.gc();
boolean renamed = f.renameTo(new File(absFile));
if (renamed)
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);
}
@ -282,7 +337,8 @@ public class InputsManager {
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
LOGGER.debug("Complex Input size after download: " + tableFile.length());
@ -308,11 +364,13 @@ public class InputsManager {
TableTemplatesMapper mapper = new TableTemplatesMapper();
String createstatement = mapper.generateCreateStatement(tableName, templatename, tableStructure);
LOGGER.debug("Creating table: " + tableName);
DatabaseUtils.createBigTable(true, tableName, supportDatabaseInfo.driver, supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url, createstatement, dbConnection);
DatabaseUtils.createRemoteTableFromFile(tableFile.getAbsolutePath(), tableName, ",", true, supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url);
DatabaseUtils.createBigTable(true, tableName, supportDatabaseInfo.driver, supportDatabaseInfo.username,
supportDatabaseInfo.password, supportDatabaseInfo.url, createstatement, dbConnection);
DatabaseUtils.createRemoteTableFromFile(tableFile.getAbsolutePath(), tableName, ",", true,
supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url);
} catch (Exception e) {
LOGGER.error("Error in database transaction " ,e);
LOGGER.error("Error in database transaction ", e);
throw new Exception("Error in creating the table for " + tableName + ": " + e.getLocalizedMessage());
} finally {
DatabaseUtils.closeDBConnection(dbConnection);
@ -368,7 +426,8 @@ public class InputsManager {
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
DatabaseInfo dbinfo = null;
@ -376,10 +435,10 @@ public class InputsManager {
for (StatisticalType type : agentInputs) {
if (type instanceof PrimitiveType) {
if (((PrimitiveType) type).getType()==PrimitiveTypes.CONSTANT){
String constant = ""+((PrimitiveType) type).getDefaultValue();
if (((PrimitiveType) type).getType() == PrimitiveTypes.CONSTANT) {
String constant = "" + ((PrimitiveType) type).getDefaultValue();
config.setParam(type.getName(), constant);
LOGGER.debug("Constant parameter: "+constant);
LOGGER.debug("Constant parameter: " + constant);
}
}
if (type instanceof ServiceType) {
@ -392,10 +451,10 @@ public class InputsManager {
String value = "";
if (sp == ServiceParameters.RANDOMSTRING)
value = "stat" + UUID.randomUUID().toString().replace("-", "");
else if (sp == ServiceParameters.USERNAME){
else if (sp == ServiceParameters.USERNAME) {
value = (String) inputs.get(ConfigurationManager.usernameParameter);
LOGGER.debug("User name used by the client: "+value);
LOGGER.debug("User name used by the client: " + value);
}
LOGGER.debug("ServiceType Adding: (" + name + "," + value + ")");
config.setParam(name, value);
@ -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;
DataProvenance provenance = DataProvenance.IMPORTED;
String creationDate = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
@ -445,18 +504,17 @@ public class InputsManager {
String type = "text/plain";
if (payload != null && (new File (payload).exists())) {
if (payload != null && (new File(payload).exists())) {
if (payload.toLowerCase().endsWith(".csv") || payload.toLowerCase().endsWith(".txt")) {
type = "text/csv";
} else
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);
}
}

View File

@ -21,7 +21,7 @@ import org.slf4j.LoggerFactory;
public class OutputsManager {
private static Logger LOGGER = LoggerFactory.getLogger(OutputsManager.class);
private AlgorithmConfiguration config;
private List<File> generatedFiles = new ArrayList<File>();
@ -29,7 +29,7 @@ public class OutputsManager {
private IClient storageclient;
private String computationsession;
private List<StoredData> provenanceData = new ArrayList<StoredData>();
public List<StoredData> getProvenanceData() {
return provenanceData;
}
@ -37,7 +37,7 @@ public class OutputsManager {
public List<File> getGeneratedData() {
return generatedFiles;
}
public List<File> getGeneratedFiles() {
return generatedFiles;
}
@ -46,12 +46,13 @@ public class OutputsManager {
return generatedTables;
}
public OutputsManager(AlgorithmConfiguration config,String computationsession) {
public OutputsManager(AlgorithmConfiguration config, String computationsession) {
this.config = config;
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>();
@ -66,10 +67,10 @@ public class OutputsManager {
StatisticalTypeToWPSType postconverter = new StatisticalTypeToWPSType();
postconverter.convert2WPSType(posterioroutput, false, config);
generatedFiles.addAll(postconverter.getGeneratedFiles());
LOGGER.debug("Generated Files "+generatedFiles);
LOGGER.debug("Generated Files " + generatedFiles);
generatedTables.addAll(postconverter.getGeneratedTables());
LOGGER.debug("Generated Tables "+generatedFiles);
LOGGER.debug("Generated Tables " + generatedFiles);
LinkedHashMap<String, IOWPSInformation> postOutput = postconverter.outputSet;
LinkedHashMap<String, IOWPSInformation> ndoutput = new LinkedHashMap<String, IOWPSInformation>();
@ -102,21 +103,23 @@ public class OutputsManager {
if (ConfigurationManager.useStorage()) {
if (postInfo.getLocalMachineContent() != null) {
// return the url from storage manager
String storageurl = uploadFileOnStorage(postInfo.getLocalMachineContent(), postInfo.getMimetype());
String storageurl = uploadFileOnStorage(postInfo.getLocalMachineContent(),
postInfo.getMimetype());
postInfo.setContent(storageurl);
}
}
/*
else if (postInfo.getLocalMachineContent() != null) {
String url = "<wps:Reference mimeType=\""+postInfo.getMimetype()+"\" xlink:href=\""+postInfo.getContent()+"\" method=\"GET\"/>";
LOGGER.debug("Reference URL: " + url);
outputs.put(okey, url);
}
else*/
* else if (postInfo.getLocalMachineContent() != null) { String
* url = "<wps:Reference mimeType=\""+postInfo.getMimetype()
* +"\" xlink:href=\""+postInfo.getContent()
* +"\" method=\"GET\"/>"; LOGGER.debug("Reference URL: " +
* url); outputs.put(okey, url); } else
*/
if (info != null) {
LOGGER.debug("Found a corresponding output: " + okey);
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) {
ndoutput.put(okey, postInfo);
}
@ -129,23 +132,23 @@ public class OutputsManager {
System.gc();
}
XmlObject ndxml = generateNonDeterministicOutput(ndoutput);
outputs.put("non_deterministic_output", ndxml);
//safety check for declared output, i.e. a priori output
for (String pkey:priorOutput.keySet()){
if (outputs.get(pkey)==null){
LOGGER.debug("Safety check: adding empty string for " + pkey+ " of type "+priorOutput.get(pkey).getClassname());
// safety check for declared output, i.e. a priori output
for (String pkey : priorOutput.keySet()) {
if (outputs.get(pkey) == null) {
LOGGER.debug("Safety check: adding empty string for " + pkey + " of type "
+ priorOutput.get(pkey).getClassname());
outputs.put(pkey, "");
}
}
LOGGER.debug("OutputsManager outputs " + outputs);
return outputs;
}
private void saveProvenanceData(IOWPSInformation info){
private void saveProvenanceData(IOWPSInformation info) {
String name = info.getName();
String id = info.getName();
DataProvenance provenance = DataProvenance.COMPUTED;
@ -153,59 +156,97 @@ public class OutputsManager {
String operator = config.getAgent();
String computationId = computationsession;
String type = info.getMimetype();
/* if (info.getLocalMachineContent() != null) {
type = StoredType.DATA;
}
*/
/*
* if (info.getLocalMachineContent() != null) { type = StoredType.DATA;
* }
*/
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);
}
private void prepareForStoring() {
LOGGER.debug("Preparing storage client");
//String scope = config.getGcubeScope();
//ScopeProvider.instance.set(scope);
// String scope = config.getGcubeScope();
// ScopeProvider.instance.set(scope);
String serviceClass = "WPS";
String serviceName = "wps.synch";
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");
}
private String uploadFileOnStorage(String localfile, String mimetype) throws Exception {
LOGGER.debug("Storing->Start uploading on storage the following file: " + localfile);
File localFile = new File(localfile);
String remotef = "/wps_synch_output/" +config.getAgent()+"/"+computationsession+"/"+ localFile.getName();
storageclient.put(true).LFile(localfile).RFile(remotef);
String url = storageclient.getHttpUrl().RFile(remotef);
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);
} else {
storageclient.put(true,contentType).LFile(localfile).RFile(remotef);
}
String url = storageclient.getHttpsUrl().RFile(remotef);
/*
if (config.getGcubeScope().startsWith("/gcube"))
url = "http://data-d.d4science.org/uri-resolver/smp?smp-uri=" + url + "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
else
url = "http://data.d4science.org/uri-resolver/smp?smp-uri=" + url+ "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
*/
* if (config.getGcubeScope().startsWith("/gcube")) url =
* "http://data-d.d4science.org/uri-resolver/smp?smp-uri=" + url +
* "&fileName=" + localFile.getName() + "&contentType=" + mimetype; else
* url = "http://data.d4science.org/uri-resolver/smp?smp-uri=" + url+
* "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
*/
LOGGER.info("Storing->Uploading finished - URL: " + 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) {
return tag.replace(" ", "_").replaceAll("[\\]\\[!\"#$%&'()*+,\\./:;<=>?@\\^`{|}~-]", "");
}
public XmlObject generateNonDeterministicOutputPlain(LinkedHashMap<String, IOWPSInformation> ndoutput) 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";
public XmlObject generateNonDeterministicOutputPlain(LinkedHashMap<String, IOWPSInformation> ndoutput)
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()) {
IOWPSInformation info = ndoutput.get(key);
String payload = info.getContent();
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";
@ -219,16 +260,21 @@ public class OutputsManager {
return xmlData;
}
public XmlObject generateNonDeterministicOutputCollection(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception {
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" + " <ogr:Result fid=\"F0\">\n" +
" <d4science:output fid=\"outputcollection\">\n";
public XmlObject generateNonDeterministicOutputCollection(LinkedHashMap<String, IOWPSInformation> ndoutput)
throws Exception {
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" + " <ogr:Result fid=\"F0\">\n"
+ " <d4science:output fid=\"outputcollection\">\n";
for (String key : ndoutput.keySet()) {
IOWPSInformation info = ndoutput.get(key);
String payload = info.getContent();
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>";
@ -241,40 +287,46 @@ public class OutputsManager {
return xmlData;
}
public XmlObject generateNonDeterministicOutput(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception {
if (ndoutput.size()==0)
if (ndoutput.size() == 0)
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\">" +
"\n<gml:featureMember>\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\">"
+ "\n<gml:featureMember>\n";
int count = 0;
for (String key : ndoutput.keySet()) {
IOWPSInformation info = ndoutput.get(key);
String payload = info.getContent();
String mimetype = info.getMimetype();
String abstractStr = info.getAbstractStr();
LOGGER.debug("IOWPS Information: " + "name "+info.getName()+","
+"abstr "+info.getAbstractStr()+","
+"content "+info.getContent()+","
+"def "+info.getDefaultVal()+",");
if ((abstractStr==null || abstractStr.trim().length()==0) && (payload!= null && payload.trim().length()>0))
LOGGER.debug("IOWPS Information [name=" + info.getName() + ", abstr=" + info.getAbstractStr() + ", content="
+ info.getContent() + ", def=" + info.getDefaultVal() + "]");
if ((abstractStr == null || abstractStr.trim().length() == 0)
&& (payload != null && payload.trim().length() > 0))
abstractStr = info.getName();
else if (abstractStr == null)
abstractStr = "";
//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+ "\">" + " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + abstractStr + "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + " </ogr:Result>\n";
// 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 + "\">" + " <d4science:Data><![CDATA[" + payload
+ "]]></d4science:Data>\n" + " <d4science:Description><![CDATA[" + abstractStr
+ "]]></d4science:Description>\n" + " <d4science:MimeType>" + mimetype
+ "</d4science:MimeType>\n" + " </ogr:Result>\n";
count++;
}
XMLString += " </gml:featureMember>\n</ogr:FeatureCollection>";
LOGGER.debug("Non deterministic output: " + XMLString);
XmlObject xmlData = XmlObject.Factory.newInstance();
@ -284,12 +336,12 @@ public class OutputsManager {
return xmlData;
}
public void shutdown(){
try{
storageclient.close();
}catch(Exception e){
public void shutdown() {
try {
storageclient.close();
} catch (Exception e) {
}
}
}

View File

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

View File

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

View File

@ -13,16 +13,15 @@ import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.gcube.common.homelibrary.home.Home;
import org.gcube.common.homelibrary.home.HomeLibrary;
import org.gcube.common.homelibrary.home.HomeManager;
import org.gcube.common.homelibrary.home.HomeManagerFactory;
import org.gcube.common.homelibrary.home.User;
import org.gcube.common.homelibrary.home.workspace.Workspace;
import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder;
import org.gcube.common.homelibrary.home.workspace.WorkspaceItem;
import org.gcube.common.homelibrary.home.workspace.folder.FolderItem;
import org.gcube.common.homelibrary.util.WorkspaceUtil;
import org.gcube.common.authorization.library.provider.AuthorizationProvider;
import org.gcube.common.storagehub.client.dsl.FileContainer;
import org.gcube.common.storagehub.client.dsl.FolderContainer;
import org.gcube.common.storagehub.client.dsl.ItemContainer;
import org.gcube.common.storagehub.client.dsl.StorageHubClient;
import org.gcube.common.storagehub.model.Metadata;
import org.gcube.common.storagehub.model.exceptions.ItemLockedException;
import org.gcube.common.storagehub.model.items.GCubeItem;
import org.gcube.common.storagehub.model.items.Item;
import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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 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.computation = computation;
this.inputData = inputData;
this.outputData = outputData;
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() {
@ -88,78 +95,102 @@ 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");
// manage folders: create the folders network
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);
StorageHubClient shc = new StorageHubClient();
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");
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");
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");
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 {
LOGGER.debug("Dataspace->Analysing " + data);
// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name, wsFolder);
String filenameonwsString = data.name ;
public String uploadData(StoredData data, FolderContainer destinationFolder, boolean changename) throws Exception {
LOGGER.debug("Dataspace->Uploaddata:"
+ " [data={},destinationFolder={}, changename={}] ", data, destinationFolder,
changename);
// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name,
// wsFolder);
String filenameonwsString = data.name;
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;
String url = "";
try {
long size = 0;
if (data.type.equals("text/csv")||data.type.equals("application/d4science")||data.type.equals("image/png")) {
// long size = 0;
if (data.type.equals("text/csv") || data.type.equals("application/d4science")
|| data.type.equals("image/png")) {
if (new File(data.payload).exists() || !data.payload.startsWith("http")) {
LOGGER.debug("Dataspace->Uploading file " + data.payload);
LOGGER.debug("Dataspace->Uploading file {}", data.payload);
in = new FileInputStream(new File(data.payload));
size = new File(data.payload).length();
// size = new File(data.payload).length();
} else {
LOGGER.debug("Dataspace->Uploading via URL " + data.payload);
LOGGER.debug("Dataspace->Uploading via URL {}", data.payload);
int tries = 10;
for (int i=0;i<tries;i++){
for (int i = 0; i < tries; i++) {
try {
URL urlc = new URL(data.payload);
url = urlc.toString();
HttpURLConnection urlConnection = (HttpURLConnection) urlc.openConnection();
urlConnection.setConnectTimeout(10000);
urlConnection.setReadTimeout(10000);
in = new BufferedInputStream(urlConnection.getInputStream());
}catch(Exception ee){
LOGGER.warn("Dataspace->Retrying connection to {} number {} ",data.payload,(i+1),ee);
in =null;
} catch (Exception ee) {
LOGGER.warn("Dataspace->Retrying connection to {} number {} ", data.payload, (i + 1), ee);
in = null;
}
if (in!=null)
if (in != null)
break;
else
Thread.sleep(10000);
}
}
if (in==null)
throw new Exception("Impossible to open stream from "+data.payload);
if (in == null)
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->WS OP saving the following file on the WS " + filenameonwsString);
LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
// 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);
Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(computation_id, data.computationId);
properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
@ -172,238 +203,231 @@ public class DataspaceManager implements Runnable {
properties.put(data_type, data.type);
properties.put(payload, url);
FolderItem fileItem = WorkspaceUtil.createExternalFile(wsFolder, filenameonwsString, data.description, in,properties,data.type,size);
//fileItem.getProperties().addProperties(properties);
LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString);
FileContainer fileContainer = destinationFolder.uploadFile(in, filenameonwsString, data.description);
LOGGER.debug("Dataspace->WS OP file uploaded on WS: " + filenameonwsString);
Metadata metadata = new Metadata(properties);
fileContainer.setMetadata(metadata);
url = fileItem.getPublicLink(false);
LOGGER.debug("Dataspace->WS OP file set metadata: " + metadata);
url = fileContainer.getPublicLink().toString();
LOGGER.debug("Dataspace->WS OP url produced for the file " + url);
data.payload = url;
try {
in.close();
} catch (Exception e) {
LOGGER.debug("Dataspace->Error creating file " + e.getMessage());
//LOGGER.debug(e);
LOGGER.debug("Dataspace->Error creating file {}", e.getMessage());
// LOGGER.debug(e);
}
LOGGER.debug("Dataspace->File created " + filenameonwsString);
LOGGER.debug("Dataspace->File created {}", filenameonwsString);
} else {
LOGGER.debug("Dataspace->String parameter " + data.payload);
LOGGER.debug("Dataspace->String parameter {}", data.payload);
url = data.payload;
}
} catch (Throwable e) {
LOGGER.error("Dataspace->Could not retrieve input payload {} ",data.payload,e);
//LOGGER.debug(e);
LOGGER.error("Dataspace->Could not retrieve input payload {} ", data.payload, e);
// LOGGER.debug(e);
url = "payload was not made available for this dataset";
data.payload = url;
}
return url;
}
public List<String> uploadInputData(List<StoredData> inputData, WorkspaceFolder dataminerFolder) throws Exception {
LOGGER.debug("Dataspace->uploading input data; Number of data: " + inputData.size());
WorkspaceItem folderItem = dataminerFolder.find(importedDataFolder);
public List<String> uploadInputData(List<StoredData> inputData, FolderContainer dataminerFolder) throws Exception {
LOGGER.debug("Dataspace->uploading input data; Number of data: {}", inputData.size());
FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(importedDataFolder)
.getContainers().get(0);
List<String> urls = new ArrayList<String>();
if (folderItem != null && folderItem.isFolder()) {
WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem;
for (StoredData input : inputData) {
WorkspaceItem item = null;
for (StoredData input : inputData) {
List<ItemContainer<? extends Item>> items = null;
if (input.type.equals("text/csv")||input.type.equals("application/d4science")||input.type.equals("image/png"))
item = destinationFolder.find(input.name);
if (input.type.equals("text/csv") || input.type.equals("application/d4science")
|| input.type.equals("image/png"))
items = destinationFolder.findByName(input.name).getContainers();
if (item==null){
String url = uploadData(input, destinationFolder,false);
LOGGER.debug("Dataspace->returning property "+url);
urls.add(url);
}
else{
LOGGER.debug("Dataspace->Input item "+input.name+" is already available in the input folder");
String url = item.getPublicLink(false);
LOGGER.debug("Dataspace->returning WS url "+url);
urls.add(url);
}
if (items == null || items.isEmpty()) {
String url = uploadData(input, destinationFolder, false);
LOGGER.debug("Dataspace->returning property {}", url);
urls.add(url);
} else {
FileContainer item = (FileContainer) items.get(0);
LOGGER.debug("Dataspace->Input item {} is already available in the input folder", input.name);
String url = item.getPublicLink().toString();
LOGGER.debug("Dataspace->returning WS url {}", url);
urls.add(url);
}
} else
LOGGER.debug("Dataspace->folder is not valid");
}
LOGGER.debug("Dataspace->finished uploading input data");
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());
WorkspaceItem folderItem = dataminerFolder.find(computedDataFolder);
FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(computedDataFolder)
.getContainers().get(0);
List<String> urls = new ArrayList<String>();
if (folderItem != null && folderItem.isFolder()) {
WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem;
for (StoredData output : outputData) {
String url = uploadData(output, destinationFolder);
urls.add(url);
}
} else
LOGGER.debug("Dataspace->folder is not valid");
for (StoredData output : outputData) {
String url = uploadData(output, destinationFolder);
urls.add(url);
}
LOGGER.debug("Dataspace->finished uploading output data");
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");
WorkspaceItem folderItem = dataminerFolder.find(computationsFolder);
if (folderItem != null && folderItem.isFolder()) {
// create a folder in here
LOGGER.debug("Dataspace->Creating computation folder " + computation.id);
WorkspaceFolder cfolder = ((WorkspaceFolder) folderItem);
String cfoldername = computation.id;
WorkspaceFolder newcomputationFolder = null;
try{
newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription);
}catch(java.lang.ClassCastException e){
LOGGER.debug("Dataspace->concurrency exception - deleting remaining item");
deleteRunningComputationData();
newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription);
}
//String itemType = "COMPUTATION";
// create IO folders
LOGGER.debug("Dataspace->creating IO folders under " + cfoldername);
newcomputationFolder.createFolder(importedDataFolder, importedDataFolder);
newcomputationFolder.createFolder(computedDataFolder, computedDataFolder);
// copy IO in those folders
LOGGER.debug("Dataspace->*****uploading inputs in IO folder*****");
List<String> inputurls = uploadInputData(inputData, newcomputationFolder);
LOGGER.debug("Dataspace->*****uploading outputs in IO folder*****");
List<String> outputurls = uploadOutputData(outputData, newcomputationFolder);
LOGGER.debug("Dataspace->*****adding properties to the folder*****");
LOGGER.debug("Dataspace->creating Folder Properties");
// write a computation item for the computation
LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
properties.put(computation_id, computation.id);
properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
properties.put(vre, computation.vre);
properties.put(operator_name, config.getAgent());
properties.put(operator_id, computation.operatorId);
properties.put(operator_description, computation.operatorDescription);
properties.put(start_date, computation.startDate);
properties.put(end_date, computation.endDate);
properties.put(status, getStatus(computation.status));
properties.put(execution_platform, computation.infrastructure);
int ninput = inputurls.size();
int noutput = outputurls.size();
LOGGER.debug("Dataspace->Adding input properties for " + ninput + " inputs");
for (int i = 1; i <= ninput; i++) {
StoredData input = inputData.get(i - 1);
if (input.payload.contains("|")){
String payload = input .payload;
LOGGER.debug("Dataspace->Managing complex input "+input.name+" : "+payload);
//delete the names that are not useful
for (StoredData subinput:inputData){
if (input.description.equals(subinput.description)){
payload = payload.replace(subinput.name,subinput.payload);
subinput.name=null;
}
}
input.name = null;
//delete last pipe character
if (payload.endsWith("|"))
payload = payload.substring(0,payload.length()-1);
LOGGER.debug("Dataspace->Complex input after processing "+payload);
properties.put("input" + i + "_" + input.description, payload);
input.payload=payload;
}
}
for (int i = 1; i <= ninput; i++) {
StoredData input = inputData.get(i - 1);
if (input.name!=null){
properties.put("input" + i + "_" + input.name, inputurls.get(i - 1));
}
}
LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs");
for (int i = 1; i <= noutput; i++) {
properties.put("output" + i + "_" + outputData.get(i - 1).name, outputurls.get(i - 1));
}
LOGGER.debug("Dataspace->Properties of the folder: " + properties);
LOGGER.debug("Dataspace->Saving properties to ProvO XML file " + noutput + " outputs");
/*
* XStream xstream = new XStream(); String xmlproperties = xstream.toXML(properties);
*/
try {
String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData);
File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID());
FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8");
InputStream sis = new FileInputStream(xmltosave);
WorkspaceUtil.createExternalFile(newcomputationFolder, computation.id + ".xml", computation.operatorDescription, sis,null,"text/xml",xmltosave.length());
sis.close();
xmltosave.delete();
} catch (Exception e) {
LOGGER.error("Dataspace->Failed creating ProvO XML file ",e);
}
//List<String> scopes = new ArrayList<String>();
//scopes.add(config.getGcubeScope());
//ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, newcomputationFolder.getId());
newcomputationFolder.getProperties().addProperties(properties);
FolderContainer computationContainer = (FolderContainer) dataminerFolder.findByName(computationsFolder)
.getContainers().get(0);
// create a folder in here
LOGGER.debug("Dataspace->Creating computation folder " + computation.id);
String cfoldername = computation.id;
FolderContainer newcomputationFolder = null;
try {
newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
} catch (java.lang.ClassCastException e) {
LOGGER.debug("Dataspace->concurrency exception - deleting remaining item");
deleteRunningComputationData();
newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
}
// String itemType = "COMPUTATION";
// create IO folders
LOGGER.debug("Dataspace->creating IO folders under " + cfoldername);
newcomputationFolder.newFolder(importedDataFolder, importedDataFolder);
newcomputationFolder.newFolder(computedDataFolder, computedDataFolder);
// copy IO in those folders
LOGGER.debug("Dataspace->*****uploading inputs in IO folder*****");
List<String> inputurls = uploadInputData(inputData, newcomputationFolder);
LOGGER.debug("Dataspace->*****uploading outputs in IO folder*****");
List<String> outputurls = uploadOutputData(outputData, newcomputationFolder);
LOGGER.debug("Dataspace->*****adding properties to the folder*****");
LOGGER.debug("Dataspace->creating Folder Properties");
// write a computation item for the computation
Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(computation_id, computation.id);
properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
properties.put(vre, computation.vre);
properties.put(operator_name, config.getAgent());
properties.put(operator_id, computation.operatorId);
properties.put(operator_description, computation.operatorDescription);
properties.put(start_date, computation.startDate);
properties.put(end_date, computation.endDate);
properties.put(status, getStatus(computation.status));
properties.put(execution_platform, computation.infrastructure);
int ninput = inputurls.size();
int noutput = outputurls.size();
LOGGER.debug("Dataspace->Adding input properties for " + ninput + " inputs");
for (int i = 1; i <= ninput; i++) {
StoredData input = inputData.get(i - 1);
if (input.payload.contains("|")) {
String payload = input.payload;
LOGGER.debug("Dataspace->Managing complex input {} : {}", input.name, payload);
// delete the names that are not useful
for (StoredData subinput : inputData) {
if (input.description.equals(subinput.description)) {
payload = payload.replace(subinput.name, subinput.payload);
subinput.name = null;
}
}
input.name = null;
// delete last pipe character
if (payload.endsWith("|"))
payload = payload.substring(0, payload.length() - 1);
LOGGER.debug("Dataspace->Complex input after processing " + payload);
properties.put("input" + i + "_" + input.description, payload);
input.payload = payload;
}
}
for (int i = 1; i <= ninput; i++) {
StoredData input = inputData.get(i - 1);
if (input.name != null) {
properties.put(String.format("input%d_%s", i, input.name), inputurls.get(i - 1));
}
}
LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs");
for (int i = 1; i <= noutput; i++) {
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->Saving properties to ProvO XML file {} outputs", noutput);
/*
* XStream xstream = new XStream(); String xmlproperties =
* xstream.toXML(properties);
*/
try {
String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData);
File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID());
FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8");
try (InputStream sis = new FileInputStream(xmltosave)) {
newcomputationFolder.uploadFile(sis, computation.id + ".xml", computation.operatorDescription);
}
xmltosave.delete();
} catch (Exception e) {
LOGGER.error("Dataspace->Failed creating ProvO XML file ", e);
}
/*
* List<String> scopes = new ArrayList<String>();
* scopes.add(config.getGcubeScope()); 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");
}
public String buildCompositePayload(List<StoredData> inputData,String payload, String inputName){
public String buildCompositePayload(List<StoredData> inputData, String payload, String inputName) {
for (StoredData input:inputData){
if (inputName.equals(input.description)){
payload = payload.replace(input.name,input.payload);
for (StoredData input : inputData) {
if (inputName.equals(input.description)) {
payload = payload.replace(input.name, input.payload);
}
}
return payload;
}
public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData) throws Exception {
public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData)
throws Exception {
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");
createFoldersNetwork(ws, root);
WorkspaceFolder dataminerItem = (WorkspaceFolder) root.find(dataminerFolder);
FolderContainer dataminerFolder = createFoldersNetwork();
LOGGER.debug("Dataspace->****uploading input files****");
uploadInputData(inputData, dataminerItem);
uploadInputData(inputData, dataminerFolder);
LOGGER.debug("Dataspace->****uploading output files****");
uploadOutputData(outputData, dataminerItem);
uploadOutputData(outputData, dataminerFolder);
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->deleting generated files");
AbstractEcologicalEngineMapper.deleteGeneratedFiles(generatedFiles);
@ -414,29 +438,20 @@ public class DataspaceManager implements Runnable {
try {
deleteRunningComputationData();
} 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");
createFoldersNetwork(ws, root);
WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder);
// LOGGER.debug("Dataspace->Creating computation item " + computation.id+" with status"+computation.status);
FolderContainer folderContainer = createFoldersNetwork();
FolderContainer computationsContainer = (FolderContainer) folderContainer.findByName(computationsFolder)
.getContainers().get(0);
// LOGGER.debug("Dataspace->Creating computation item " +
// computation.id+" with status"+computation.status);
String itemType = "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(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
properties.put(vre, computation.vre);
@ -452,24 +467,34 @@ public class DataspaceManager implements Runnable {
List<String> scopes = new ArrayList<String>();
scopes.add(config.getGcubeScope());
ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, 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");
}
public String getStatus(String status){
public String getStatus(String status) {
double statusD = 0;
try{
try {
statusD = Double.parseDouble(status);
}catch(Exception e){
} catch (Exception e) {
return status;
}
if (statusD==100)
if (statusD == 100)
return "completed";
else if (statusD==-2)
else if (statusD == -2)
return "error";
else if (statusD==-1)
else if (statusD == -1)
return "cancelled";
else
return status;
@ -479,66 +504,75 @@ public class DataspaceManager implements Runnable {
LOGGER.debug("Dataspace->deleting computation item");
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();
WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder);
StorageHubClient shc = new StorageHubClient();
FolderContainer dataminerContainer = (FolderContainer) shc.getWSRoot().findByName(dataminerFolder)
.getContainers().get(0);
FolderContainer computationContainer = (FolderContainer) dataminerContainer.findByName(computationsFolder)
.getContainers().get(0);
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;
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++;
}
List<ItemContainer<? extends Item>> wi = computationContainer.findByName(this.statusComputationName)
.getContainers();
if (!wi.isEmpty()) {
for (ItemContainer<? extends Item> container : wi) {
boolean retry = false;
do {
try {
container.forceDelete();
retry = false;
} catch (ItemLockedException e) {
LOGGER.warn("item locked, retrying");
Thread.sleep(1000);
retry = true;
}
} while (retry);
}
} else
LOGGER.debug("Dataspace->Warning Could not find {} under {}", this.statusComputationName,
computationContainer.get().getName());
LOGGER.debug("Dataspace->finished removing computation data - success "+!ws.exists(computation.id,computationsFolderWs.getId()));
/*
* 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 ");
}
public static String getExtension(String payload, String type){
// TODO
public static String getExtension(String payload) {
LOGGER.debug("DataSpace->Get Extension from: " + payload);
String extension = "";
if (type.toLowerCase().equals("text/plain")){}
else if (payload.toLowerCase().startsWith("http")){
if (payload.toLowerCase().startsWith("http")) {
try {
URL obj= new URL(payload);
URL obj = new URL(payload);
URLConnection conn = obj.openConnection();
// get all headers
Map<String, List<String>> map = conn.getHeaderFields();
for (Map.Entry<String, List<String>> entry : map.entrySet()) {
String value = entry.getValue().toString();
if (value.toLowerCase().contains("filename=")){
System.out.println("DataSpace->Searching in http header: found "+value);
extension = value.substring(value.lastIndexOf("."),value.lastIndexOf("\""));
LOGGER.debug("Header value: " + value);
if (value.toLowerCase().contains("filename")) {
LOGGER.debug("DataSpace->Searching in http header: found " + value);
extension = value.substring(value.lastIndexOf("."), value.lastIndexOf("\""));
break;
}
}
conn.getInputStream().close();
} 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);
if (paylFile.exists()){
if (paylFile.exists()) {
String paylname = paylFile.getName();
extension = paylname.substring(paylname.lastIndexOf("."));
}
}
LOGGER.debug("DataSpace->Extension retrieved: " + 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.StringWriter;
import java.util.ArrayList;
import java.util.List;
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
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"
updateSequence="1">
<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:Keywords>
<ows:Keyword>WPS</ows:Keyword>
@ -19,8 +19,8 @@
<ows:AccessConstraints>NONE</ows:AccessConstraints>
</ows:ServiceIdentification>
<ows:ServiceProvider>
<ows:ProviderName>National Research Council of Italy</ows:ProviderName>
<ows:ProviderSite xlink:href="www.d4science.org" />
<ows:ProviderName>D4Science</ows:ProviderName>
<ows:ProviderSite xlink:href="https://www.d4science.org" />
<ows:ServiceContact>
<ows:IndividualName>Gianpaolo Coro</ows:IndividualName>
<ows:PositionName>Researcher</ows:PositionName>
@ -34,7 +34,7 @@
<ows:AdministrativeArea>Istituto di Scienza e Tecnologie dell'Informazione A. Faedo</ows:AdministrativeArea>
<ows:PostalCode>56124</ows:PostalCode>
<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:ContactInfo>
</ows:ServiceContact>
@ -43,31 +43,29 @@
<ows:Operation name="GetCapabilities">
<ows:DCP>
<ows:HTTP>
<ows:Get xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Post xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Get xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Post xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
</ows:HTTP>
</ows:DCP>
</ows:Operation>
<ows:Operation name="DescribeProcess">
<ows:DCP>
<ows:HTTP>
<ows:Get xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Post xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Get xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Post xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
</ows:HTTP>
</ows:DCP>
</ows:Operation>
<ows:Operation name="Execute">
<ows:DCP>
<ows:HTTP>
<ows:Get xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Post xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Get xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
<ows:Post xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
</ows:HTTP>
</ows:DCP>
</ows:Operation>
</ows:OperationsMetadata>
<wps:ProcessOfferings>
#PROCESSES#
</wps:ProcessOfferings>
<wps:ProcessOfferings>#PROCESSES#</wps:ProcessOfferings>
<wps:Languages>
<wps:Default>
<ows:Language>en-GB</ows:Language>

View File

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

View File

@ -17,22 +17,22 @@ import org.junit.Test;
public class AlgorithmTest {
List<String> executeOnly = Arrays.asList();
List<String> executeOnly = Arrays.asList("#BIONYM", "#AQUAMAPS_SUITABLE", "#AQUAMAPS_SUITABLE 21 sp", "#BIONYM1024","#CMSY2");
@Test
public void executeAlgorithmsFromFile() throws Exception{
String env = "dev";
Properties prop = new Properties();
/*Properties prop = new Properties();
prop.load(AlgorithmTest.class.getResourceAsStream("/test_params.properties"));
*/
String protocol = "http";
String hostname = prop.getProperty(env+".host");
String token = prop.getProperty(env+".token");
String layerID = prop.getProperty(env+".layer");
String hostname = "dataminer-genericworkers.d4science.org";
String token = "xxx-xxx-xxx-xxx";
String layerID = "08ee0d70-4d8b-4f42-8b06-d709482bca95";
Iterator<String> uris = getUrisIterator();
HttpClient client = new HttpClient();
@ -43,7 +43,7 @@ public class AlgorithmTest {
if (nextLine.startsWith("#"))
algorithmName = nextLine;
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);
try{
long start = System.currentTimeMillis();

View File

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

View File

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

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

@ -5,58 +5,58 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ESRI_GRID_EXTRACTION&DataInputs=Layer={LAYERID};YResolution=0.5;XResolution=0.5;BBox_LowerLeftLong=-50;BBox_UpperRightLat=60;BBox_LowerLeftLat=-60;BBox_UpperRightLong=50;Z=0;TimeIndex=0;
#DBSCAN
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.DBSCAN
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.DBSCAN&DataInputs=OccurrencePointsClusterLabel=OccClustersTest;epsilon=10;min_points=1;OccurrencePointsTable={PROTOCOL}://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
{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
{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
{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
{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
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIONYM_LOCAL
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIONYM_LOCAL&DataInputs=Matcher_1=LEVENSHTEIN;Matcher_4=NONE;Matcher_5=NONE;Matcher_2=NONE;Matcher_3=NONE;Threshold_1=0.6;Threshold_2=0.6;Accuracy_vs_Speed=MAX_ACCURACY;MaxResults_2=10;MaxResults_1=10;Threshold_3=0.4;Taxa_Authority_File=FISHBASE;Parser_Name=SIMPLE;MaxResults_4=0;Threshold_4=0;MaxResults_3=0;MaxResults_5=0;Threshold_5=0;Use_Stemmed_Genus_and_Species=false;Activate_Preparsing_Processing=true;SpeciesAuthorName=Gadus morhua
#ABSENCE CELLS FROM AQUAMAPS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ABSENCE_CELLS_FROM_AQUAMAPS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ABSENCE_CELLS_FROM_AQUAMAPS&DataInputs=Number_of_Points=20;Table_Label=hcaf_filtered_wps;Aquamaps_HSPEC={PROTOCOL}://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
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.HCAF_FILTER
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.HCAF_FILTER&DataInputs=B_Box_Left_Lower_Lat=-17;B_Box_Right_Upper_Long=147;B_Box_Right_Upper_Lat=25;B_Box_Left_Lower_Long=89;Table_Label=wps_hcaf_filter;
#MAX_ENT_NICHE_MODELLING
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.MAX_ENT_NICHE_MODELLING
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.MAX_ENT_NICHE_MODELLING&DataInputs=LongitudeColumn=decimallongitude;LatitudeColumn=decimallatitude;Z=0;Layers={LAYERID};TimeIndex=0;MaxIterations=100;SpeciesName=Latimeria%20chalumnae;DefaultPrevalence=0.5;YResolution=0.5;OccurrencesTable=http://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
#{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
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.PRESENCE_CELLS_GENERATION
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.PRESENCE_CELLS_GENERATION&DataInputs=Number_of_Points=20;Table_Label=hcaf_filtered_wps;Species_Code=Fis-30189;
#FAO_OCEAN_AREA_COLUMN_CREATOR
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.FAO_OCEAN_AREA_COLUMN_CREATOR
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.FAO_OCEAN_AREA_COLUMN_CREATOR&DataInputs=Resolution=5;Latitude_Column=decimallatitude;InputTable={PROTOCOL}://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
{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
{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
{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
{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
{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
{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
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SPECIES_OBSERVATION_MEOW_AREA_PER_YEAR
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.SPECIES_OBSERVATION_MEOW_AREA_PER_YEAR&DataInputs=Selected species=Gadus morhua;End_year=2015;Start_year=2000;Area_type=NORTH SEA;
@ -80,16 +80,16 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.MOST_OBSERVED_TAXA&DataInputs=Level=GENUS;Taxa_number=10;End_year=2015;Start_year=2000;
#TIME_SERIES_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_SERIES_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.TIME_SERIES_ANALYSIS&DataInputs=FFT_Window_Samples=12;SSA_Points_to_Forecast=3;AggregationFunction=SUM;TimeSeriesTable={PROTOCOL}://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
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.MAPS_COMPARISON
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.MAPS_COMPARISON&DataInputs=TimeIndex_1=0;ValuesComparisonThreshold=0.1;TimeIndex_2=0;Z=0;KThreshold=0.5;Layer_1=483a4a32-729e-422b-b5e4-49f27ba93ec2;Layer_2=483a4a32-729e-422b-b5e4-49f27ba93ec2;
#QUALITY_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.QUALITY_ANALYSIS
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.evaluators.QUALITY_ANALYSIS&DataInputs=NegativeCasesTableKeyColumn=csquarecode;DistributionTableProbabilityColumn=probability;PositiveCasesTableKeyColumn=csquarecode;PositiveThreshold=0.8;PositiveCasesTable={PROTOCOL}://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
{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
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.XYEXTRACTOR
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.XYEXTRACTOR&DataInputs=OutputTableLabel=wps_xy_extractor;Layer={LAYERID};YResolution=0.5;XResolution=0.5;BBox_LowerLeftLong=-50;BBox_UpperRightLat=60;BBox_LowerLeftLat=-60;BBox_UpperRightLong=50;Z=0;TimeIndex=0;
@ -101,22 +101,22 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.ZEXTRACTION&DataInputs=OutputTableLabel=wps_z_extractor;Layer={LAYERID};Resolution=100;Y=38;TimeIndex=0;X=28
#XYEXTRACTOR_TABLE
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.XYEXTRACTOR_TABLE
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.XYEXTRACTOR_TABLE&DataInputs=TimeIndex=0;Z=0;filter= ;zColumn=lme;timeColumn=lme;xColumn=centerlong;yColumn=centerlat;geoReferencedTableName={PROTOCOL}://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
{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
{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
{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
{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
{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
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIOCLIMATE_HSPEN
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.BIOCLIMATE_HSPEN&DataInputs=HSPEN_Table_List={PROTOCOL}://data-d.d4science.org/dDRpendoOEpnUE5nRzM4WHQ3RWVlVUorb3lwa2wzNWJHbWJQNStIS0N6Yz0|{PROTOCOL}://data-d.d4science.org/dDRpendoOEpnUE5nRzM4WHQ3RWVlVUorb3lwa2wzNWJHbWJQNStIS0N6Yz0;HSPEN_Table_Names=h1|h2;
@ -131,7 +131,7 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.modellers.FEED_FORWARD_ANN&DataInputs=TrainingDataSet={PROTOCOL}://data-d.d4science.org/UndsT051bEZwbEpnRzM4WHQ3RWVlVDQ0eHNITWgzRXdHbWJQNStIS0N6Yz0;TrainingColumns=a|b;TargetColumn=t;LayersNeurons=1;Reference=1;LearningThreshold=0.001;MaxIterations=1000;ModelName=neuralnet_t;
#FEED_FORWARD_A_N_N_DISTRIBUTION
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.generators.FEED_FORWARD_A_N_N_DISTRIBUTION
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.generators.FEED_FORWARD_A_N_N_DISTRIBUTION&DataInputs=FeaturesTable={PROTOCOL}://data-d.d4science.org/UndsT051bEZwbEpnRzM4WHQ3RWVlVDQ0eHNITWgzRXdHbWJQNStIS0N6Yz0;FeaturesColumnNames=a|b;FinalTableLabel=Distrib_t;ModelName={PROTOCOL}://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
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.OCCURRENCES_DUPLICATES_DELETER
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.OCCURRENCES_DUPLICATES_DELETER&DataInputs=final_Table_Name=DeletedOcc_;OccurrencePointsTableName={PROTOCOL}://data-d.d4science.org/KzI1TmN5TCtJT2hnRzM4WHQ3RWVlZlZLdCttTThpUnRHbWJQNStIS0N6Yz0;longitudeColumn=decimalLongitude;latitudeColumn=decimalLatitude;recordedByColumn=recordedBy;scientificNameColumn=scientificName;eventDateColumn=eventDate;lastModificationColumn=modified;spatialTolerance=0.5;confidence=80;
@ -170,7 +170,7 @@
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.RASTER_DATA_PUBLISHER&DataInputs=PublicationLevel=PUBLIC;DatasetAbstract=Abstract;DatasetTitle=Generic Raster Layer Test3;RasterFile={PROTOCOL}://data.d4science.org/QTVNbXp5cmI0MG52TTE0K2paNzhXZWlCTHhweU8rUCtHbWJQNStIS0N6Yz0;InnerLayerName=analyzed_field;FileNameOnInfra=raster-1465493226242.nc;Topics=analyzed_field;SpatialResolution=-1;
#Web app publisher
{PROTOCOL}://{HOST}/wps/WebProcessingService?Request=DescribeProcess&Service=WPS&Version=1.0.0&gcube-token={TOKEN}&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.WEB_APP_PUBLISHER
{PROTOCOL}://{HOST}/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token={TOKEN}&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.WEB_APP_PUBLISHER&DataInputs=ZipFile={PROTOCOL}://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
{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;