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-"72.25","-43.75","2232.874","642","0","0","51","0","0","0","0","0","412","34.7202","34.17","34.85","","34.52","1.15","6.28","9.59","15.87","0.32","12.17","38.76","3709","3819","3550","3407:132:3" -"-1.75","-87.25","0","0","0","","-1","","","","","","0","","","","","","","","","","","","","0","0","0","5800:371:2" diff --git a/SampleResult.txt b/SampleResult.txt deleted file mode 100644 index 4fc4040..0000000 --- a/SampleResult.txt +++ /dev/null @@ -1,101 +0,0 @@ -percentage, isofficial, language, countrycode -52.4,true,Pashto,AFG -95.6,true,Dutch,NLD -86.2,true,Papiamento,ANT -97.9,true,Albaniana,ALB -86,true,Arabic,DZA -90.6,true,Samoan,ASM -44.6,false,Spanish,AND -37.2,false,Ovimbundu,AGO -0,true,English,AIA -95.7,false,Creole English,ATG -42,true,Arabic,ARE -96.8,true,Spanish,ARG -93.4,true,Armenian,ARM -76.7,false,Papiamento,ABW -81.2,true,English,AUS -89,true,Azerbaijani,AZE -89.7,false,Creole English,BHS -67.7,true,Arabic,BHR -97.7,true,Bengali,BGD -95.1,false,Bajan,BRB -59.2,true,Dutch,BEL -50.8,true,English,BLZ -39.8,false,Fon,BEN -100,true,English,BMU -50,true,Dzongkha,BTN -87.7,true,Spanish,BOL -99.2,true,Serbo-Croatian,BIH -75.5,false,Tswana,BWA -97.5,true,Portuguese,BRA -97.3,true,English,GBR -0,true,English,VGB -45.5,true,Malay,BRN -83.2,true,Bulgariana,BGR -50.2,false,Mossi,BFA -98.1,true,Kirundi,BDI -0,true,English,CYM -89.7,true,Spanish,CHL -0,true,Maori,COK -97.5,true,Spanish,CRI -43.9,false,Somali,DJI -100,false,Creole English,DMA -98,true,Spanish,DOM -93,true,Spanish,ECU -98.8,true,Arabic,EGY -100,true,Spanish,SLV -49.1,true,Tigrinja,ERI -74.4,true,Spanish,ESP -22.7,true,Zulu,ZAF -31,false,Oromo,ETH -0,true,English,FLK -50.8,true,Fijian,FJI -29.3,true,Pilipino,PHL -100,true,Faroese,FRO -35.8,false,Fang,GAB -34.1,false,Malinke,GMB -71.7,true,Georgiana,GEO -52.4,false,Akan,GHA -88.9,true,English,GIB -100,false,Creole English,GRD -87.5,true,Greenlandic,GRL -95,false,Creole French,GLP -37.5,true,English,GUM -64.7,true,Spanish,GTM -38.6,false,Ful,GIN -36.4,false,Crioulo,GNB -96.4,false,Creole English,GUY -100,false,Haiti Creole,HTI -97.2,true,Spanish,HND -88.7,false,Canton Chinese,HKG -0,true,Norwegian,SJM -39.4,false,Javanese,IDN -39.9,true,Hindi,IND -77.2,true,Arabic,IRQ -45.7,true,Persian,IRN -98.4,true,English,IRL -95.7,true,Icelandic,ISL -63.1,true,Hebrew,ISR -94.1,true,Italian,ITA -0,false,Sunda,TMP -92,true,German,AUT -94.2,false,Creole English,JAM -99.1,true,Japanese,JPN -99.6,true,Arabic,YEM -97.9,true,Arabic,JOR -0,false,Chinese,CXR -75.2,true,Serbo-Croatian,YUG -88.6,true,Khmer,KHM -19.7,false,Fang,CMR -60.4,true,English,CAN -100,false,Crioulo,CPV -46,true,Kazakh,KAZ -20.9,false,Kikuyu,KEN -23.8,false,Gbaya,CAF -92,true,Chinese,CHN -59.7,true,Kirgiz,KGZ -98.9,true,Kiribati,KIR -99,true,Spanish,COL -75,true,Comorian,COM -51.5,false,Kongo,COG -18,false,Luba,COD diff --git a/TestAlgDeployment/DatabasesResourcesManagerAlgorithms-1.0.0-SNAPSHOT.jar b/TestAlgDeployment/DatabasesResourcesManagerAlgorithms-1.0.0-SNAPSHOT.jar deleted file mode 100644 index 5c3a4fc..0000000 Binary files a/TestAlgDeployment/DatabasesResourcesManagerAlgorithms-1.0.0-SNAPSHOT.jar and /dev/null differ diff --git a/TestAlgDeployment/TestAlg.jar b/TestAlgDeployment/TestAlg.jar deleted file mode 100644 index 7ab9c6c..0000000 Binary files a/TestAlgDeployment/TestAlg.jar and /dev/null differ diff --git a/TestAlgDeployment/TestAlg.properties b/TestAlgDeployment/TestAlg.properties deleted file mode 100644 index cbc0334..0000000 --- a/TestAlgDeployment/TestAlg.properties +++ /dev/null @@ -1 +0,0 @@ -TEST_ALGORITHM=org.gcube.test.algorithm.SimpleAlg diff --git a/cfg/ALog.properties b/cfg/ALog.properties deleted file mode 100644 index 41feb3e..0000000 --- a/cfg/ALog.properties +++ /dev/null @@ -1,30 +0,0 @@ -#### Use two appenders, one to log to console, another to log to a file -log4j.rootCategory= R - -#### First appender writes to console -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n -#log4j.appender.stdout.layout.ConversionPattern=%m%n -#log4j.appender.stdout.File=Analysis.log - -#### Second appender writes to a file -log4j.logger.AnalysisLogger=trace, stdout,R -log4j.appender.R=org.apache.log4j.RollingFileAppender -log4j.appender.R.File=Analysis.log -log4j.appender.R.MaxFileSize=50000KB -log4j.appender.R.MaxBackupIndex=2 -log4j.appender.R.layout=org.apache.log4j.PatternLayout -log4j.appender.R.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n -#log4j.appender.R.layout.ConversionPattern=%m%n - -#### Third appender writes to a file -log4j.logger.org.hibernate=H -#log4j.appender.H=org.apache.log4j.RollingFileAppender -log4j.appender.H=org.apache.log4j.AsyncAppender -#log4j.appender.H.File=HibernateLog.log -#log4j.appender.H.MaxFileSize=1024KB -#log4j.appender.H.MaxBackupIndex=2 -log4j.appender.H.layout=org.apache.log4j.PatternLayout -log4j.appender.H.layout.ConversionPattern=%d{dd/MM/yyyy HH:mm:ss} %p %t %c - %m%n - diff --git a/cfg/DestinationDBHibernate.cfg.xml b/cfg/DestinationDBHibernate.cfg.xml deleted file mode 100644 index 47a0416..0000000 --- a/cfg/DestinationDBHibernate.cfg.xml +++ /dev/null @@ -1,23 +0,0 @@ - - - - org.postgresql.Driver - org.hibernate.connection.C3P0ConnectionProvider - - - jdbc:postgresql://obis2.i-marine.research-infrastructures.eu:5432/obis - gcube --> - d4science2 - 1 - org.hibernate.dialect.PostgreSQLDialect - org.hibernate.transaction.JDBCTransactionFactory - - 1 - 0 - 1 - - 1 - thread - - - \ No newline at end of file diff --git a/cfg/DestinationDBHibernateDBManager.cfg.xml b/cfg/DestinationDBHibernateDBManager.cfg.xml deleted file mode 100644 index 8b2db9e..0000000 --- a/cfg/DestinationDBHibernateDBManager.cfg.xml +++ /dev/null @@ -1,20 +0,0 @@ - - - - com.mysql.jdbc.Driver - org.hibernate.connection.C3P0ConnectionProvider - jdbc:mysql://146.48.87.169/timeseries - root - test - org.hibernate.dialect.MySQLDialect - org.hibernate.transaction.JDBCTransactionFactory - 0 - 0 - 1 - 1 - 0 - 1 - thread - - - diff --git a/cfg/QueryResult.txt b/cfg/QueryResult.txt deleted file mode 100644 index 77b4049..0000000 --- a/cfg/QueryResult.txt +++ /dev/null @@ -1,3 +0,0 @@ -1,AFD-Pul-1838,pinhead spot,English,USA,52836,7,0 -16,Alg-111,Piedra de mar,Spanish,Spain,52834,7,0 -17,Alg-111,Pierre vermiculée,French,France,52834,7,0 diff --git a/cfg/RandomSampleOnTable.txt b/cfg/RandomSampleOnTable.txt deleted file mode 100644 index e69de29..0000000 diff --git a/cfg/SampleOnTable.txt b/cfg/SampleOnTable.txt deleted file mode 100644 index 821689e..0000000 --- a/cfg/SampleOnTable.txt +++ /dev/null @@ -1,680 +0,0 @@ -9.7703E-7,0.00563891 -1.4364E-4,0.0510053 -4.19937E-5,0.0279353 -2.17743E-5,0.0185856 -1.944E-4,0.0632979 -3.44589E-6,0.00799436 -4.25587E-6,0.00841894 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-AQUAMAPS_NATIVE=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNative -AQUAMAPS_NATIVE_2050=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNative2050 -AQUAMAPS_SUITABLE_2050=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsSuitable2050 -AQUAMAPS_NATIVE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNN -AQUAMAPS_SUITABLE_NEURALNETWORK=org.gcube.dataanalysis.ecoengine.spatialdistributions.AquamapsNNSuitable -FEED_FORWARD_A_N_N_DISTRIBUTION=org.gcube.dataanalysis.ecoengine.spatialdistributions.FeedForwardNeuralNetworkDistribution \ No newline at end of file diff --git a/cfg/clusterers.properties b/cfg/clusterers.properties deleted file mode 100644 index c2801e9..0000000 --- a/cfg/clusterers.properties +++ /dev/null @@ -1,3 +0,0 @@ -DBSCAN=org.gcube.dataanalysis.ecoengine.clustering.DBScan -KMEANS=org.gcube.dataanalysis.ecoengine.clustering.KMeans -XMEANS=org.gcube.dataanalysis.ecoengine.clustering.XMeansWrapper \ No newline at end of file diff --git a/cfg/dynamictransducerers.properties b/cfg/dynamictransducerers.properties deleted file mode 100644 index e69de29..0000000 diff --git a/cfg/evaluators.properties b/cfg/evaluators.properties deleted file mode 100644 index 1245533..0000000 --- a/cfg/evaluators.properties +++ /dev/null @@ -1,3 +0,0 @@ -DISCREPANCY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis -QUALITY_ANALYSIS=org.gcube.dataanalysis.ecoengine.evaluation.DistributionQualityAnalysis -HRS=org.gcube.dataanalysis.ecoengine.evaluation.HabitatRepresentativeness \ No newline at end of file diff --git a/cfg/generators.properties b/cfg/generators.properties deleted file mode 100644 index 4efd8af..0000000 --- a/cfg/generators.properties +++ /dev/null @@ -1,2 +0,0 @@ -LOCAL_WITH_DATABASE=org.gcube.dataanalysis.ecoengine.processing.LocalSplitGenerator -SIMPLE_LOCAL=org.gcube.dataanalysis.ecoengine.processing.LocalSimpleSplitGenerator diff --git a/cfg/loredana.txt b/cfg/loredana.txt deleted file mode 100644 index e69de29..0000000 diff --git a/cfg/modelers.properties b/cfg/modelers.properties deleted file mode 100644 index d5c652e..0000000 --- a/cfg/modelers.properties +++ /dev/null @@ -1 +0,0 @@ -HSPEN_MODELER=org.gcube.dataanalysis.ecoengine.modeling.SimpleModeler \ No newline at end of file diff --git a/cfg/models.properties b/cfg/models.properties deleted file mode 100644 index 479b406..0000000 --- a/cfg/models.properties +++ /dev/null @@ -1,4 +0,0 @@ -HSPEN=org.gcube.dataanalysis.ecoengine.models.ModelHSPEN -AQUAMAPSNN=org.gcube.dataanalysis.ecoengine.models.ModelAquamapsNN -FEED_FORWARD_ANN=org.gcube.dataanalysis.ecoengine.models.FeedForwardNN -FEED_FORWARD_ANN_FILE=org.gcube.dataanalysis.ecoengine.models.testing.FeedForwardNNFile \ No newline at end of file diff --git a/cfg/nodealgorithms.properties b/cfg/nodealgorithms.properties deleted file mode 100644 index 4493d3b..0000000 --- a/cfg/nodealgorithms.properties +++ /dev/null @@ -1 +0,0 @@ -AQUAMAPS_SUITABLE=org.gcube.dataanalysis.peeng.models.AquamapsSuitableNode diff --git a/cfg/operators.xml b/cfg/operators.xml deleted file mode 100644 index 93b465c..0000000 --- a/cfg/operators.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/cfg/results.csv b/cfg/results.csv deleted file mode 100644 index 00aa4aa..0000000 --- a/cfg/results.csv +++ /dev/null @@ -1 +0,0 @@ -1,2.87747E-6,2,1.603E-7,3,2.84254E-6,4,1.06799E-5,5,8.2902E-7,6,9.5606E-7,7,12.5088,8,2.8121E-6,9,3.62395E-6,10,15.2436,11,27.0718,12,62.4943,13,27.2604,14,38.4655,15,0.00185396,16,8.42477E-4,17,0.00539245,18,5.84188E-4,19,1.00963E-5,20,1.65052E-5,21,4.22465E-4,22,4.83264E-6,23,2.82366E-4,24,3.37542E-5,25,2.26395E-5,26,1.51102E-5,27,9.59838E-6,28,3.44589E-6,29,1.96001E-4,30,4.7696E-6, \ No newline at end of file diff --git a/cfg/results.txt b/cfg/results.txt deleted file mode 100644 index e69de29..0000000 diff --git a/cfg/transducerers.properties b/cfg/transducerers.properties deleted file mode 100644 index 0ac5ff4..0000000 --- a/cfg/transducerers.properties +++ /dev/null @@ -1,25 +0,0 @@ -ABSENCE_CELLS_FROM_AQUAMAPS=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarineAbsencePointsFromAquamapsDistribution -BIOCLIMATE_HSPEC=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPECTransducer -BIOCLIMATE_HCAF=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHCAFTransducer -BIOCLIMATE_HSPEN=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPENTransducer -HCAF_INTERPOLATION=org.gcube.dataanalysis.ecoengine.transducers.InterpolationTransducer -HCAF_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HcafFilter -HSPEN_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HspenFilter -OCCURRENCES_MERGER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsMerger -OCCURRENCES_INTERSECTOR=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsIntersector -OCCURRENCES_MARINE_TERRESTRIAL=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsInSeaOnEarth -OCCURRENCES_DUPLICATES_DELETER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsDuplicatesDeleter -OCCURRENCES_SUBTRACTION=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsSubtraction -PRESENCE_CELLS_GENERATION=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarinePresencePoints -FIN_TAXA_MATCH=org.gcube.dataanalysis.fin.taxamatch.TaxaMatchTransducer -LISTNAMES_TABLES=org.gcube.dataacces.algorithms.DatabasesResourcesManagerAlgorithms.AbsoluteSpeciesBarChartsAlgorithm -TEST_ALG=org.gcube.dataacces.algorithms.DatabasesResourcesManagerAlgorithms.SimpleAlg -LISTDBINFO=org.gcube.dataaccess.algorithms.drmalgorithms.ListDBInfo -LISTDBNAMES=org.gcube.dataaccess.algorithms.drmalgorithms.ListNames -LISTDBSCHEMA=org.gcube.dataaccess.algorithms.drmalgorithms.ListSchemas -LISTTABLES=org.gcube.dataaccess.algorithms.drmalgorithms.ListTables -GETTABLEDETAILS=org.gcube.dataaccess.algorithms.drmalgorithms.GetTableDetails -LISTSUBMITQUERY=org.gcube.dataaccess.algorithms.drmalgorithms.SubmitQuery -SAMPLEONTABLE=org.gcube.dataaccess.algorithms.drmalgorithms.SampleOnTable -SMARTSAMPLEONTABLE=org.gcube.dataaccess.algorithms.drmalgorithms.SmartSampleOnTable -RANDOMSAMPLEONTABLE=org.gcube.dataaccess.algorithms.drmalgorithms.RandomSampleOnTable \ No newline at end of file diff --git a/cfg/userperspective.properties b/cfg/userperspective.properties deleted file mode 100644 index 8374202..0000000 --- a/cfg/userperspective.properties +++ /dev/null @@ -1,12 +0,0 @@ -ANOMALIES_DETECTION=DBSCAN,KMEANS,XMEANS -CLASSIFICATION=FEED_FORWARD_A_N_N_DISTRIBUTION -CLIMATE=BIOCLIMATE_HSPEC,BIOCLIMATE_HCAF,BIOCLIMATE_HSPEN,HCAF_INTERPOLATION -CORRELATION_ANALYSIS=HRS -DATA_CLUSTERING=DBSCAN,KMEANS,XMEANS -FILTERING=HCAF_FILTER,HSPEN_FILTER -FUNCTION_SIMULATION=FEED_FORWARD_A_N_N_DISTRIBUTION -OCCURRENCES=ABSENCE_CELLS_FROM_AQUAMAPS,PRESENCE_CELLS_GENERATION,OCCURRENCES_MERGER,OCCURRENCES_INTERSECTOR,OCCURRENCES_MARINE_TERRESTRIAL,OCCURRENCES_DUPLICATES_DELETER,OCCURRENCES_SUBTRACTION -PERFORMANCES_EVALUATION=QUALITY_ANALYSIS,DISCREPANCY_ANALYSIS -SPECIES_SIMULATION=AQUAMAPS_SUITABLE,AQUAMAPS_NATIVE,AQUAMAPS_NATIVE_2050,AQUAMAPS_SUITABLE_2050,AQUAMAPS_NATIVE_NEURALNETWORK,AQUAMAPS_SUITABLE_NEURALNETWORK -TRAINING=HSPEN,AQUAMAPSNN,FEED_FORWARD_ANN -TIME_SERIES=HCAF_INTERPOLATION \ No newline at end of file diff --git a/distro/CHANGELOG b/distro/CHANGELOG deleted file mode 100644 index ed9cbcb..0000000 --- a/distro/CHANGELOG +++ /dev/null @@ -1,2 +0,0 @@ -v. 1.0.0 (09-06-2014) - * First release \ No newline at end of file diff --git a/distro/INSTALL b/distro/INSTALL deleted file mode 100644 index e69de29..0000000 diff --git a/distro/LICENSE b/distro/LICENSE deleted file mode 100644 index cc51139..0000000 --- a/distro/LICENSE +++ /dev/null @@ -1,6 +0,0 @@ -gCube System - License ------------------------------------------------------------- - -The gCube/gCore software is licensed as Free Open Source software conveying to the EUPL (http://ec.europa.eu/idabc/eupl). -The software and documentation is provided by its authors/distributors "as is" and no expressed or -implied warranty is given for its use, quality or fitness for a particular case. \ No newline at end of file diff --git a/distro/MAINTAINERS b/distro/MAINTAINERS deleted file mode 100644 index 9f65049..0000000 --- a/distro/MAINTAINERS +++ /dev/null @@ -1 +0,0 @@ -* Loredana Liccardo (loredana.liccardo@isti.cnr.it), CNR Pisa, Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" \ No newline at end of file diff --git a/distro/README b/distro/README deleted file mode 100644 index eb0e7e3..0000000 --- a/distro/README +++ /dev/null @@ -1,52 +0,0 @@ -The gCube System - Database Resource Manager algorithms ------------------------------------------------------------- - -This work is partially funded by the European Commission in the -context of the iMarine project (www.d4science.eu), under the 1st call of FP7 IST priority. - - -Authors -------- - -* Loredana Liccardo (loredana.liccardo@isti.cnr.it), CNR Pisa, - Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo". - - -Version and Release Date ------------------------- - -${version} - -Description ------------ - -The Database Resource Manager algorithms manage the heterogeneity of the Databases resources indexed -in the infrastructure by means of the Database Resource Manager library. - - -Download information --------------------- - -Source code is available from SVN: -http://svn.d4science.research-infrastructures.eu/gcube/trunk/data-access/DatabasesResourcesManagerAlgorithms - -Binaries can be downloaded from: -n/a - - -Documentation -------------- -For installation and using please referer to INSTALL. - -Documentation is also available on-line from the Projects Documentation Wiki: -https://gcube.wiki.gcube-system.org/gcube/index.php - - -Licensing ---------- - -This software is licensed under the terms you may find in the file named "LICENSE" in this directory. - - - - diff --git a/distro/changelog.xml b/distro/changelog.xml deleted file mode 100644 index 92418f9..0000000 --- a/distro/changelog.xml +++ /dev/null @@ -1,71 +0,0 @@ - - - - algorithm SubmitQuery modified in order to pass the string - pathfile to the submitQuery method of class DatabaseManagement in - order to generate a file and retrieve it from the statistical manager - with the map as output. - - Algorithms RandomSampleOnTable, SampleOnTable, - SmartSampleOnTable and SubmitQuery modified in order to manage the - file as output. - - total number rows returned as output for the result of the - submit Query operation: algorithm SubmitQuery modified - - - - some algorithms modified to cope modifications applied in the - database-resource-manager component and regarding the management of - the same access - point for a resource and the database connection - shutdown. - - - - SubmitQuery algorithm updated because input parameters - in the - SubmitQuery method of DatabaseManagement class have been updated - - timer added in the SubmitQuery algorithm that stops the query - execution after 30 minutes - - hibernate bug fixed and related to a join tables with same - columns names. Bug resolved using JDBC. GetConnection - method changed - in the SubmitQuery algorithm to create - the connection with JDBC - - method shutdown of algorithm SubmitQuery implemented in order - to allow a user to cancel a submit query operation - - bug fixed when two algorithms are submitted concurrently.Bug - related to map result's name. Bug fixed generating the name as - ResultsMap"+UUID.randomUUID() - - classes SubmitQuery, SampleOnTable, SmartSampleOnTable, - RandomSampleOnTable modified in order to not make available the - file - as result - - file DestinationDBHibernate modified to insert the property on - the timeout - - bug fixed on table names that are keywords.Method - GetTableDetails corrected to consider the name as schema.table for - postgres and database.table for mysql - - - - first release - - - \ No newline at end of file diff --git a/distro/descriptor.xml b/distro/descriptor.xml deleted file mode 100644 index 21d8c88..0000000 --- a/distro/descriptor.xml +++ /dev/null @@ -1,42 +0,0 @@ - - servicearchive - - tar.gz - - / - - - ${distroDirectory} - / - true - - README - LICENSE - INSTALL - MAINTAINERS - changelog.xml - - 755 - true - - - - - ${distroDirectory}/profile.xml - / - true - - - target/${build.finalName}.jar - /${artifactId} - - - ${distroDirectory}/svnpath.txt - /${artifactId} - true - - - \ No newline at end of file diff --git a/distro/profile.xml b/distro/profile.xml deleted file mode 100644 index 0844a74..0000000 --- a/distro/profile.xml +++ /dev/null @@ -1,25 +0,0 @@ - - - - Service - - Database Resource Manager algorithms - DataAccess - ${artifactId} - 1.0.0 - - - ${artifactId} - ${version} - - ${groupId} - ${artifactId} - ${version} - - - ${build.finalName}.jar - - - - - diff --git a/distro/svnpath.txt b/distro/svnpath.txt deleted file mode 100644 index d354a17..0000000 --- a/distro/svnpath.txt +++ /dev/null @@ -1 +0,0 @@ -http://svn.d4science.research-infrastructures.eu/gcube/trunk/data-access/DatabasesResourcesManagerAlgorithms \ No newline at end of file diff --git a/nullresults.csv b/nullresults.csv deleted file mode 100644 index 19f640a..0000000 --- a/nullresults.csv +++ /dev/null @@ -1,10 +0,0 @@ -Xiphias gladius,135638 -Fulmarus glacialis,131885 -Thunnus albacares,124076 -Pachymetopon blochii,113597 -Aptenodytes patagonicus,112605 -Gadus morhua,101777 -Caretta caretta,101769 -Thyrsites atun,97986 -Loligo vulgaris reynaudi,96672 -Argyrozona argyrozona,96278 diff --git a/pom.xml b/pom.xml deleted file mode 100644 index 140c325..0000000 --- a/pom.xml +++ /dev/null @@ -1,112 +0,0 @@ - - - 4.0.0 - - - org.gcube.tools - maven-parent - 1.0.0 - - - org.gcube.dataaccess.algorithms - database-rm-algorithms - 1.3.0-SNAPSHOT - DatabasesResourcesManagerAlgorithms - Databases Resources Manager Algorithms - - - ${project.basedir}/distro - UTF-8 - UTF-8 - - - - - - - - - - - - - - - - - - - - org.gcube.dataaccess - database-resource-manager - [1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT) - - - - - - - - - - - - - - - - - - - - - org.apache.maven.plugins - maven-resources-plugin - 2.5 - - - copy-profile - install - - copy-resources - - - target - - - ${distroDirectory} - true - - profile.xml - - - - - - - - - - org.apache.maven.plugins - maven-assembly-plugin - 2.2 - - - ${distroDirectory}/descriptor.xml - - - - - servicearchive - install - - single - - - - - - - - diff --git a/results.csv b/results.csv deleted file mode 100644 index 19f640a..0000000 --- a/results.csv +++ /dev/null @@ -1,10 +0,0 @@ -Xiphias gladius,135638 -Fulmarus glacialis,131885 -Thunnus albacares,124076 -Pachymetopon blochii,113597 -Aptenodytes patagonicus,112605 -Gadus morhua,101777 -Caretta caretta,101769 -Thyrsites atun,97986 -Loligo vulgaris reynaudi,96672 -Argyrozona argyrozona,96278 diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/GetTableDetails.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/GetTableDetails.java deleted file mode 100644 index 91eda20..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/GetTableDetails.java +++ /dev/null @@ -1,539 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -import java.io.IOException; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.UUID; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataaccess.databases.access.DatabasesDiscoverer; -import org.gcube.dataaccess.databases.resources.DBResource; -import org.gcube.dataaccess.databases.utils.DatabaseManagement; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.gcube.resources.discovery.client.api.DiscoveryException; -import org.gcube.resources.discovery.client.api.InvalidResultException; -import org.hibernate.HibernateException; -import org.hibernate.SessionFactory; - -/** Class that allows to retrieve some information about the chosen table */ -public class GetTableDetails extends StandardLocalExternalAlgorithm { - - private LinkedHashMap map = new LinkedHashMap(); - // object that allows to manage some operations on a database - private DatabaseManagement mgt; - // variable that keeps track of the database's type - private String driverInfo; - - // database's parameters specified by the user - private String resourceName = null; - private String databaseName = null; - private String schemaName = null; - private String tableName = null; - - private SessionFactory sf; - - @Override - public void init() throws Exception { - - mgt = new DatabaseManagement(config.getConfigPath()); - - AnalysisLogger.getLogger().debug("In GetTableDetails->Initialization"); - - String scope = config.getGcubeScope(); - - AnalysisLogger.getLogger().debug("In GetTableDetails->scope set by config: " + scope); - -// AnalysisLogger.getLogger().debug("In TableDetails->scope set by config: " + config.getGcubeScope()); - - if (scope == null || scope.length() == 0) { - - - scope = ScopeProvider.instance.get(); - - AnalysisLogger.getLogger().debug("In GetTableDetails->scope set by ScopeProvider: " + scope); - - - } else { - - ScopeProvider.instance.set(scope); - - } - - } - - @Override - public String getDescription() { - // add a simple description for the algorithm - - return "Algorithm that allows to view table details of a chosen database"; - - } - - @Override - protected void process() throws Exception, IOException, - IllegalStateException, DiscoveryException, InvalidResultException, - HibernateException { - - AnalysisLogger.getLogger().debug("In GetTableDetails->Processing"); - - try { - - // retrieve information - List Info = retrieveInfo(); - - // create the connection - getConnection(Info); - - // get table's details - - // recover information about the "CreateTableStatement" and - // "Number of rows" of the table chosen by the user - - map = getDetails(); - - } catch (HibernateException h) { - - AnalysisLogger.getLogger().debug( - "In GetTableDetails-> ERROR " + h.getMessage()); - throw h; - } catch (IllegalStateException e) { - // e.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails-> ERROR " + e.getMessage()); - - throw e; - - } catch (DiscoveryException e1) { - // e1.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails-> ERROR " + e1.getMessage()); - - throw e1; - - } catch (InvalidResultException e2) { - // e2.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails-> ERROR " + e2.getMessage()); - - throw e2; - - } catch (IOException e3) { - // e3.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails-> Exception " + e3.getMessage()); - - throw e3; - } - - catch (Exception e4) { - // e4.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In GetTableDetails-> Exception " + e4.getMessage()); - - throw e4; - - } finally { - // close the connection - mgt.closeConnection(); - } - - } - - @Override - protected void setInputParameters() { - -// AnalysisLogger.getLogger().debug("In GetTableDetails->setting inputs"); - - // parameters specified by the user - addStringInput("ResourceName", "The name of the resource", ""); - addStringInput("DatabaseName", "The name of the database", ""); - addStringInput("SchemaName", "The name of the schema", ""); - addStringInput("TableName", "The name of the table", ""); - - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("In GetTableDetails->Shutdown"); - - } - - @Override - public StatisticalType getOutput() { - - AnalysisLogger.getLogger().debug("In GetTableDetails->retrieving outputs"); - - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(), - map, PrimitiveTypes.MAP, "ResultsMap"+UUID.randomUUID(), "Results Map"); - - return output; - - } - - // create the database's connection - private void getConnection(List Info) throws IOException { - - // create the connection - Iterator iterator = Info.iterator(); - - String DatabaseUserName = iterator.next(); - String DatabasePassword = iterator.next(); - String DatabaseDriver = iterator.next(); - String DatabaseDialect = iterator.next(); - String DatabaseURL = iterator.next(); - String DatabaseName = iterator.next(); - - mgt.createConnection(DatabaseUserName, - DatabasePassword, DatabaseDriver, DatabaseDialect, DatabaseURL, - DatabaseName); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->database " + DatabaseName + ": connected"); - } - - // Method that recover the info useful for the connection - private List retrieveInfo() throws Exception, - IllegalStateException, DiscoveryException, InvalidResultException { - - resourceName = getInputParameter("ResourceName"); - - if(resourceName != null){ - resourceName = getInputParameter("ResourceName").trim(); - } - - if ((resourceName == null) || (resourceName.equals(""))) { - throw new Exception("Warning: insert the resource name"); - } - - - databaseName = getInputParameter("DatabaseName"); - - if(databaseName != null){ - databaseName = getInputParameter("DatabaseName").trim(); - } - if ((databaseName == null) || (databaseName.equals(""))) { - throw new Exception("Warning: insert the database name"); - } - - // retrieve the chosen resource - DatabasesDiscoverer discovery = new DatabasesDiscoverer(); - - List resources = discovery.discover(); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->number of database resources: " - + resources.size()); - - for (int i = 0; i < resources.size(); i++) { - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->Resource's name: " - + resources.get(i).getResourceName()); - - } - - // list that contains information useful for the connection - List info = new ArrayList(); - - check: for (int i = 0; i < resources.size(); i++) { - - if (resources.get(i).getResourceName().toLowerCase().equals(resourceName.toLowerCase())) { - - normalizeDBInfo(resources.get(i)); - - for (int j = 0; j < resources.get(i).getAccessPoints().size(); j++) { - - // if (resources.get(i).getAccessPoints().get(j) - // .getDatabaseName().equals(databaseName)) { - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getUsername()); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getPassword()); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getDriver()); - // - // // driverInfo = - // // resources.get(i).getAccessPoints().get(j) - // // .getDriver(); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getDialect()); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .address()); - // - // info.add(databaseName); - // - // break check; - // - // } - - // if (resources.get(i).getAccessPoints().get(j) - // .address().equals(url)){ - // - // System.out.println("url selezionato"); - // - // - // - // } - - if (resources.get(i).getAccessPoints().get(j) - .getDatabaseName().toLowerCase().equals(databaseName.toLowerCase())) { - - info.add(resources.get(i).getAccessPoints().get(j) - .getUsername()); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->username: " - + resources.get(i).getAccessPoints() - .get(j).getUsername()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getPassword()); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->password: " - + resources.get(i).getAccessPoints() - .get(j).getPassword()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDriver()); - - driverInfo = resources.get(i).getAccessPoints().get(j) - .getDriver(); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->driver: " - + resources.get(i).getAccessPoints() - .get(j).getDriver()); - - // driverInfo = - // resources.get(i).getAccessPoints().get(j) - // .getDriver(); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDialect()); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->dialect: " - + resources.get(i).getAccessPoints() - .get(j).getDialect()); - - info.add(resources.get(i).getAccessPoints().get(j) - .address()); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->url: " - + resources.get(i).getAccessPoints() - .get(j).address()); - - info.add(databaseName); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->databasename: " - + resources.get(i).getAccessPoints() - .get(j).getDatabaseName()); - - break check; - - } - - } - - } - - } - - AnalysisLogger - .getLogger() - .debug("In GetTableDetails->information useful for connection: retrieved"); - return info; - - } - - // method that retrieves information such as "CreateTableStatement" and the - // number of rows about the table chosen by the user - private LinkedHashMap getDetails() - throws Exception { - - - tableName = getInputParameter("TableName"); - - if(tableName != null){ - tableName = getInputParameter("TableName").trim(); - } - if ((tableName == null) || (tableName.equals(""))) { - throw new Exception("Warning: insert the table name"); - } - - if (driverInfo.toLowerCase().contains("postgres")) { - - schemaName = getInputParameter("SchemaName"); - if(schemaName != null){ - schemaName = getInputParameter("SchemaName").trim(); - } - if ((schemaName == null) || (schemaName.equals(""))) { - throw new Exception("Warning: insert the schema name"); - } - } - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->getting details on the table: " + tableName); - - // recover metadata of the table - - // recover the "show create" statement - - String createTable = null; - - if ((driverInfo.toLowerCase().contains("postgres"))) { - - createTable = mgt.getCreateTable(tableName, schemaName); - - } - - if ((driverInfo.toLowerCase().contains("mysql"))) { - - createTable = mgt.getCreateTable(tableName, databaseName); - - } - - PrimitiveType valCreateTable = new PrimitiveType( - String.class.getName(), createTable, PrimitiveTypes.STRING, - "Create Table Statement", "Create Table Statement"); - - map.put("CreateTable", valCreateTable); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->getting the \"CreateTableStatement\": " - + createTable); - - // to retrieve the column names of a table - List listColumnNamesTable = mgt.getListColumnNamesTable(); - - String ColumnName = ""; - - for (int i = 0; i < listColumnNamesTable.size(); i++) { - - if (i != listColumnNamesTable.size() - 1) { - ColumnName = ColumnName + listColumnNamesTable.get(i) + ","; - } else { - ColumnName = ColumnName + listColumnNamesTable.get(i); - - } - - } - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->column names: " - + ColumnName); - - PrimitiveType valListColumnNamesTable = new PrimitiveType( - String.class.getName(), ColumnName, PrimitiveTypes.STRING, - "Column Name", "Column Name"); - - map.put("Column Names", valListColumnNamesTable); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->getting the column names list: " - + createTable); - - // recover the number of rows - // BigInteger rows = mgt.getNumberOfRows(tableName); - - long rows = 0; - - if ((driverInfo.toLowerCase().contains("postgres"))) { - AnalysisLogger.getLogger().debug( - "In GetTableDetails->schemaName:" + schemaName);; - - rows = mgt.getNumberOfRows(tableName, schemaName); - - } - - if ((driverInfo.toLowerCase().contains("mysql"))) { - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->*databasename:" + databaseName);; - - rows = mgt.getNumberOfRows(tableName, databaseName); - - } - -// long rows = mgt.getNumberOfRows(tableName); - - // PrimitiveType valRows = new PrimitiveType( - // String.class.getName(), rows.toString(), - // PrimitiveTypes.STRING, "NumberRows", "Rows' Number"); - - PrimitiveType valRows = new PrimitiveType(String.class.getName(), - Long.toString(rows), PrimitiveTypes.STRING, "Number Rows", - "Rows' Number"); - - map.put("NumberRows", valRows); - - // AnalysisLogger - // .getLogger() - // .debug("In TableDetails->getting the number of rows: " + - // rows.toString()); - - AnalysisLogger.getLogger().debug( - "In GetTableDetails->getting the number of rows: " - + Long.toString(rows)); - - return map; - - } - - private void normalizeDBInfo(DBResource resource) throws Exception { - - try{ - int ap = resource.getAccessPoints().size(); - - for (int i = 0; i < ap; i++) { - resource.normalize(i); - } - - }catch (Exception e) { - AnalysisLogger.getLogger().debug( - "In GetTableDetails->: Error in normalization process" - + e.getMessage()); - - throw e; - } - -// int ap = resource.getAccessPoints().size(); -// -// for (int i = 0; i < ap; i++) { -// -// try { -// resource.normalize(i); -// } catch (IOException e) { -// -// // e.printStackTrace(); -// AnalysisLogger.getLogger().debug( -// "In GetTableDetails->: Error in normalization process" -// + e.getMessage()); -// -// throw e; -// -// } -// -// } - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListDBInfo.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListDBInfo.java deleted file mode 100644 index 2835736..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListDBInfo.java +++ /dev/null @@ -1,290 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -import java.io.IOException; -import java.util.ArrayList; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.UUID; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataaccess.databases.access.DatabasesDiscoverer; -import org.gcube.dataaccess.databases.resources.DBResource; -import org.gcube.dataaccess.databases.resources.DBResource.AccessPoint; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.gcube.resources.discovery.client.api.DiscoveryException; -import org.gcube.resources.discovery.client.api.InvalidResultException; - -/** Class that allows to retrieve information about the chosen resource */ -public class ListDBInfo extends StandardLocalExternalAlgorithm { - - private LinkedHashMap map = new LinkedHashMap(); - - // database's parameters specified by the user - private String resourceName = null; - - // list that contains information about the resource - private List ap = new ArrayList(); - - // variable that keeps track of database platform version - private String platformVersion = ""; - - @Override - public void init() throws Exception { - - AnalysisLogger.getLogger().debug("In ListDBInfo->Initialization"); - - String scope = config.getGcubeScope(); - - AnalysisLogger.getLogger().debug("In ListDBInfo->scope set by config object: " + scope); - - - - if (scope == null || scope.length() == 0) { - - scope = ScopeProvider.instance.get(); - AnalysisLogger.getLogger().debug("In ListDBInfo->scope set by ScopeProvider: " + scope); - - - }else{ - - ScopeProvider.instance.set(scope); - - } - } - - @Override - public String getDescription() { - // add a simple description for the algorithm - return "Algorithm that allows to view information about one chosen resource of Database Type in the Infrastructure"; - } - - @Override - protected void process() throws Exception, IOException, IllegalStateException, DiscoveryException, InvalidResultException { - AnalysisLogger.getLogger().debug("In ListDBInfo->Processing"); - - AnalysisLogger.getLogger().debug("Scope: " + ScopeProvider.instance.get()); - - - try{ - // retrieve information - List apInfo = retrieveInfo(); - - AnalysisLogger.getLogger().debug("access point dimension: " + apInfo.size()); - - for (int i = 0; i < apInfo.size(); i++) { - - PrimitiveType DBName = new PrimitiveType(String.class.getName(), - apInfo.get(i).getDatabaseName(), PrimitiveTypes.STRING, - "Database Name " - , "Database Name"); - - int index = i+1; - - map.put("Database Name "+index, DBName); - - AnalysisLogger.getLogger().debug( - "In ListDBInfo->Database Name: " - + apInfo.get(i).getDatabaseName()); - - PrimitiveType url = new PrimitiveType(String.class.getName(), - apInfo.get(i).address(), PrimitiveTypes.STRING, "URL", - "URL"); - - map.put("URL " +index, url); - - AnalysisLogger.getLogger().debug( - "In ListDBInfo->URL: " + apInfo.get(i).address()); - - PrimitiveType driver = new PrimitiveType(String.class.getName(), - apInfo.get(i).getDriver(), PrimitiveTypes.STRING, - "Driver Name", "Driver Name"); - - map.put("Driver Name "+index, driver); - - AnalysisLogger.getLogger().debug( - "In ListDBInfo->Driver Name: " - + apInfo.get(i).getDriver()); - - PrimitiveType dialect = new PrimitiveType(String.class.getName(), - apInfo.get(i).getDialect(), PrimitiveTypes.STRING, - "Dialect Name", "Dialect Name"); - - map.put("Dialect Name " +index, dialect); - - AnalysisLogger.getLogger().debug( - "In ListDBInfo->Dialect Name: " - + apInfo.get(i).getDialect()); - - PrimitiveType platformVersionValue = new PrimitiveType(String.class.getName(), - platformVersion, PrimitiveTypes.STRING, - "Platform Version", "Platform Version"); - - map.put("Platform Version " +index, platformVersionValue); - - AnalysisLogger.getLogger().debug( - "In ListDBInfo->Platform Version: " - + platformVersion); - - - - } - - } - - catch (IllegalStateException e) { -// e.printStackTrace(); - - AnalysisLogger.getLogger().debug("In ListDBInfo-> ERROR " + e.getMessage()); - throw e; - - } catch (DiscoveryException e1) { -// e1.printStackTrace(); - - AnalysisLogger.getLogger().debug("In ListDBInfo-> ERROR " + e1.getMessage()); - - throw e1; - - } catch (InvalidResultException e2) { -// e2.printStackTrace(); - - AnalysisLogger.getLogger().debug("In ListDBInfo-> ERROR " + e2.getMessage()); - - - throw e2; - - } -// catch(IOException e3){ -//// e3.printStackTrace(); -// -// AnalysisLogger.getLogger().debug("In ListDBInfo-> Exception " + e3.getMessage()); -// -// throw e3; -// } - - catch(Exception e4){ - -// e4.printStackTrace(); - AnalysisLogger.getLogger().debug("In ListDBInfo-> Exception " + e4.getMessage()); - - throw e4; - - } - - - } - - @Override - protected void setInputParameters() { - -// AnalysisLogger.getLogger().debug("In ListDBInfo->setting inputs"); - - // resource name specified by the user - addStringInput("ResourceName", "The name of the resource", ""); - - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("In ListDBInfo->Shutdown"); - - } - - @Override - public StatisticalType getOutput() { - - AnalysisLogger.getLogger().debug("In ListDBInfo->retrieving outputs"); - - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(), - map, PrimitiveTypes.MAP, "ResultsMap"+UUID.randomUUID(), "Results Map"); - - return output; - - } - - private List retrieveInfo() throws Exception, IllegalStateException, DiscoveryException, InvalidResultException { - - resourceName = getInputParameter("ResourceName"); - - if (resourceName != null) { - resourceName = getInputParameter("ResourceName").trim(); - } - - if ((resourceName == null) || (resourceName.equals(""))) { - throw new Exception("Warning: insert the resource name"); - } - - // retrieve information about the chosen resource - DatabasesDiscoverer discovery = new DatabasesDiscoverer(); - - List resources = discovery.discover(); - - AnalysisLogger.getLogger().debug( - "In ListDBInfo->number of database resources: " - + resources.size()); - - check: for (int i = 0; i < resources.size(); i++) { - - if (resources.get(i).getResourceName().toLowerCase().equals(resourceName.toLowerCase())) { - - platformVersion = resources.get(i).getPlatformVersion(); - - // ap = resources.get(i).getAccessPoints(); - - normalizeDBInfo(resources.get(i)); - - ap = resources.get(i).getAccessPoints(); - - break check; - - } - - } - return ap; - - } - - private void normalizeDBInfo(DBResource resource) throws Exception { - - try{ - int ap = resource.getAccessPoints().size(); - - for (int i = 0; i < ap; i++) { - resource.normalize(i); - } - - }catch (Exception e) { - AnalysisLogger.getLogger().debug( - "In ListDBInfo->: Error in normalization process" - + e.getMessage()); - - throw e; - } - -// int ap = resource.getAccessPoints().size(); -// -// for (int i = 0; i < ap; i++) { -// -// try { -// resource.normalize(i); -// } -//// catch (IOException e) { -// catch (IOException e) { -// // TODO Auto-generated catch block -//// e.printStackTrace(); -// AnalysisLogger.getLogger().debug( -// "In ListDBInfo->: Error in normalization process" -// + e.getMessage()); -// throw e; -// -// } -// -// } - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListNames.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListNames.java deleted file mode 100644 index 1b7ff89..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListNames.java +++ /dev/null @@ -1,174 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -import java.util.ArrayList; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.UUID; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataaccess.databases.access.DatabasesDiscoverer; -import org.gcube.dataaccess.databases.resources.DBResource; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.gcube.resources.discovery.client.api.DiscoveryException; -import org.gcube.resources.discovery.client.api.InvalidResultException; - -/** Class that allows to retrieve a list of database resources */ -public class ListNames extends StandardLocalExternalAlgorithm { - - private LinkedHashMap map = new LinkedHashMap(); - - @Override - public void init() throws Exception { - - AnalysisLogger.getLogger().debug("In ListNames->Initialization"); - - String scope = config.getGcubeScope(); - - AnalysisLogger.getLogger().debug( - "In ListNames->scope set by config object: " + scope); - - if (scope == null || scope.length() == 0) { - - scope = ScopeProvider.instance.get(); - - AnalysisLogger.getLogger().debug( - "In ListNames->scope set by ScopeProvider: " + scope); - - } else { - - ScopeProvider.instance.set(scope); - - } - } - - @Override - public String getDescription() { - // add a simple description for the algorithm - return "Algorithm that allows to view the available database resources names in the Infrastructure"; - - } - - @Override - protected void process() throws Exception { - - AnalysisLogger.getLogger().debug("In ListNames->Processing"); - - String scope = ScopeProvider.instance.get(); - - if (scope != null) { - - AnalysisLogger.getLogger().debug("getting scope: " + scope); - - AnalysisLogger.getLogger().debug( - "getting scope through config: " + config.getGcubeScope()); - - } - - try { - // retrieve resources - List resources = this.retrieveResources(); - - // add the name to the list - - // list that contains the resource's names - ArrayList listnames = new ArrayList(); - - for (int i = 0; i < resources.size(); i++) { - PrimitiveType val = new PrimitiveType(String.class.getName(), - null, PrimitiveTypes.STRING, "Resource's name", - "Resource's name"); - - AnalysisLogger.getLogger().debug( - "In ListNames->Resource's name: " - + resources.get(i).getResourceName()); - - listnames.add(resources.get(i).getResourceName()); - - val.setContent(listnames.get(i)); - - map.put(String.valueOf(i), val); - - } - - AnalysisLogger.getLogger().debug( - "In ListNames->Output Map Size: " + map.size()); - - } catch (IllegalStateException e) { - // e.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListNames-> ERROR " + e.getMessage()); - throw e; - - } catch (DiscoveryException e1) { - // e1.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListNames-> ERROR " + e1.getMessage()); - - throw e1; - - } catch (InvalidResultException e2) { - // e2.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListNames-> ERROR " + e2.getMessage()); - - throw e2; - - } - - } - - @Override - protected void setInputParameters() { - -// AnalysisLogger.getLogger().debug("In ListNames->setting inputs"); - addStringInput("MaxNumber", "Max Number of Resources (-1 for all)", - "-1"); - - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("In ListNames->Shutdown"); - - } - - @Override - public StatisticalType getOutput() { - - AnalysisLogger.getLogger().debug("In ListNames->retrieving outputs"); - - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(), - map, PrimitiveTypes.MAP, "ResultsMap"+UUID.randomUUID(), "Results Map"); - - return output; - - } - - private List retrieveResources() throws IllegalStateException, - DiscoveryException, InvalidResultException { - - AnalysisLogger.getLogger().debug("In ListNames->retrieving resources"); - List resources = new ArrayList(); - - // retrieve the resources - DatabasesDiscoverer discovery = new DatabasesDiscoverer(); - - resources = discovery.discover(); - - AnalysisLogger.getLogger().debug( - "In ListNames->number of database resources: " - + resources.size()); - - return resources; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListSchemas.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListSchemas.java deleted file mode 100644 index 3ab6410..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListSchemas.java +++ /dev/null @@ -1,473 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -import java.io.IOException; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.UUID; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataaccess.databases.access.DatabasesDiscoverer; -import org.gcube.dataaccess.databases.resources.DBResource; -import org.gcube.dataaccess.databases.utils.DatabaseManagement; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.gcube.resources.discovery.client.api.DiscoveryException; -import org.gcube.resources.discovery.client.api.InvalidResultException; -import org.hibernate.HibernateException; -import org.hibernate.SessionFactory; - -/** - * class that allows to retrieve schema's names of a chosen database. In this - * case the database's type is "postgresql" - */ -public class ListSchemas extends StandardLocalExternalAlgorithm { - - private LinkedHashMap map = new LinkedHashMap(); - private DatabaseManagement mgt; - - // database's parameters specified by the user - private String resourceName = null; - private String databaseName = null; - - private SessionFactory sf; - - @Override - public void init() throws Exception { - mgt = new DatabaseManagement(config.getConfigPath()); - AnalysisLogger.getLogger().debug("In ListSchemas->Initialization"); - - String scope = config.getGcubeScope(); - - AnalysisLogger.getLogger().debug( - "In ListSchemas->scope set by config object: " + scope); - - if (scope == null || scope.length() == 0) { - - scope = ScopeProvider.instance.get(); - - AnalysisLogger.getLogger().debug( - "In ListSchemas->scope set by ScopeProvider: " + scope); - - } else { - - ScopeProvider.instance.set(scope); - - } - } - - @Override - public String getDescription() { - // add a simple description for the algorithm - - return "Algorithm that allows to view the schema names of a chosen database for which the type is Postgres"; - - } - - @Override - protected void process() throws Exception, IOException, - IllegalStateException, DiscoveryException, InvalidResultException, - HibernateException { - - AnalysisLogger.getLogger().debug("In ListSchemas->Processing"); - - try { - - // retrieve information useful for connection - - List Info = retrieveInfo(); - - // create the connection - getConnection(Info); - - // get the schema's list - - List listSchemas = new ArrayList(); - listSchemas = getSchemas(); - - if (listSchemas.size() == 0) { - - AnalysisLogger.getLogger().debug( - "In ListSchemas->Warning: no schema available"); - - } - - for (int i = 0; i < listSchemas.size(); i++) { - - PrimitiveType val = new PrimitiveType(String.class.getName(), - null, PrimitiveTypes.STRING, "schema's name", - "schema's name"); - - val.setContent(listSchemas.get(i)); - - map.put(String.valueOf(i), val); - - // AnalysisLogger.getLogger().debug( - // "In ListSchemas->getting schema's name: " - // + val.getContent()); - - } - - } catch (HibernateException h) { - - AnalysisLogger.getLogger().debug( - "In ListSchemas-> ERROR " + h.getMessage()); - throw h; - } - - catch (IllegalStateException e) { - // e.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListSchemas-> ERROR " + e.getMessage()); - - throw e; - - } catch (DiscoveryException e1) { - // e1.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListSchemas-> ERROR " + e1.getMessage()); - - throw e1; - - } catch (InvalidResultException e2) { - // e2.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListSchemas-> ERROR " + e2.getMessage()); - - throw e2; - - } catch (IOException e3) { - // e3.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListSchemas-> Exception " + e3.getMessage()); - - throw e3; - } - - catch (Exception e4) { - // e4.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListSchemas-> Exception " + e4.getMessage()); - - throw e4; - - } finally { - // close the connection - mgt.closeConnection(); - } - } - - @Override - protected void setInputParameters() { - - // AnalysisLogger.getLogger().debug("In ListSchemas->setting inputs"); - - // resource and database's name specified by the user - - addStringInput("ResourceName", "The name of the resource", ""); - addStringInput("DatabaseName", "The name of the database", ""); - - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("In ListSchemas->Shutdown"); - - } - - @Override - public StatisticalType getOutput() { - - AnalysisLogger.getLogger().debug("In ListSchemas->retrieving outputs"); - - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(), - map, PrimitiveTypes.MAP, "ResultsMap" + UUID.randomUUID(), - "Results Map"); - - return output; - - } - - // method that retrieves the schema's list - private List getSchemas() throws Exception { - - List listSchemas = new ArrayList(); - - try { - - listSchemas = mgt.getSchemas(); - - } catch (Exception e) { - - // e.printStackTrace(); - - // System.out.println(e.getMessage()); - - throw e; - - } - -// finally { -// if (sf.isClosed() == false) { -// mgt.closeConnection(); -// } -// } - - return listSchemas; - - } - - // method that retrieves information useful for the connection - private List retrieveInfo() throws Exception, - IllegalStateException, DiscoveryException, InvalidResultException { - - // the user specifies the resource and the database'name - - resourceName = getInputParameter("ResourceName"); - - if (resourceName != null) { - resourceName = getInputParameter("ResourceName").trim(); - } - - if ((resourceName == null) || (resourceName.equals(""))) { - throw new Exception("Warning: insert the resource name"); - } - - databaseName = getInputParameter("DatabaseName"); - - if (databaseName != null) { - databaseName = getInputParameter("DatabaseName").trim(); - } - if ((databaseName == null) || (databaseName.equals(""))) { - throw new Exception("Warning: insert the database name"); - } - - // retrieve the chosen resource - DatabasesDiscoverer discovery = new DatabasesDiscoverer(); - - // list that contains information useful for the connection - List info = new ArrayList(); - - // try{ - - List resources = discovery.discover(); - - AnalysisLogger.getLogger().debug( - "In ListSchemas->number of database resources: " - + resources.size()); - - for (int i = 0; i < resources.size(); i++) { - - AnalysisLogger.getLogger().debug( - "In ListSchemas->Resource's name: " - + resources.get(i).getResourceName()); - - } - - check: for (int i = 0; i < resources.size(); i++) { - - if (resources.get(i).getResourceName().toLowerCase() - .equals(resourceName.toLowerCase())) { - - normalizeDBInfo(resources.get(i)); - - for (int j = 0; j < resources.get(i).getAccessPoints().size(); j++) { - - // if (resources.get(i).getAccessPoints().get(j) - // .getDatabaseName().equals(databaseName)) { - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getUsername()); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getPassword()); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getDriver()); - // - // // driverInfo = - // // resources.get(i).getAccessPoints().get(j) - // // .getDriver(); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getDialect()); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .address()); - // - // info.add(databaseName); - // - // break check; - // - // } - - // if (resources.get(i).getAccessPoints().get(j) - // .address().equals(url)){ - // - // System.out.println("url selezionato"); - // - // - // - // } - - if (resources.get(i).getAccessPoints().get(j) - .getDatabaseName().toLowerCase() - .equals(databaseName.toLowerCase())) { - - info.add(resources.get(i).getAccessPoints().get(j) - .getUsername()); - - AnalysisLogger.getLogger().debug( - "In ListSchemas->username: " - + resources.get(i).getAccessPoints() - .get(j).getUsername()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getPassword()); - - AnalysisLogger.getLogger().debug( - "In ListSchemas->password: " - + resources.get(i).getAccessPoints() - .get(j).getPassword()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDriver()); - - AnalysisLogger.getLogger().debug( - "In ListSchemas->driver: " - + resources.get(i).getAccessPoints() - .get(j).getDriver()); - - // driverInfo = - // resources.get(i).getAccessPoints().get(j) - // .getDriver(); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDialect()); - - AnalysisLogger.getLogger().debug( - "In ListSchemas->dialect: " - + resources.get(i).getAccessPoints() - .get(j).getDialect()); - - info.add(resources.get(i).getAccessPoints().get(j) - .address()); - - AnalysisLogger.getLogger().debug( - "In ListSchemas->url: " - + resources.get(i).getAccessPoints() - .get(j).address()); - - info.add(databaseName); - - AnalysisLogger.getLogger().debug( - "In ListSchemas->databasename: " - + resources.get(i).getAccessPoints() - .get(j).getDatabaseName()); - - break check; - - } - - } - - } - - } - - AnalysisLogger.getLogger().debug( - "In ListSchemas->information useful for connection: retrieved"); - - // } - // catch(IllegalStateException e) - // { - // // e.printStackTrace(); - // throw e; - // } - // catch(DiscoveryException e1) - // { - // e1.printStackTrace(); - // throw e1; - // } - // catch(InvalidResultException e2) - // { - // e2.printStackTrace(); - // throw e2; - // } - - return info; - - } - - // method that allows to create the connection - private void getConnection(List Info) throws IOException { - - // create the connection - Iterator iterator = Info.iterator(); - - String DatabaseUserName = iterator.next(); - String DatabasePassword = iterator.next(); - String DatabaseDriver = iterator.next(); - String DatabaseDialect = iterator.next(); - String DatabaseURL = iterator.next(); - String DatabaseName = iterator.next(); - - mgt.createConnection(DatabaseUserName, - DatabasePassword, DatabaseDriver, DatabaseDialect, DatabaseURL, - DatabaseName); - - // if (sf.isClosed()){ - - // AnalysisLogger.getLogger().debug("In ListSchemas->database "+DatabaseName+": connected"); - - // } - } - - private void normalizeDBInfo(DBResource resource) throws Exception { - - try{ - int ap = resource.getAccessPoints().size(); - - for (int i = 0; i < ap; i++) { - resource.normalize(i); - } - - }catch (Exception e) { - AnalysisLogger.getLogger().debug( - "In ListSchemas->: Error in normalization process" - + e.getMessage()); - - throw e; - } - -// int ap = resource.getAccessPoints().size(); -// -// for (int i = 0; i < ap; i++) { -// -//// try { -// resource.normalize(i); -//// } catch (IOException e) { -// -// // e.printStackTrace(); -//// AnalysisLogger.getLogger().debug( -//// "In ListTables->: Error in normalization process" -//// + e.getMessage()); -// -//// throw e; -// -//// } -// -// } - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListTables.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListTables.java deleted file mode 100644 index cc46fd6..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/ListTables.java +++ /dev/null @@ -1,460 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -import java.io.IOException; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.UUID; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataaccess.databases.access.DatabasesDiscoverer; -import org.gcube.dataaccess.databases.resources.DBResource; -import org.gcube.dataaccess.databases.utils.DatabaseManagement; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.gcube.resources.discovery.client.api.DiscoveryException; -import org.gcube.resources.discovery.client.api.InvalidResultException; -import org.hibernate.HibernateException; -import org.hibernate.SessionFactory; - -/** Class that allows to retrieve the tables's names of a chosen database */ -public class ListTables extends StandardLocalExternalAlgorithm { - - private LinkedHashMap map = new LinkedHashMap(); - private DatabaseManagement mgt; - // variable that keeps track of the database's type - private String driverInfo; - - // database's parameters specified by the user - private String resourceName = null; - private String databaseName = null; - private String schemaName = null; - - private SessionFactory sf; - - @Override - public void init() throws Exception { - mgt = new DatabaseManagement(config.getConfigPath()); - AnalysisLogger.getLogger().debug("In ListTables->Initialization"); - - String scope = config.getGcubeScope(); - - AnalysisLogger.getLogger().debug( - "In ListTables->scope set by config object: " + scope); - - if (scope == null || scope.length() == 0) { - - scope = ScopeProvider.instance.get(); - - AnalysisLogger.getLogger().debug( - "In ListTables->scope set by ScopeProvider: " + scope); - - } else { - - ScopeProvider.instance.set(scope); - - } - - } - - @Override - public String getDescription() { - // add a simple description for the algorithm - - return "Algorithm that allows to view the table names of a chosen database"; - - } - - @Override - protected void process() throws Exception, IOException, - IllegalStateException, DiscoveryException, InvalidResultException, - HibernateException { - - AnalysisLogger.getLogger().debug("In ListTables->Processing"); - - try { - - // retrieve information useful for the connection - - List Info = retrieveInfo(); - - // create the connection - getConnection(Info); - - // get the table' list - - List listTables = new ArrayList(); - - if (driverInfo.toLowerCase().contains("postgres")) { - - schemaName = getInputParameter("SchemaName"); - if(schemaName != null){ - schemaName = getInputParameter("SchemaName").trim(); - } - if ((schemaName == null) || (schemaName.equals(""))) { - throw new Exception("Warning: insert the schema name"); - } - - // if (!schemaName.equals("")) { - - listTables = mgt.getTables(databaseName, schemaName); - - AnalysisLogger - .getLogger() - .debug("In ListTables->getting table's name for database postgres"); - - // } - - } - - if (driverInfo.toLowerCase().contains("mysql")) { - - listTables = mgt.getTables(databaseName, null); - - AnalysisLogger - .getLogger() - .debug("In ListTables->getting table's name for database mysql"); - - } - - // if (listTables.size()==0){ - // - // AnalysisLogger.getLogger().debug("In ListTables->Warning: no table available"); - // - // } - - // TODO: manage also the oracle type - - if (listTables == null) { - - AnalysisLogger.getLogger().debug( - "In ListTables->Warning: no tables available"); - - } else { - - for (int i = 0; i < listTables.size(); i++) { - - PrimitiveType val = new PrimitiveType( - String.class.getName(), null, - PrimitiveTypes.STRING, "Table's name", - "Table's name"); - - val.setContent(listTables.get(i)); - - map.put(String.valueOf(i), val); - - // AnalysisLogger.getLogger().debug( - // "In ListTables->getting table's name: " - // + val.getContent()); - - } - } - - } catch (HibernateException h) { - - AnalysisLogger.getLogger().debug( - "In ListTables-> ERROR " + h.getMessage()); - throw h; - } catch (IllegalStateException e) { - // e.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListTables-> ERROR " + e.getMessage()); - throw e; - - } catch (DiscoveryException e1) { - // e1.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListTables-> ERROR " + e1.getMessage()); - - throw e1; - - } catch (InvalidResultException e2) { - // e2.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListTables-> ERROR " + e2.getMessage()); - - throw e2; - - } catch (IOException e3) { - // e3.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListTables-> Exception " + e3.getMessage()); - - throw e3; - } - - catch (Exception e4) { - // e4.printStackTrace(); - - AnalysisLogger.getLogger().debug( - "In ListTables-> Exception " + e4.getMessage()); - - throw e4; - - } finally { - // close the connection - mgt.closeConnection(); - } - } - - @Override - protected void setInputParameters() { - - // AnalysisLogger.getLogger().debug("In ListTables->setting inputs"); - - // parameters specified by the user - addStringInput("ResourceName", "The name of the resource", ""); - addStringInput("DatabaseName", "The name of the database", ""); - addStringInput("SchemaName", "The name of the schema", ""); - - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("In ListTables->Shutdown"); - - } - - @Override - public StatisticalType getOutput() { - - AnalysisLogger.getLogger().debug("In ListTables->retrieving outputs"); - - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(), - map, PrimitiveTypes.MAP, "ResultsMap" + UUID.randomUUID(), - "Results Map"); - - return output; - - } - - private List retrieveInfo() throws Exception, - IllegalStateException, DiscoveryException, InvalidResultException { - - // parameters specified by the user - resourceName = getInputParameter("ResourceName"); - - if (resourceName != null) { - resourceName = getInputParameter("ResourceName").trim(); - } - - if ((resourceName == null) || (resourceName.equals(""))) { - throw new Exception("Warning: insert the resource name"); - } - - databaseName = getInputParameter("DatabaseName"); - - if (databaseName != null) { - databaseName = getInputParameter("DatabaseName").trim(); - } - if ((databaseName == null) || (databaseName.equals(""))) { - throw new Exception("Warning: insert the database name"); - } - - // retrieve the chosen resource - DatabasesDiscoverer discovery = new DatabasesDiscoverer(); - - List resources = discovery.discover(); - - AnalysisLogger.getLogger().debug( - "In ListTables->number of database resources: " - + resources.size()); - - for (int i = 0; i < resources.size(); i++) { - - AnalysisLogger.getLogger().debug( - "In ListTables->Resource's name: " - + resources.get(i).getResourceName()); - - } - - // list that contains information useful for the connection - List info = new ArrayList(); - - check: for (int i = 0; i < resources.size(); i++) { - - if (resources.get(i).getResourceName().toLowerCase() - .equals(resourceName.toLowerCase())) { - - normalizeDBInfo(resources.get(i)); - - for (int j = 0; j < resources.get(i).getAccessPoints().size(); j++) { - - // if (resources.get(i).getAccessPoints().get(j) - // .getDatabaseName().equals(databaseName)) { - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getUsername()); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getPassword()); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getDriver()); - // - // // driverInfo = - // // resources.get(i).getAccessPoints().get(j) - // // .getDriver(); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .getDialect()); - // - // info.add(resources.get(i).getAccessPoints().get(j) - // .address()); - // - // info.add(databaseName); - // - // break check; - // - // } - - // if (resources.get(i).getAccessPoints().get(j) - // .address().equals(url)){ - // - // System.out.println("url selezionato"); - // - // - // - // } - - if (resources.get(i).getAccessPoints().get(j) - .getDatabaseName().toLowerCase() - .equals(databaseName.toLowerCase())) { - - info.add(resources.get(i).getAccessPoints().get(j) - .getUsername()); - - AnalysisLogger.getLogger().debug( - "In ListTables->username: " - + resources.get(i).getAccessPoints() - .get(j).getUsername()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getPassword()); - - AnalysisLogger.getLogger().debug( - "In ListTables->password: " - + resources.get(i).getAccessPoints() - .get(j).getPassword()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDriver()); - - driverInfo = resources.get(i).getAccessPoints().get(j) - .getDriver(); - - AnalysisLogger.getLogger().debug( - "In ListTables->driver: " - + resources.get(i).getAccessPoints() - .get(j).getDriver()); - - // driverInfo = - // resources.get(i).getAccessPoints().get(j) - // .getDriver(); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDialect()); - - AnalysisLogger.getLogger().debug( - "In ListTables->dialect: " - + resources.get(i).getAccessPoints() - .get(j).getDialect()); - - info.add(resources.get(i).getAccessPoints().get(j) - .address()); - - AnalysisLogger.getLogger().debug( - "In ListTables->url: " - + resources.get(i).getAccessPoints() - .get(j).address()); - - info.add(databaseName); - - AnalysisLogger.getLogger().debug( - "In ListTables->databasename: " - + resources.get(i).getAccessPoints() - .get(j).getDatabaseName()); - - break check; - - } - - } - - } - - } - - AnalysisLogger.getLogger().debug( - "In ListTables->information useful for connection: retrieved"); - - return info; - - } - - private void getConnection(List Info) throws IOException { - - // create the connection - Iterator iterator = Info.iterator(); - - String DatabaseUserName = iterator.next(); - String DatabasePassword = iterator.next(); - String DatabaseDriver = iterator.next(); - String DatabaseDialect = iterator.next(); - String DatabaseURL = iterator.next(); - String DatabaseName = iterator.next(); - - mgt.createConnection(DatabaseUserName, - DatabasePassword, DatabaseDriver, DatabaseDialect, DatabaseURL, - DatabaseName); - - AnalysisLogger.getLogger().debug( - "In ListTables->database " + DatabaseName + ": connected"); - } - - private void normalizeDBInfo(DBResource resource) throws Exception { - - try{ - int ap = resource.getAccessPoints().size(); - - for (int i = 0; i < ap; i++) { - resource.normalize(i); - } - - }catch (Exception e) { - AnalysisLogger.getLogger().debug( - "In ListTables->: Error in normalization process" - + e.getMessage()); - - throw e; - } - -// int ap = resource.getAccessPoints().size(); -// -// for (int i = 0; i < ap; i++) { -// -// try { -// resource.normalize(i); -// } catch (IOException e) { -// // e.printStackTrace(); -// -// AnalysisLogger.getLogger().debug( -// "In ListTables->: Error in normalization process" -// + e.getMessage()); -// -// throw e; -// } -// -// } - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/RandomSampleOnTable.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/RandomSampleOnTable.java deleted file mode 100644 index abc1e54..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/RandomSampleOnTable.java +++ /dev/null @@ -1,411 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.UUID; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataaccess.databases.access.DatabasesDiscoverer; -import org.gcube.dataaccess.databases.resources.DBResource; -import org.gcube.dataaccess.databases.utils.DatabaseManagement; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.gcube.resources.discovery.client.api.DiscoveryException; -import org.gcube.resources.discovery.client.api.InvalidResultException; -import org.hibernate.HibernateException; -import org.hibernate.SessionFactory; - -/** - * Class that allows to perform a random sample operation on a table of a chosen - * database. It retrieves 100 rows of a table randomly. - */ - -public class RandomSampleOnTable extends StandardLocalExternalAlgorithm { - - private LinkedHashMap map = new LinkedHashMap(); - - // object that allows to manage some operations on a database - private DatabaseManagement mgt; - // database's parameters specified by the user - private String resourceName = null; - private String databaseName = null; - private String schemaName = null; - private String tableName = null; - - private SessionFactory sf; - // variable that keeps track of the driver information - private String driverInfo; - - @Override - public void init() throws Exception { - - mgt = new DatabaseManagement(config.getConfigPath()); - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable->Initialization"); - - String scope = config.getGcubeScope(); - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable->scope set by config object: " - + scope); - - if (scope == null || scope.length() == 0) { - scope = ScopeProvider.instance.get(); - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable->scope set by ScopeProvider: " - + scope); - } else { - ScopeProvider.instance.set(scope); - } - } - - @Override - public String getDescription() { - return "Algorithm that allows to perform a sample operation on a table randomly"; - } - - @Override - protected void process() throws Exception { - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable->Processing"); - - try { - // retrieve information - List Info = retrieveInfo(); - - // check on table name field - tableName = getInputParameter("TableName"); - if(tableName != null){ - tableName = getInputParameter("TableName").trim(); - } - if ((tableName == null) || (tableName.equals(""))) { - throw new Exception("Warning: insert the table name"); - } - - // check on schema name field - if (driverInfo.toLowerCase().contains("postgres")) { - schemaName = getInputParameter("SchemaName"); - if(schemaName != null){ - schemaName = getInputParameter("SchemaName").trim(); - } - if ((schemaName == null) || (schemaName.equals(""))) { - throw new Exception("Warning: insert the schema name"); - } - } - - // create the connection - getConnection(Info); - - // smart sample operation on table - map = randomSampleOnTable(); - - } catch (HibernateException h) { - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable-> ERROR " + h.getMessage()); - throw h; - } - - catch (IllegalStateException e) { - // e.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable-> ERROR " + e.getMessage()); - throw e; - - } catch (DiscoveryException e1) { - // e1.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable-> ERROR " + e1.getMessage()); - throw e1; - - } catch (InvalidResultException e2) { - // e2.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable-> ERROR " + e2.getMessage()); - throw e2; - - } catch (IOException e3) { - // e3.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable-> ERROR " + e3.getMessage()); - throw e3; - } - - catch (Exception e4) { - // e4.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In RandomSmartSampleOnTable-> Exception " - + e4.getMessage()); - throw e4; - - } finally { - // close the connection - mgt.closeConnection(); - } - } - - @Override - protected void setInputParameters() { - // parameters specified by the user - addStringInput("ResourceName", "The name of the resource", ""); - addStringInput("DatabaseName", "The name of the database", ""); - addStringInput("SchemaName", "The name of the schema", ""); - addStringInput("TableName", "The name of the table", ""); - } - - public StatisticalType getOutput() { - - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->retrieving outputs"); - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(), - map, PrimitiveTypes.MAP, "ResultsMap" + UUID.randomUUID(), - "Results Map"); - return output; - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("In RandomSampleOnTable->Shutdown"); - } - - // Method that recovers the info useful for the connection - private List retrieveInfo() throws Exception, - IllegalStateException, DiscoveryException, InvalidResultException { - - resourceName = getInputParameter("ResourceName"); - - if (resourceName != null) { - resourceName = getInputParameter("ResourceName").trim(); - } - - if ((resourceName == null) || (resourceName.equals(""))) { - throw new Exception("Warning: insert the resource name"); - } - - databaseName = getInputParameter("DatabaseName"); - - if (databaseName != null) { - databaseName = getInputParameter("DatabaseName").trim(); - } - if ((databaseName == null) || (databaseName.equals(""))) { - throw new Exception("Warning: insert the database name"); - } - - // retrieve the chosen resource - DatabasesDiscoverer discovery = new DatabasesDiscoverer(); - List resources = discovery.discover(); - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->number of elements: " - + resources.size()); - - // list that contains information useful for the connection - List info = new ArrayList(); - - check: for (int i = 0; i < resources.size(); i++) { - if (resources.get(i).getResourceName().toLowerCase() - .equals(resourceName.toLowerCase())) { - normalizeDBInfo(resources.get(i)); - for (int j = 0; j < resources.get(i).getAccessPoints().size(); j++) { - - if (resources.get(i).getAccessPoints().get(j) - .getDatabaseName().toLowerCase() - .equals(databaseName.toLowerCase())) { - - info.add(resources.get(i).getAccessPoints().get(j) - .getUsername()); - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->username: " - + resources.get(i).getAccessPoints() - .get(j).getUsername()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getPassword()); - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->password: " - + resources.get(i).getAccessPoints() - .get(j).getPassword()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDriver()); - driverInfo = resources.get(i).getAccessPoints().get(j) - .getDriver(); - - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->driver: " - + resources.get(i).getAccessPoints() - .get(j).getDriver()); - - // driverInfo = - // resources.get(i).getAccessPoints().get(j) - // .getDriver(); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDialect()); - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->dialect: " - + resources.get(i).getAccessPoints() - .get(j).getDialect()); - - info.add(resources.get(i).getAccessPoints().get(j) - .address()); - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->url: " - + resources.get(i).getAccessPoints() - .get(j).address()); - - info.add(databaseName); - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->databasename: " - + resources.get(i).getAccessPoints() - .get(j).getDatabaseName()); - break check; - } - } - } - } - - AnalysisLogger - .getLogger() - .debug("In RandomSampleOnTable->information useful for connection: retrieved"); - return info; - } - - // to normalize the information related to a database - private void normalizeDBInfo(DBResource resource) throws Exception { - - try{ - int ap = resource.getAccessPoints().size(); - - for (int i = 0; i < ap; i++) { - resource.normalize(i); - } - - }catch (Exception e) { - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->: Error in normalization process" - + e.getMessage()); - - throw e; - } - -// int ap = resource.getAccessPoints().size(); -// for (int i = 0; i < ap; i++) { -// try { -// resource.normalize(i); -// } catch (IOException e) { -// // e.printStackTrace(); -// AnalysisLogger.getLogger().debug( -// "In RandomSampleOnTable->: Error in normalization process" -// + e.getMessage()); -// throw e; -// } -// } - } - - // create the database's connection - private void getConnection(List Info) throws IOException { - - // create the connection - Iterator iterator = Info.iterator(); - - String DatabaseUserName = iterator.next(); - String DatabasePassword = iterator.next(); - String DatabaseDriver = iterator.next(); - String DatabaseDialect = iterator.next(); - String DatabaseURL = iterator.next(); - String DatabaseName = iterator.next(); - - mgt.createConnection(DatabaseUserName, - DatabasePassword, DatabaseDriver, DatabaseDialect, DatabaseURL, - DatabaseName); - - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->database " + DatabaseName - + ": connected"); - - } - - // to perform the sample operation on the table randomly - private LinkedHashMap randomSampleOnTable() - throws Exception { - - LinkedHashMap mapResults = new LinkedHashMap(); - AnalysisLogger - .getLogger() - .debug("In RandomSampleOnTable->starting the sample operation on table randomly"); - - // sample on table operation - // List resultSet = null; - - if (driverInfo.toLowerCase().contains("postgres")) { - // for a postgres database the second parameter is the schema name - // resultSet = mgt.randomSampleOnTable(tableName, schemaName, - // config.getPersistencePath()); - mgt.randomSampleOnTable(tableName, schemaName, - config.getPersistencePath()); - } - - if (driverInfo.toLowerCase().contains("mysql")) { - // for a mysql database the second parameter is the database name - // resultSet = mgt.randomSampleOnTable(tableName, databaseName, - // config.getPersistencePath()); - mgt.randomSampleOnTable(tableName, databaseName, - config.getPersistencePath()); - } - - AnalysisLogger.getLogger().debug( - "In RandomSampleOnTable->result retrieved"); - - // to add the results to the variable map - // to add the map - - HashMap mapResult = new HashMap(); - mapResult = mgt.getMapSampleTableResult(); - - String encoded = null; - encoded = new String(mapResult.get("HEADERS").getBytes(), "UTF-8"); - - // // check the encoded value - // AnalysisLogger.getLogger().debug( - // "In RandomSampleOnTable->string encoded: " + encoded); - - PrimitiveType val = new PrimitiveType(String.class.getName(), encoded, - PrimitiveTypes.STRING, "Row", "Row"); - mapResults.put("HEADERS", val); - - for (int i = 0; i < mapResult.size() - 1; i++) { - encoded = new String(mapResult.get(String.valueOf(i)).getBytes(), - "UTF-8"); - - // // check the encoded value - // AnalysisLogger.getLogger().debug( - // "In RandomSampleOnTable->string encoded: " + encoded); - - PrimitiveType val1 = new PrimitiveType(String.class.getName(), - encoded, PrimitiveTypes.STRING, "Row", "Row"); - mapResults.put(String.valueOf(i), val1); - // //check value contained in map - // String value = (String) val1.getContent(); - // - // AnalysisLogger.getLogger().debug( - // "In RandomSampleOnTable->value: " + value); - } - - // to add the file - PrimitiveType fileResult = new PrimitiveType(File.class.getName(), - mgt.getFile(), PrimitiveTypes.FILE, "File", - "File"); - mapResults.put("File", fileResult); - - return mapResults; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SampleOnTable.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SampleOnTable.java deleted file mode 100644 index 4c4baf7..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SampleOnTable.java +++ /dev/null @@ -1,407 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -import java.io.File; -import java.io.IOException; -import java.io.UnsupportedEncodingException; -import java.net.URLDecoder; -import java.net.URLEncoder; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.UUID; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataaccess.databases.access.DatabasesDiscoverer; -import org.gcube.dataaccess.databases.resources.DBResource; -import org.gcube.dataaccess.databases.utils.DatabaseManagement; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.gcube.resources.discovery.client.api.DiscoveryException; -import org.gcube.resources.discovery.client.api.InvalidResultException; -import org.hibernate.HibernateException; -import org.hibernate.SessionFactory; - -/** - * Class that allows to perform a sample operation on a table of a chosen - * database. It retrieves the first 100 rows of a table. - */ -public class SampleOnTable extends StandardLocalExternalAlgorithm { - - private LinkedHashMap map = new LinkedHashMap(); - - // object that allows to manage some operations on a database - private DatabaseManagement mgt; - // database's parameters specified by the user - private String resourceName = null; - private String databaseName = null; - private String schemaName = null; - private String tableName = null; - - private SessionFactory sf; - // variable that keeps track of the driver information - private String driverInfo; - - @Override - public void init() throws Exception { - - mgt = new DatabaseManagement(config.getConfigPath()); - AnalysisLogger.getLogger().debug("In SampleOnTable->Initialization"); - - String scope = config.getGcubeScope(); - AnalysisLogger.getLogger().debug( - "In SampleOnTable->scope set by config object: " + scope); - - if (scope == null || scope.length() == 0) { - scope = ScopeProvider.instance.get(); - AnalysisLogger.getLogger().debug( - "In SampleOnTable->scope set by ScopeProvider: " + scope); - } else { - ScopeProvider.instance.set(scope); - } - } - - @Override - public String getDescription() { - return "Algorithm that allows to perform a sample operation on a table"; - } - - @Override - protected void process() throws Exception { - AnalysisLogger.getLogger().debug("In SampleOnTable->Processing"); - - try { - // retrieve information - List Info = retrieveInfo(); - - // check on table name field - tableName = getInputParameter("TableName"); - if(tableName != null){ - tableName = getInputParameter("TableName").trim(); - } - if ((tableName == null) || (tableName.equals(""))) { - throw new Exception("Warning: insert the table name"); - } - - // check on schema name field - if (driverInfo.toLowerCase().contains("postgres")) { - schemaName = getInputParameter("SchemaName"); - if(schemaName != null){ - schemaName = getInputParameter("SchemaName").trim(); - } - if ((schemaName == null) || (schemaName.equals(""))) { - throw new Exception("Warning: insert the schema name"); - } - } - - // create the connection - getConnection(Info); - - // sample operation on table - map = sampleOnTable(); - - } catch (HibernateException h) { - AnalysisLogger.getLogger().debug( - "In SampleOnTable-> ERROR " + h.getMessage()); - throw h; - } - - catch (IllegalStateException e) { - // e.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SampleOnTable-> ERROR " + e.getMessage()); - throw e; - - } catch (DiscoveryException e1) { - // e1.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SampleOnTable-> ERROR " + e1.getMessage()); - throw e1; - - } catch (InvalidResultException e2) { - // e2.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SampleOnTable-> ERROR " + e2.getMessage()); - throw e2; - - } catch (IOException e3) { - // e3.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SampleOnTable-> ERROR " + e3.getMessage()); - throw e3; - } - - catch (Exception e4) { - // e4.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SampleOnTable-> Exception " + e4.getMessage()); - throw e4; - - } finally { - // close the connection - mgt.closeConnection(); - } - } - - @Override - protected void setInputParameters() { - // parameters specified by the user - addStringInput("ResourceName", "The name of the resource", ""); - addStringInput("DatabaseName", "The name of the database", ""); - addStringInput("SchemaName", "The name of the schema", ""); - addStringInput("TableName", "The name of the table", ""); - } - - public StatisticalType getOutput() { - - AnalysisLogger.getLogger() - .debug("In SampleOnTable->retrieving outputs"); - - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(), - map, PrimitiveTypes.MAP, "ResultsMap"+UUID.randomUUID(), "Results Map"); - - return output; - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("In SampleOnTable->Shutdown"); - - } - - // Method that recovers the info useful for the connection - private List retrieveInfo() throws Exception, - IllegalStateException, DiscoveryException, InvalidResultException { - - resourceName = getInputParameter("ResourceName"); - - if (resourceName != null) { - resourceName = getInputParameter("ResourceName").trim(); - } - - if ((resourceName == null) || (resourceName.equals(""))) { - throw new Exception("Warning: insert the resource name"); - } - - databaseName = getInputParameter("DatabaseName"); - - if (databaseName != null) { - databaseName = getInputParameter("DatabaseName").trim(); - } - if ((databaseName == null) || (databaseName.equals(""))) { - throw new Exception("Warning: insert the database name"); - } - - // retrieve the chosen resource - DatabasesDiscoverer discovery = new DatabasesDiscoverer(); - List resources = discovery.discover(); - - AnalysisLogger.getLogger().debug( - "In SampleOnTable->number of elements: " + resources.size()); - - // list that contains information useful for the connection - List info = new ArrayList(); - - check: for (int i = 0; i < resources.size(); i++) { - if (resources.get(i).getResourceName().toLowerCase() - .equals(resourceName.toLowerCase())) { - normalizeDBInfo(resources.get(i)); - for (int j = 0; j < resources.get(i).getAccessPoints().size(); j++) { - - if (resources.get(i).getAccessPoints().get(j) - .getDatabaseName().toLowerCase() - .equals(databaseName.toLowerCase())) { - - info.add(resources.get(i).getAccessPoints().get(j) - .getUsername()); - AnalysisLogger.getLogger().debug( - "In SampleOnTable->username: " - + resources.get(i).getAccessPoints() - .get(j).getUsername()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getPassword()); - AnalysisLogger.getLogger().debug( - "In SampleOnTable->password: " - + resources.get(i).getAccessPoints() - .get(j).getPassword()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDriver()); - driverInfo = resources.get(i).getAccessPoints().get(j) - .getDriver(); - AnalysisLogger.getLogger().debug( - "In SampleOnTable->driver: " - + resources.get(i).getAccessPoints() - .get(j).getDriver()); - - // driverInfo = - // resources.get(i).getAccessPoints().get(j) - // .getDriver(); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDialect()); - AnalysisLogger.getLogger().debug( - "In SampleOnTable->dialect: " - + resources.get(i).getAccessPoints() - .get(j).getDialect()); - - info.add(resources.get(i).getAccessPoints().get(j) - .address()); - AnalysisLogger.getLogger().debug( - "In SampleOnTable->url: " - + resources.get(i).getAccessPoints() - .get(j).address()); - - info.add(databaseName); - AnalysisLogger.getLogger().debug( - "In SampleOnTable->databasename: " - + resources.get(i).getAccessPoints() - .get(j).getDatabaseName()); - break check; - } - } - } - } - - AnalysisLogger - .getLogger() - .debug("In SampleOnTable->information useful for connection: retrieved"); - - return info; - } - - // to normalize the information related to a database - private void normalizeDBInfo(DBResource resource) throws Exception { - - try{ - int ap = resource.getAccessPoints().size(); - - for (int i = 0; i < ap; i++) { - resource.normalize(i); - } - - }catch (Exception e) { - AnalysisLogger.getLogger().debug( - "In SampleOnTable->: Error in normalization process" - + e.getMessage()); - - throw e; - } - -// int ap = resource.getAccessPoints().size(); -// for (int i = 0; i < ap; i++) { -// try { -// resource.normalize(i); -// } catch (IOException e) { -// // e.printStackTrace(); -// AnalysisLogger.getLogger().debug( -// "In SampleOnTable->: Error in normalization process" -// + e.getMessage()); -// throw e; -// } -// } - } - - // create the database's connection - private void getConnection(List Info) throws IOException { - - // create the connection - Iterator iterator = Info.iterator(); - - String DatabaseUserName = iterator.next(); - String DatabasePassword = iterator.next(); - String DatabaseDriver = iterator.next(); - String DatabaseDialect = iterator.next(); - String DatabaseURL = iterator.next(); - String DatabaseName = iterator.next(); - - mgt.createConnection(DatabaseUserName, - DatabasePassword, DatabaseDriver, DatabaseDialect, DatabaseURL, - DatabaseName); - - AnalysisLogger.getLogger().debug( - "In SampleOnTable->database " + DatabaseName + ": connected"); - } - - // to perform the sample operation on the table - private LinkedHashMap sampleOnTable() - throws Exception { - - LinkedHashMap mapResults = new LinkedHashMap(); - AnalysisLogger.getLogger().debug( - "In SampleOnTable->starting the sample operation on table"); - - // sample on table operation - // List resultSet = null; - - if (driverInfo.toLowerCase().contains("postgres")) { - // for a postgres database the second parameter is the schema name - // resultSet = mgt.sampleOnTable(tableName, schemaName, - // config.getPersistencePath()); - mgt.sampleOnTable(tableName, schemaName, - config.getPersistencePath()); - } - - if (driverInfo.toLowerCase().contains("mysql")) { - // for a mysql database the second parameter is the database name - // resultSet = mgt.sampleOnTable(tableName, databaseName, - // config.getPersistencePath()); - mgt.sampleOnTable(tableName, databaseName, - config.getPersistencePath()); - } - - AnalysisLogger.getLogger().debug("In SampleOnTable->result retrieved"); - - // to add the results to the variable map - // to add the map - - HashMap mapResult = new HashMap(); - mapResult = mgt.getMapSampleTableResult(); - - String encoded = null; - encoded = new String(mapResult.get("HEADERS").getBytes(), "UTF-8"); - - // // check encoded value - // - // AnalysisLogger.getLogger().debug( - // "In SampleOnTable->string encoded: " + encoded); - - PrimitiveType val = new PrimitiveType(String.class.getName(), encoded, - PrimitiveTypes.STRING, "Row", "Row"); - mapResults.put("HEADERS", val); - - for (int i = 0; i < mapResult.size() - 1; i++) { - encoded = new String(mapResult.get(String.valueOf(i)).getBytes(), - "UTF-8"); - - // // check encoded value - // AnalysisLogger.getLogger().debug( - // "In SampleOnTable->string encoded: " + encoded); - - PrimitiveType val1 = new PrimitiveType(String.class.getName(), - encoded, PrimitiveTypes.STRING, "Row", "Row"); - mapResults.put(String.valueOf(i), val1); - // //check value contained in the map - // String value = (String) val1.getContent(); - // - // AnalysisLogger.getLogger().debug( - // "In SampleOnTable->value: " + value); - - } - - // to add the file - PrimitiveType fileResult = new PrimitiveType(File.class.getName(), - mgt.getFile(), PrimitiveTypes.FILE, "File", - "File"); - mapResults.put("File", fileResult); - - return mapResults; - - } -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SmartCorrectionEnum.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SmartCorrectionEnum.java deleted file mode 100644 index e53e35d..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SmartCorrectionEnum.java +++ /dev/null @@ -1,7 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -public enum SmartCorrectionEnum { - NONE, - POSTGRES, - MYSQL, -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SmartSampleOnTable.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SmartSampleOnTable.java deleted file mode 100644 index 0ac0d37..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SmartSampleOnTable.java +++ /dev/null @@ -1,409 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.UUID; - -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataaccess.databases.access.DatabasesDiscoverer; -import org.gcube.dataaccess.databases.resources.DBResource; -import org.gcube.dataaccess.databases.utils.DatabaseManagement; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.gcube.resources.discovery.client.api.DiscoveryException; -import org.gcube.resources.discovery.client.api.InvalidResultException; -import org.hibernate.HibernateException; -import org.hibernate.SessionFactory; - -/** - * Class that allows to perform a smart sample operation on a table of a chosen - * database. It retrieves 100 rows of a table randomly that have the maximum - * number of columns not null. - */ - -public class SmartSampleOnTable extends StandardLocalExternalAlgorithm { - - private LinkedHashMap map = new LinkedHashMap(); - - // object that allows to manage some operations on a database - private DatabaseManagement mgt; - // database's parameters specified by the user - private String resourceName = null; - private String databaseName = null; - private String schemaName = null; - private String tableName = null; - - private SessionFactory sf; - // variable that keeps track of the driver information - private String driverInfo; - - @Override - public void init() throws Exception { - - mgt = new DatabaseManagement(config.getConfigPath()); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->Initialization"); - - String scope = config.getGcubeScope(); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->scope set by config object: " + scope); - - if (scope == null || scope.length() == 0) { - scope = ScopeProvider.instance.get(); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->scope set by ScopeProvider: " - + scope); - } else { - ScopeProvider.instance.set(scope); - } - } - - @Override - public String getDescription() { - return "Algorithm that allows to perform a smart sample operation on a table"; - } - - @Override - protected void process() throws Exception { - AnalysisLogger.getLogger().debug("In SmartSampleOnTable->Processing"); - - try { - - // retrieve information - List Info = retrieveInfo(); - - // check on table name field - tableName = getInputParameter("TableName"); - if(tableName != null){ - tableName = getInputParameter("TableName").trim(); - } - if ((tableName == null) || (tableName.equals(""))) { - throw new Exception("Warning: insert the table name"); - } - - // check on schema name field - if (driverInfo.toLowerCase().contains("postgres")) { - schemaName = getInputParameter("SchemaName"); - if(schemaName != null){ - schemaName = getInputParameter("SchemaName").trim(); - } - if ((schemaName == null) || (schemaName.equals(""))) { - throw new Exception("Warning: insert the schema name"); - } - } - - // create the connection - getConnection(Info); - - // smart sample operation on table - map = smartSampleOnTable(); - - } catch (HibernateException h) { - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable-> ERROR " + h.getMessage()); - throw h; - } - - catch (IllegalStateException e) { - // e.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable-> ERROR " + e.getMessage()); - throw e; - - } catch (DiscoveryException e1) { - // e1.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable-> ERROR " + e1.getMessage()); - throw e1; - - } catch (InvalidResultException e2) { - // e2.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable-> ERROR " + e2.getMessage()); - throw e2; - - } catch (IOException e3) { - // e3.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable-> ERROR " + e3.getMessage()); - throw e3; - } - - catch (Exception e4) { - // e4.printStackTrace(); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable-> Exception " + e4.getMessage()); - throw e4; - - } finally { - mgt.closeConnection(); - } - } - - @Override - protected void setInputParameters() { - // parameters specified by the user - addStringInput("ResourceName", "The name of the resource", ""); - addStringInput("DatabaseName", "The name of the database", ""); - addStringInput("SchemaName", "The name of the schema", ""); - addStringInput("TableName", "The name of the table", ""); - } - - public StatisticalType getOutput() { - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->retrieving outputs"); - - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(), - map, PrimitiveTypes.MAP, "ResultsMap"+UUID.randomUUID(), "Results Map"); - return output; - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("In SmartSampleOnTable->Shutdown"); - } - - // Method that recovers the info useful for the connection - private List retrieveInfo() throws Exception, - IllegalStateException, DiscoveryException, InvalidResultException { - - resourceName = getInputParameter("ResourceName"); - - if (resourceName != null) { - resourceName = getInputParameter("ResourceName").trim(); - } - - if ((resourceName == null) || (resourceName.equals(""))) { - throw new Exception("Warning: insert the resource name"); - } - - databaseName = getInputParameter("DatabaseName"); - - if (databaseName != null) { - databaseName = getInputParameter("DatabaseName").trim(); - } - if ((databaseName == null) || (databaseName.equals(""))) { - throw new Exception("Warning: insert the database name"); - } - - // retrieve the chosen resource - DatabasesDiscoverer discovery = new DatabasesDiscoverer(); - List resources = discovery.discover(); - - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->number of elements: " - + resources.size()); - - // list that contains information useful for the connection - List info = new ArrayList(); - - check: for (int i = 0; i < resources.size(); i++) { - - if (resources.get(i).getResourceName().toLowerCase() - .equals(resourceName.toLowerCase())) { - - normalizeDBInfo(resources.get(i)); - - for (int j = 0; j < resources.get(i).getAccessPoints().size(); j++) { - - if (resources.get(i).getAccessPoints().get(j) - .getDatabaseName().toLowerCase() - .equals(databaseName.toLowerCase())) { - - info.add(resources.get(i).getAccessPoints().get(j) - .getUsername()); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->username: " - + resources.get(i).getAccessPoints() - .get(j).getUsername()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getPassword()); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->password: " - + resources.get(i).getAccessPoints() - .get(j).getPassword()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDriver()); - driverInfo = resources.get(i).getAccessPoints().get(j) - .getDriver(); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->driver: " - + resources.get(i).getAccessPoints() - .get(j).getDriver()); - - // driverInfo = - // resources.get(i).getAccessPoints().get(j) - // .getDriver(); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDialect()); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->dialect: " - + resources.get(i).getAccessPoints() - .get(j).getDialect()); - - info.add(resources.get(i).getAccessPoints().get(j) - .address()); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->url: " - + resources.get(i).getAccessPoints() - .get(j).address()); - - info.add(databaseName); - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->databasename: " - + resources.get(i).getAccessPoints() - .get(j).getDatabaseName()); - break check; - } - } - } - } - - AnalysisLogger - .getLogger() - .debug("In SmartSampleOnTable->information useful for connection: retrieved"); - return info; - } - - // to normalize the information related to a database - private void normalizeDBInfo(DBResource resource) throws Exception { - - try{ - int ap = resource.getAccessPoints().size(); - - for (int i = 0; i < ap; i++) { - resource.normalize(i); - } - - }catch (Exception e) { - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->: Error in normalization process" - + e.getMessage()); - - throw e; - } - -// int ap = resource.getAccessPoints().size(); -// for (int i = 0; i < ap; i++) { -// try { -// resource.normalize(i); -// } catch (IOException e) { -// // e.printStackTrace(); -// AnalysisLogger.getLogger().debug( -// "In SmartSampleOnTable->: Error in normalization process" -// + e.getMessage()); -// throw e; -// } -// } - } - - // create the database's connection - private void getConnection(List Info) throws IOException { - - // create the connection - Iterator iterator = Info.iterator(); - - String DatabaseUserName = iterator.next(); - String DatabasePassword = iterator.next(); - String DatabaseDriver = iterator.next(); - String DatabaseDialect = iterator.next(); - String DatabaseURL = iterator.next(); - String DatabaseName = iterator.next(); - - mgt.createConnection(DatabaseUserName, - DatabasePassword, DatabaseDriver, DatabaseDialect, DatabaseURL, - DatabaseName); - - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->database " + DatabaseName - + ": connected"); - } - - // to perform the sample operation on the table - private LinkedHashMap smartSampleOnTable() - throws Exception { - - LinkedHashMap mapResults = new LinkedHashMap(); - - AnalysisLogger - .getLogger() - .debug("In SmartSampleOnTable->starting the smart sample operation on table"); - - // sample on table operation - // List resultSet = null; - - if (driverInfo.toLowerCase().contains("postgres")) { - // for a postgres database the second parameter is the schema name - // resultSet = mgt.smartSampleOnTable(tableName, schemaName, - // config.getPersistencePath()); - mgt.smartSampleOnTable(tableName, schemaName, - config.getPersistencePath()); - } - - if (driverInfo.toLowerCase().contains("mysql")) { - // for a mysql database the second parameter is the database name - // resultSet = mgt.smartSampleOnTable(tableName, databaseName, - // config.getPersistencePath()); - mgt.smartSampleOnTable(tableName, databaseName, - config.getPersistencePath()); - } - - AnalysisLogger.getLogger().debug( - "In SmartSampleOnTable->result retrieved"); - - // to add the results to the variable map - // to add the map - HashMap mapResult = new HashMap(); - mapResult = mgt.getMapSampleTableResult(); - - String encoded = null; - encoded = new String(mapResult.get("HEADERS").getBytes(), "UTF-8"); - - // //check encoded value - // AnalysisLogger.getLogger().debug( - // "In SmartSampleOnTable->string encoded: " + encoded); - - PrimitiveType val = new PrimitiveType(String.class.getName(), encoded, - PrimitiveTypes.STRING, "Row", "Row"); - mapResults.put("HEADERS", val); - - for (int i = 0; i < mapResult.size() - 1; i++) { - encoded = new String(mapResult.get(String.valueOf(i)).getBytes(), - "UTF-8"); - - // // check encoded value - // AnalysisLogger.getLogger().debug( - // "In SmartSampleOnTable->string encoded: " + encoded); - - PrimitiveType val1 = new PrimitiveType(String.class.getName(), - encoded, PrimitiveTypes.STRING, "Row", "Row"); - mapResults.put(String.valueOf(i), val1); - // //check value - // String value = (String) val1.getContent(); - // - // AnalysisLogger.getLogger().debug( - // "In SmartSampleOnTable->value: " + value); - - } - - // to add the file - PrimitiveType fileResult = new PrimitiveType(File.class.getName(), - mgt.getFile(), PrimitiveTypes.FILE, "File", - "File"); - mapResults.put("File", fileResult); - - return mapResults; - } -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SubmitQuery.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SubmitQuery.java deleted file mode 100644 index b373b1b..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SubmitQuery.java +++ /dev/null @@ -1,691 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -import java.io.File; -import java.io.IOException; -import java.sql.Connection; -import java.sql.DriverManager; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Iterator; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Timer; -import java.util.TimerTask; -import java.util.UUID; - -import org.apache.commons.httpclient.UsernamePasswordCredentials; -import org.gcube.common.scope.api.ScopeProvider; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataaccess.databases.access.DatabasesDiscoverer; -import org.gcube.dataaccess.databases.lexer.MySQLLexicalAnalyzer; -import org.gcube.dataaccess.databases.lexer.PostgresLexicalAnalyzer; -import org.gcube.dataaccess.databases.resources.DBResource; -import org.gcube.dataaccess.databases.utils.DatabaseManagement; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.gcube.resources.discovery.client.api.DiscoveryException; -import org.gcube.resources.discovery.client.api.InvalidResultException; -import org.hibernate.HibernateException; -import org.hibernate.SessionFactory; - -import com.adventnet.swissqlapi.sql.exception.ConvertException; -import com.adventnet.swissqlapi.sql.parser.ParseException; - -/** - * Class that allows to submit a query. It retrieves results in a file and in a - * map. - */ -public class SubmitQuery extends StandardLocalExternalAlgorithm { - - static long maximum_execution_time = 30*60*1000; //time to stop execution query - private LinkedHashMap map = new LinkedHashMap(); - // object that allows to manage some operations on a database - private DatabaseManagement mgt; - // variable that keeps track of the database's type - private String driverInfo; - - private Connection dbconnection; - // database's parameters specified by the user - private String resourceName = null; - private String databaseName = null; - private String schemaName = null; - private String tableName = null; - private String query = null; - - private String valueReadOnly = "Read-Only Query"; - private String smartCorrection = "Apply Smart Correction"; - private String dialect = "Language"; - - private String valueRO; - private String valueSC; - private String valueDialect = ""; - - // variable used to filter the disallowed queries - private boolean NotAllowedQuery = false; - - //class for the timer to stop execution query - private class ExecutionStopper extends TimerTask { - @Override - public void run() { - AnalysisLogger.getLogger().debug("ExecutionStopper: Stopping execution"); - shutdown(); - } - } - - - @Override - public void init() throws Exception { - - mgt = new DatabaseManagement(config.getConfigPath()); - AnalysisLogger.getLogger().debug("In SubmitQuery->Initialization"); - - String scope = config.getGcubeScope(); - AnalysisLogger.getLogger().debug( - "In SubmitQuery->scope set by config object: " + scope); - - if (scope == null || scope.length() == 0) { - scope = ScopeProvider.instance.get(); - AnalysisLogger.getLogger().debug( - "In SubmitQuery->scope set by ScopeProvider: " + scope); - } else { - ScopeProvider.instance.set(scope); - } - - valueRO = config.getParam(valueReadOnly); - valueSC = config.getParam(smartCorrection); - } - - @Override - public String getDescription() { - return "Algorithm that allows to submit a query"; - } - - @Override - protected void process() throws Exception, IOException, - IllegalStateException, DiscoveryException, InvalidResultException, - HibernateException { - - AnalysisLogger.getLogger().debug("In SubmitQuery->Processing"); - - Timer stopper = new Timer(); - stopper.schedule(new ExecutionStopper(),maximum_execution_time); - - try { - // retrieve information - List Info = retrieveInfo(); - - // create the connection - dbconnection = getConnection(Info); - - // submit a query - map = submitQuery(); - -// // close the connection -// dbconnection.close(); - - } catch (HibernateException h) { - - // AnalysisLogger.getLogger().debug( - // "In SubmitQuery-> ERROR " + h.getMessage()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery-> " + h.getMessage()); - throw h; - } - - catch (IllegalStateException e) { - // e.printStackTrace(); - - // AnalysisLogger.getLogger().debug( - // "In SubmitQuery-> ERROR " + e.getMessage()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery-> " + e.getMessage()); - throw e; - - } catch (DiscoveryException e1) { - // e1.printStackTrace(); - - // AnalysisLogger.getLogger().debug( - // "In SubmitQuery-> ERROR " + e1.getMessage()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery-> " + e1.getMessage()); - throw e1; - - } catch (InvalidResultException e2) { - // e2.printStackTrace(); - - // AnalysisLogger.getLogger().debug( - // "In SubmitQuery-> ERROR " + e2.getMessage()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery-> " + e2.getMessage()); - throw e2; - - } catch (IOException e3) { - // e3.printStackTrace(); - - // AnalysisLogger.getLogger().debug( - // "In SubmitQuery-> ERROR " + e3.getMessage()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery-> " + e3.getMessage()); - throw e3; - } - - catch (Exception e4) { - // e4.printStackTrace(); - - // AnalysisLogger.getLogger().debug( - // "In SubmitQuery-> Exception " + e4.getMessage()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery-> " + e4.getMessage()); - throw e4; - - } finally { - if (dbconnection!=null) { - dbconnection.close(); - AnalysisLogger.getLogger().debug("In SubmitQuery-> Connection closed"); - dbconnection=null; - } - //remove the timer if the execution query has already terminated - if (stopper!=null){ - try{ - stopper.cancel(); - stopper.purge(); - AnalysisLogger.getLogger().debug("In SubmitQuery-> Execution stopper terminated"); - }catch(Exception e){ - AnalysisLogger.getLogger().debug("In SubmitQuery-> Could not stop execution stopper "+e.getMessage() ); - } - } - } - } - - public StatisticalType getOutput() { - - AnalysisLogger.getLogger().debug("In SubmitQuery->retrieving outputs"); - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(), - map, PrimitiveTypes.MAP, "ResultsMap"+UUID.randomUUID(), "Results Map"); - return output; - } - - public List getInputParameters() { - List parameters = new ArrayList(); - - // parameters specified by the user - PrimitiveType p0 = new PrimitiveType(String.class.getName(), "", - PrimitiveTypes.STRING, "ResourceName", - "The name of the resource"); - - PrimitiveType p1 = new PrimitiveType(String.class.getName(), "", - PrimitiveTypes.STRING, "DatabaseName", - "The name of the database"); - - PrimitiveType p2 = new PrimitiveType(Boolean.class.getName(), null, - PrimitiveTypes.BOOLEAN, valueReadOnly, - "Check the box if the query must be read-only", "true"); - - PrimitiveType p3 = new PrimitiveType(Boolean.class.getName(), null, - PrimitiveTypes.BOOLEAN, smartCorrection, - "Check the box for smart correction", "true"); - - // addEnumerateInput(SmartCorrectionEnum.values(), dialect, "Language", - // ""); - PrimitiveType p4 = new PrimitiveType(Enum.class.getName(), - SmartCorrectionEnum.values(), PrimitiveTypes.ENUMERATED, - dialect, "Language", SmartCorrectionEnum.NONE.name()); - - PrimitiveType p5 = new PrimitiveType(String.class.getName(), "", - PrimitiveTypes.STRING, "Query", "query"); - - parameters.add(p0); - parameters.add(p1); - parameters.add(p2); - parameters.add(p3); - parameters.add(p4); - parameters.add(p5); - - return parameters; - - } - - @Override - protected void setInputParameters() { - - // AnalysisLogger.getLogger().debug("In SubmitQuery->setting inputs"); - - // parameters specified by the user - // addStringInput("ResourceName", "The name of the resource", ""); - // addStringInput("DatabaseName", "The name of the database", ""); - - // PrimitiveType p2 = new PrimitiveType(Boolean.class.getName(), null, - // PrimitiveTypes.BOOLEAN, valueReadOnly, - // "Check the box if the query must be read-only","true"); - - // addEnumerateInput(SubmitQueryEnum.values(), valueReadOnly, - // "Check the box if the query must be read-only", - // SubmitQueryEnum.TRUE.name()); - // addStringInput("SchemaName", "The name of the schema", ""); - // addStringInput("TableName", "The name of the table", ""); - - // PrimitiveType p3 = new PrimitiveType(Boolean.class.getName(), null, - // PrimitiveTypes.BOOLEAN, smartCorrection, - // "Check the box for smart correction","true"); - // List parameters = new ArrayList(); - // parameters.add(p2); - // parameters.add(p3); - - // addEnumerateInput( - // SubmitQueryEnum.values(), - // smartCorrection, - // "Check the box for smart correction", - // SubmitQueryEnum.TRUE.name()); - - // addEnumerateInput(SmartCorrectionEnum.values(), dialect, "Language)", - // SmartCorrectionEnum.POSTGRES.name()); - - // addEnumerateInput(SmartCorrectionEnum.values(), dialect, "Language", - // ""); - // addEnumerateInput(SmartCorrectionEnum.values(), dialect, "Language", - // ""); - - // addStringInput("Query", "query", ""); - - } - - @Override - public void shutdown() { - - AnalysisLogger.getLogger().debug("In SubmitQuery->Shutdown"); - try{ - if (dbconnection!=null) { - dbconnection.close(); - AnalysisLogger.getLogger().debug("In SubmitQuery-> Connection closed"); - dbconnection=null; - } - }catch(Exception e){ - AnalysisLogger.getLogger().debug("In SubmitQuery->Unable to close connection "+e.getMessage()); - } - } - - // Method that recovers the info useful for the connection - private List retrieveInfo() throws Exception, - IllegalStateException, DiscoveryException, InvalidResultException { - - resourceName = getInputParameter("ResourceName"); - - if (resourceName != null) { - resourceName = getInputParameter("ResourceName").trim(); - } - - if ((resourceName == null) || (resourceName.equals(""))) { - throw new Exception("Warning: insert the resource name"); - } - - databaseName = getInputParameter("DatabaseName"); - - if (databaseName != null) { - databaseName = getInputParameter("DatabaseName").trim(); - } - if ((databaseName == null) || (databaseName.equals(""))) { - throw new Exception("Warning: insert the database name"); - } - - // retrieve the chosen resource - DatabasesDiscoverer discovery = new DatabasesDiscoverer(); - List resources = discovery.discover(); - AnalysisLogger.getLogger().debug( - "In SubmitQuery->number of elements: " + resources.size()); - - // list that contains information useful for the connection - List info = new ArrayList(); - - check: for (int i = 0; i < resources.size(); i++) { - if (resources.get(i).getResourceName().toLowerCase() - .equals(resourceName.toLowerCase())) { - normalizeDBInfo(resources.get(i)); - for (int j = 0; j < resources.get(i).getAccessPoints().size(); j++) { - - if (resources.get(i).getAccessPoints().get(j) - .getDatabaseName().toLowerCase() - .equals(databaseName.toLowerCase())) { - - info.add(resources.get(i).getAccessPoints().get(j) - .getUsername()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery->username: " - + resources.get(i).getAccessPoints() - .get(j).getUsername()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getPassword()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery->password: " - + resources.get(i).getAccessPoints() - .get(j).getPassword()); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDriver()); - driverInfo = resources.get(i).getAccessPoints().get(j) - .getDriver(); - AnalysisLogger.getLogger().debug( - "In SubmitQuery->driver: " - + resources.get(i).getAccessPoints() - .get(j).getDriver()); - - // driverInfo = - // resources.get(i).getAccessPoints().get(j) - // .getDriver(); - - info.add(resources.get(i).getAccessPoints().get(j) - .getDialect()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery->dialect: " - + resources.get(i).getAccessPoints() - .get(j).getDialect()); - - info.add(resources.get(i).getAccessPoints().get(j) - .address()); - AnalysisLogger.getLogger().debug( - "In SubmitQuery->url: " - + resources.get(i).getAccessPoints() - .get(j).address()); - - info.add(databaseName); - AnalysisLogger.getLogger().debug( - "In SubmitQuery->databasename: " - + resources.get(i).getAccessPoints() - .get(j).getDatabaseName()); - - break check; - } - } - } - } - - AnalysisLogger.getLogger().debug( - "In SubmitQuery->information useful for connection: retrieved"); - return info; - } - - // create the database's connection - private Connection getConnection(List Info) throws Exception { - - // create the connection - Iterator iterator = Info.iterator(); - - String DatabaseUserName = iterator.next(); - String DatabasePassword = iterator.next(); - String DatabaseDriver = iterator.next(); - String DatabaseDialect = iterator.next(); - String DatabaseURL = iterator.next(); - String DatabaseName = iterator.next(); - - // Load the database driver - Class.forName(DatabaseDriver) ; - // Get a connection to the database - Connection conn = DriverManager.getConnection(DatabaseURL,DatabaseUserName,DatabasePassword) ; - if (conn!=null){ - AnalysisLogger.getLogger().debug( - "In SubmitQuery->database " + DatabaseName + ": connected"); - } - return conn; - } - - // Method that allows to submit a query - private LinkedHashMap submitQuery() - throws Exception, ParseException, ConvertException { - - // LinkedHashMap results = new - // LinkedHashMap(); - - LinkedHashMap mapResults = new LinkedHashMap(); - - query = getInputParameter("Query"); - if ((query == null) || (query.equals(""))) { - throw new Exception("Warning: insert the query"); - } - - // analyze the query to filter it if it is not read-only compliant - // String valueRO = getInputParameter(valueReadOnly); - - // //print check - AnalysisLogger.getLogger().debug("In SubmitQuery->valueRO: " + valueRO); - - if (valueRO.equals("true")) { - AnalysisLogger.getLogger().debug( - "In SubmitQuery->Analyzing the query: " + query); - NotAllowedQuery = analyzeQuery(query); - - // //print check - // AnalysisLogger.getLogger().debug( - // "In SubmitQuery->NotAllowedQuery valueRO: " + NotAllowedQuery); - } - - if (NotAllowedQuery == false) { - - // formatWithQuotes(query); - - // submit query - List result = new ArrayList(); - - // path file - // AnalysisLogger.getLogger() - // .debug("In SubmitQuery->path file: " - // + config.getPersistencePath()); - - // if user specifies to use the smart correction a translation in - // applied on the query - // String valueSC = getInputParameter(smartCorrection); - - // //print check - AnalysisLogger.getLogger().debug( - "In SubmitQuery->valueSC: " + valueSC); - - // dialect to which a query is converted - // String valueDialect = getInputParameter(dialect); - valueDialect = getInputParameter(dialect); - - // //print check - AnalysisLogger.getLogger().debug( - "In SubmitQuery->valueDialect: " + valueDialect); - - if ((valueSC.equals("true")) && (!(valueDialect.equals("NONE")))) { - String smartCorrectedQuery = ""; - - AnalysisLogger.getLogger().debug( - "In SubmitQuery->applying smart correction on the query: " - + query); - - if (valueDialect.equals("POSTGRES")) { - - // //print check - // AnalysisLogger.getLogger().debug( - // "In SubmitQuery->query: " + query); - // - // AnalysisLogger.getLogger().debug( - // "In SubmitQuery->dialect: " + - // DatabaseManagement.POSTGRESQLDialect); - - // call the SwisSQL library functionality - smartCorrectedQuery = mgt.smartCorrectionOnQuery(query, - DatabaseManagement.POSTGRESQLDialect); - } - - if (valueDialect.equals("MYSQL")) { - // call the SwisSQL library functionality - smartCorrectedQuery = mgt.smartCorrectionOnQuery(query, - DatabaseManagement.MYSQLDialect); - } - - AnalysisLogger.getLogger().debug( - "In SubmitQuery-> query converted: " - + smartCorrectedQuery); - query = smartCorrectedQuery; - - if (!(smartCorrectedQuery.equals(""))) { - PrimitiveType valQuery = new PrimitiveType( - String.class.getName(), smartCorrectedQuery, - PrimitiveTypes.STRING, "Converted Query", - "Query Converted"); - - mapResults.put("Query Converted", valQuery); - } - } - - // else if ((valueSC.equals("true")) && - // (valueDialect.equals("NONE"))) { - // - // throw new Exception("Warning: specify the language"); - // - // } - - AnalysisLogger.getLogger().debug( - "In SubmitQuery->Submitting the query: " + query); - - if (driverInfo.toLowerCase().contains("postgres")) { - - // for a postgres database the second parameter is the - // schema - // name - - // result = mgt.submitQuery(query, tableName, schemaName, - // sf, config.getPersistencePath()); - - result = mgt - .submitQuery(query, dbconnection, config.getPersistencePath()); - } - - if (driverInfo.toLowerCase().contains("mysql")) { - // for a mysql database the second parameter is the database - // name - - // result = mgt.submitQuery(query, tableName, databaseName, - // sf, config.getPersistencePath()); - - result = mgt - .submitQuery(query, dbconnection, config.getPersistencePath()); - } - - if (result == null) { - throw new Exception("Warning: the table has not rows"); - } - - AnalysisLogger.getLogger().debug( - "In SubmitQuery->Query's Result retrieved"); - - HashMap mapResult = new HashMap(); - mapResult = mgt.getMapQueryResult(); -// System.out.println("map size alg with header: " + mapResult.size()); - - String encoded = null; - encoded = new String(mapResult.get("HEADERS").getBytes(), "UTF-8"); - - // // check the encoded value - // AnalysisLogger.getLogger().debug( - // "In RandomSampleOnTable->string encoded: " + encoded); - - PrimitiveType val = new PrimitiveType(String.class.getName(), - encoded, PrimitiveTypes.STRING, "Row", "Row"); - - mapResults.put("HEADERS", val); - - // to add the rows (result of the query) - for (int i = 0; i < mapResult.size() - 1; i++) { - encoded = new String(mapResult.get(String.valueOf(i)) - .getBytes(), "UTF-8"); - - // // check the encoded value -// AnalysisLogger.getLogger().debug( -// "In RandomSampleOnTable->string encoded: " + encoded); - - PrimitiveType val1 = new PrimitiveType(String.class.getName(), - encoded, PrimitiveTypes.STRING, "Row", "Row"); - mapResults.put(String.valueOf(i), val1); - // //check value contained in map - // String value = (String) val1.getContent(); - // -// AnalysisLogger.getLogger().debug( -// "In RandomSampleOnTable->value: " + value); - } - - // to add the file - PrimitiveType fileResult = new - PrimitiveType(File.class.getName(), - mgt.getFile(), PrimitiveTypes.FILE, "File", - "File"); - mapResults.put("File", fileResult); - -// //to add the number of total rows for a result of a submit query operation - PrimitiveType totalRows = new PrimitiveType(String.class.getName(), - String.valueOf(mgt.getSubmitQueryTotalRows()), PrimitiveTypes.STRING, "Total Rows", - "Total Rows"); - mapResults.put("Total Rows", totalRows); - - } - return mapResults; - } - - // method that allows to analyze the query in order to filter it if it is - // not read-only compliant - private boolean analyzeQuery(String query) throws Exception { - boolean NotAllowed = false; - // check if the query is allowed - - // TODO: check also the oracle case - if (driverInfo.toLowerCase().contains("postgres")) { - PostgresLexicalAnalyzer obj = new PostgresLexicalAnalyzer(); - NotAllowed = obj.analyze(query); - } - if (driverInfo.toLowerCase().contains("mysql")) { - MySQLLexicalAnalyzer obj = new MySQLLexicalAnalyzer(); - NotAllowed = obj.analyze(query); - } - - AnalysisLogger.getLogger().debug( - "In SubmitQuery->Warning: query filtered: " + NotAllowed); - return NotAllowed; - } - - private void normalizeDBInfo(DBResource resource) throws Exception { - - - try{ - int ap = resource.getAccessPoints().size(); - - for (int i = 0; i < ap; i++) { - resource.normalize(i); - } - - }catch (Exception e) { - AnalysisLogger.getLogger().debug( - "In SubmitQuery->: Error in normalization process" - + e.getMessage()); - - throw e; - } - -// int ap = resource.getAccessPoints().size(); -// for (int i = 0; i < ap; i++) { -// try { -// resource.normalize(i); -// } catch (IOException e) { -// // e.printStackTrace(); -// AnalysisLogger.getLogger().debug( -// "In SubmitQuery->: Error in normalization process" -// + e.getMessage()); -// throw e; -// } -// } - } - -// private void formatWithQuotes(String Query) { -// if (driverInfo.toLowerCase().contains("postgres")) { -// if (Query.contains(tableName)) { -// query = Query.replaceAll(tableName, "\"" + tableName + "\""); -// } -// if (driverInfo.toLowerCase().contains("mysql")) { -// query = Query.replaceAll(tableName, "\"" + tableName + "\""); -// } -// } -// } -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SubmitQueryEnum.java b/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SubmitQueryEnum.java deleted file mode 100644 index 9a914f4..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/drmalgorithms/SubmitQueryEnum.java +++ /dev/null @@ -1,6 +0,0 @@ -package org.gcube.dataaccess.algorithms.drmalgorithms; - -public enum SubmitQueryEnum { - TRUE, - FALSE -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/examples/AbsoluteSpeciesBarChartsAlgorithm.java b/src/main/java/org/gcube/dataaccess/algorithms/examples/AbsoluteSpeciesBarChartsAlgorithm.java deleted file mode 100644 index f9e882b..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/examples/AbsoluteSpeciesBarChartsAlgorithm.java +++ /dev/null @@ -1,358 +0,0 @@ -package org.gcube.dataaccess.algorithms.examples; - -import java.awt.Image; -import java.io.BufferedWriter; -import java.io.File; -import java.io.FileWriter; -import java.io.IOException; -import java.sql.Connection; -import java.sql.DriverManager; -import java.sql.ResultSet; -import java.sql.SQLException; -import java.sql.Statement; -import java.util.HashMap; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; - -import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools; -import org.gcube.contentmanagement.graphtools.plotting.graphs.HistogramGraph; -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; -import org.jfree.chart.JFreeChart; -import org.jfree.data.category.DefaultCategoryDataset; - -public class AbsoluteSpeciesBarChartsAlgorithm extends - StandardLocalExternalAlgorithm { - - LinkedHashMap map = new LinkedHashMap(); - - static String databaseName = "DatabaseName"; - static String userParameterName = "DatabaseUserName"; - static String passwordParameterName = "DatabasePassword"; - static String urlParameterName = "DatabaseURL"; - - // static String databaseName = "Obis2Repository"; - // static String userParameterName = "postgres"; - // static String passwordParameterName = "0b1s@d4sc13nc3"; - // static String urlParameterName = - // "jdbc:postgresql://obis2.i-marine.research-infrastructures.eu:5432/obis"; - - protected String fileName; - BufferedWriter out; - private String firstSpeciesNumber = " SpeciesNumber :"; - private String yearStart = "Start year :"; - private String yearEnd = "End year :"; - private int speciesNumber; - String databaseJdbc; - String year_start; - String year_end; - String databaseUser; - String databasePwd; - private Connection connection = null; - private DefaultCategoryDataset defaultcategorydataset; - - @Override - public void init() throws Exception { - AnalysisLogger.getLogger().debug("Initialization"); - } - - @Override - public String getDescription() { - return ": A transducer algorithm that produces the list of top n most observed taxa, i.e. the species taxa having the largest number of occurrence records, in the OBIS database in a given time interval"; - } - - public void fulfilParameters() { - - AnalysisLogger.getLogger().debug("fulfilParameters method"); - - // String tmp = getInputParameter(firstSpeciesNumber); - - List list = getInputParameters(); - - System.out.println("size: " + list.size()); - - for (int i = 0; i < list.size(); i++) { - - System.out.println(list.get(i).getName()+" "+list.get(i).getDefaultValue()); - - if (list.get(i).getName().equals(firstSpeciesNumber)) { - // System.out.println(list.get(i).getName()); - String tmp = list.get(i).getDefaultValue(); - speciesNumber = Integer.parseInt(tmp); - - } - - if (list.get(i).getName().equals(yearStart)) { - - year_start = list.get(i).getDefaultValue(); - - } - - if (list.get(i).getName().equals(yearEnd)) { - - year_end = list.get(i).getDefaultValue(); - - } -// if (list.get(i).getName().equals(urlParameterName)) { -// -// databaseJdbc = list.get(i).getDefaultValue(); -// -// } -// if (list.get(i).getName().equals(userParameterName)) { -// -// databaseUser = list.get(i).getDefaultValue(); -// -// } -// if (list.get(i).getName().equals(passwordParameterName)) { -// -// databasePwd = list.get(i).getDefaultValue(); -// -// } - - databaseJdbc = getInputParameter("DatabaseURL"); - databaseUser= getInputParameter("DatabaseUserName"); - databasePwd= getInputParameter("DatabasePassword"); - - - } - - // System.out.println(tmp); - -// databaseJdbc = getInputParameter(urlParameterName); - // year_start = getInputParameter(yearStart); -// year_end = getInputParameter(yearEnd); -// databaseUser = getInputParameter(userParameterName); -// databasePwd = getInputParameter(passwordParameterName); - -// fileName = super.config.getPersistencePath() + "results.csv"; - - fileName = config.getConfigPath() + "results.csv"; - -// fileName = "./cfg/" + "results.csv"; - - - AnalysisLogger.getLogger().debug("Percorso file: " + fileName); - - AnalysisLogger.getLogger().debug("fulfilParameters method"); - } - - private ResultSet performeQuery() throws SQLException { - - connection = DriverManager.getConnection(databaseJdbc, databaseUser, - databasePwd); - - Statement stmt = connection.createStatement(); - String query = "SELECT tname, sum(count)AS count FROM public.count_species_per_year WHERE year::integer >=" - + year_start - + "AND year::integer <=" - + year_end - + "GROUP BY tname ORDER BY count desc;"; - return stmt.executeQuery(query); - } - - @Override - protected void process() throws Exception { - - - - System.out.println("In the process"); - - defaultcategorydataset = new DefaultCategoryDataset(); -// String driverName = "org.postgresql.Driver"; -// Class driverClass = Class.forName(driverName); -// Driver driver = (Driver) driverClass.newInstance(); - - System.out.println("pre fulfill"); - fulfilParameters(); - System.out.println("post fulfill"); - -// String tmp = getInputParameter(firstSpeciesNumber); -// System.out.println("process-> speciesnumber value: " + tmp); - - // String tmp="10"; -// speciesNumber = Integer.parseInt(tmp); - -// year_start = getInputParameter(yearStart); - // year_start="1800"; - -// year_end = getInputParameter(yearEnd); - // year_end="2020"; - - // fileName = super.config.getPersistencePath() + "results.csv"; - -// fileName = "results.csv"; - - out = new BufferedWriter(new FileWriter(fileName)); - - System.out.println("pre query"); - ResultSet rs = performeQuery(); - System.out.println("post query"); - - // connection = - // DriverManager.getConnection("jdbc:postgresql://obis2.i-marine.research-infrastructures.eu:5432/obis", - // "postgres", - // "0b1s@d4sc13nc3"); - // Statement stmt = connection.createStatement(); - // String query = - // "SELECT tname, sum(count)AS count FROM public.count_species_per_year WHERE year::integer >=" - // + year_start - // + "AND year::integer <=" - // + year_end - // + "GROUP BY tname ORDER BY count desc;"; - - // - // System.out.println("pre query"); - // ResultSet rs=stmt.executeQuery(query); - // - // System.out.println("post query"); - // - int i = 0; - String s = "Species"; - while (rs.next() && i < speciesNumber) { - - System.out.println(rs.toString()); - - String tname = rs.getString("tname"); - String count = rs.getString("count"); - - System.out.println("tname:" + tname); - - System.out.println("count:" + count); - - write(tname + "," + count); - int countOcc = Integer.parseInt(count); - - PrimitiveType val = new PrimitiveType(String.class.getName(), - count, PrimitiveTypes.STRING, tname, tname); - - - if (i < 100) - map.put(tname, val); - if (i < 16) - defaultcategorydataset.addValue(countOcc, s, tname); - i++; - - } - out.close(); - connection.close(); - - } - - @Override - protected void setInputParameters() { - - System.out.println("Sono in SetParameters"); - - addStringInput( - firstSpeciesNumber, - "Number of species to report (max 17 will be visualized on the chart)", - "10"); - - // System.out.println(firstSpeciesNumber); - - addStringInput(yearStart, "Starting year of the analysis", "1800"); - // System.out.println(yearStart); - - addStringInput(yearEnd, "Ending year of the analysis", "2020"); - // System.out.println(yearEnd); - - // addRemoteDatabaseInput("Obis2Repository", urlParameterName, - // userParameterName, passwordParameterName, "driver", "dialect"); - - // addRemoteDatabaseInput("Obis2Repository", urlParameterName, - // userParameterName, passwordParameterName, "org.postgresql.Driver", - // "org.hibernate.dialect.PostgreSQLDialect"); - - System.out.println("pre addRemoteDB"); -// addRemoteDatabaseInput( -// "Obis2Repository", -// "jdbc:postgresql://obis2.i-marine.research-infrastructures.eu:5432/obis", -// "postgres", "0b1s@d4sc13nc3", "org.postgresql.Driver", -// "org.hibernate.dialect.PostgreSQLDialect"); - -// addRemoteDatabaseInput("Obis2Repository", urlParameterName, -// userParameterName, passwordParameterName, "driver", "dialect"); - - - System.out.println("post addRemoteDB"); - - // super.config.setConfigPath("./cfg/"); - // config.setConfigPath(); - - // super.config.setParam("DatabaseUserName","gcube"); - // super.config.setParam("DatabasePassword","d4science2"); - // super.config.setParam("DatabaseURL","jdbc:postgresql://obis2.i-marine.research-infrastructures.eu:5432/obis"); - // super.config.setParam("DatabaseDriver","org.postgresql.Driver"); - - // System.out.println("URL: "+ super.config.getDatabaseURL()); - - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("Shutdown"); - } - - @Override - public StatisticalType getOutput() { - - AnalysisLogger.getLogger().debug("In getOutput"); - - PrimitiveType p = new PrimitiveType(Map.class.getName(), - PrimitiveType.stringMap2StatisticalMap(outputParameters), - PrimitiveTypes.MAP, "Discrepancy Analysis", ""); - - - AnalysisLogger - .getLogger() - .debug("MapsComparator: Producing Gaussian Distribution for the errors"); - // build image: - HashMap producedImages = new HashMap(); - - JFreeChart chart = HistogramGraph - .createStaticChart(defaultcategorydataset); - Image image = ImageTools.toImage(chart.createBufferedImage(680, 420)); - - producedImages.put("Species Observations", image); - - PrimitiveType images = new PrimitiveType(HashMap.class.getName(), - producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation", - "Graphical representation of the error spread"); - // PrimitiveType images = new PrimitiveType("Species Observations", - // producedImages, PrimitiveTypes.IMAGES, "ErrorRepresentation", - // "Graphical representation of the error spread"); - PrimitiveType f = new PrimitiveType(File.class.getName(), new File( - fileName), PrimitiveTypes.FILE, "OccFile", "OccFile"); - // end build image - AnalysisLogger.getLogger().debug( - "Bar Charts Species Occurrences Produced"); - // collect all the outputs - map.put("File", f); - map.put("Result", p); - map.put("Images", images); - - // generate a primitive type for the collection - PrimitiveType output = new PrimitiveType(HashMap.class.getName(), map, - PrimitiveTypes.MAP, "ResultsMap", "Results Map"); - -// PrimitiveType output=null; - - return output; - } - - public void write(String writeSt) { - try { - out.write(writeSt); - out.newLine(); - } catch (IOException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/examples/SimpleAlg.java b/src/main/java/org/gcube/dataaccess/algorithms/examples/SimpleAlg.java deleted file mode 100644 index c26a9c9..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/examples/SimpleAlg.java +++ /dev/null @@ -1,107 +0,0 @@ -package org.gcube.dataaccess.algorithms.examples; - -import java.util.LinkedHashMap; -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes; -import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm; - - -public class SimpleAlg extends -StandardLocalExternalAlgorithm{ - - - @Override - public void init() throws Exception { - AnalysisLogger.getLogger().debug("Initialization"); - } - - @Override - public String getDescription() { - return "An algorithm for testing"; - } - - @Override - protected void process() throws Exception { - - AnalysisLogger.getLogger().debug("in process"); - - } - - @Override - protected void setInputParameters() { - addStringInput("Name","name",""); - - addStringInput("Surname","surname","Liccardo"); - - } - - @Override - public void shutdown() { - AnalysisLogger.getLogger().debug("Shutdown"); - - // closes database's connection - - } - - @Override - public StatisticalType getOutput() { - - - AnalysisLogger.getLogger().debug("retrieving results"); - - String name= getInputParameter("Name"); - - String surname= getInputParameter("Surname"); - - - - - List list = getInputParameters(); - - System.out.println("size: " + list.size()); - - for (int i = 0; i < list.size(); i++) { - - System.out.println(list.get(i).getName()+" "+list.get(i).getDefaultValue()); - - } - - - - PrimitiveType n = new PrimitiveType( - String.class.getName(), - getInputParameter("Name") , - PrimitiveTypes.STRING, - "Name", - "name"); - - PrimitiveType s = new PrimitiveType( - String.class.getName(), - getInputParameter("Surname") , - PrimitiveTypes.STRING, - "Surname", - "surname"); - - - - - LinkedHashMap map = new LinkedHashMap(); - - map.put("Name", n); - - map.put("Surname", s); - - - AnalysisLogger.getLogger().debug("name: " + name); - - AnalysisLogger.getLogger().debug("surname: " + surname); - - return null; - } - - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/examples/TestSimpleAlg.java b/src/main/java/org/gcube/dataaccess/algorithms/examples/TestSimpleAlg.java deleted file mode 100644 index 91abb38..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/examples/TestSimpleAlg.java +++ /dev/null @@ -1,38 +0,0 @@ -package org.gcube.dataaccess.algorithms.examples; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class TestSimpleAlg { - - public static void main(String[] args) throws Exception { - System.out.println("TEST 1"); - List trans = null; - trans = TransducerersFactory.getTransducerers(testConfigLocal()); - trans.get(0).init(); - - - Regressor.process(trans.get(0)); - trans.get(0).getOutput(); - - trans = null; - } - - private static AlgorithmConfiguration testConfigLocal() { - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("TEST_ALG"); - -// AlgorithmConfiguration config=new AlgorithmConfiguration(); - - - return config; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/examples/TestTransducers.java b/src/main/java/org/gcube/dataaccess/algorithms/examples/TestTransducers.java deleted file mode 100644 index f187b2a..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/examples/TestTransducers.java +++ /dev/null @@ -1,67 +0,0 @@ -package org.gcube.dataaccess.algorithms.examples; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class TestTransducers { - -public static void main(String[] args) throws Exception { -System.out.println("TEST 1"); -List trans = null; -trans = TransducerersFactory.getTransducerers(testConfigLocal()); -trans.get(0).init(); - - -Regressor.process(trans.get(0)); -trans.get(0).getOutput(); - -trans = null; -} - -private static AlgorithmConfiguration testConfigLocal() { - - AlgorithmConfiguration config = Regressor.getConfig(); - -// AlgorithmConfiguration config=new AlgorithmConfiguration(); - - - config.setConfigPath("./cfg"); - - config.setParam("DatabaseName", "Obis2Repository"); - config.setParam("DatabaseUserName","postgres"); - config.setParam("DatabasePassword","0b1s@d4sc13nc3"); - config.setParam("databaseNamebaseDriver","org.postgresql.Driver"); - config.setParam("DatabaseURL", "jdbc:postgresql://obis2.i-marine.research-infrastructures.eu:5432/obis"); - - - System.out.println("config: " + config.getParam("DatabaseUserName")); - - - - -// System.out.println(config.getDatabaseURL()); - - config.setAgent("LISTNAMES_TABLES"); - - config.setParam("longitudeColumn", "decimallongitude"); - config.setParam("latitudeColumn", "decimallatitude"); - config.setParam("recordedByColumn", "recordedby"); - config.setParam("scientificNameColumn", "scientificname"); - config.setParam("eventDateColumn", "eventdate"); - config.setParam("lastModificationColumn", "modified"); - config.setParam("OccurrencePointsTableName", "whitesharkoccurrences2"); - config.setParam("finalTableName", "whitesharkoccurrencesnoduplicates"); - config.setParam("spatialTolerance", "0.5"); - config.setParam("confidence", "80"); - - - - return config; - -} - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/TestListDBInfo.java b/src/main/java/org/gcube/dataaccess/algorithms/test/TestListDBInfo.java deleted file mode 100644 index eb3f344..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/TestListDBInfo.java +++ /dev/null @@ -1,38 +0,0 @@ -package org.gcube.dataaccess.algorithms.test; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class TestListDBInfo { - - public static void main(String[] args) throws Exception { - System.out.println("TEST 1"); - List trans = null; - trans = TransducerersFactory.getTransducerers(testConfigLocal()); - trans.get(0).init(); - - - Regressor.process(trans.get(0)); - trans.get(0).getOutput(); - - trans = null; - } - - private static AlgorithmConfiguration testConfigLocal() { - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTDBINFO"); -// config.setParam("ResourceName", "TabularData Database"); - - - config.setGcubeScope("/gcube"); - return config; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/TestListNames.java b/src/main/java/org/gcube/dataaccess/algorithms/test/TestListNames.java deleted file mode 100644 index bab18a5..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/TestListNames.java +++ /dev/null @@ -1,36 +0,0 @@ -package org.gcube.dataaccess.algorithms.test; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class TestListNames { - - public static void main(String[] args) throws Exception { - System.out.println("TEST 1"); - List trans = null; - trans = TransducerersFactory.getTransducerers(testConfigLocal()); - trans.get(0).init(); - - - Regressor.process(trans.get(0)); - StatisticalType output = trans.get(0).getOutput(); - System.out.println(output); - trans = null; - } - - private static AlgorithmConfiguration testConfigLocal() { - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTDBNAMES"); - config.setGcubeScope("/gcube"); - return config; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/TestListSchemas.java b/src/main/java/org/gcube/dataaccess/algorithms/test/TestListSchemas.java deleted file mode 100644 index 069b05e..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/TestListSchemas.java +++ /dev/null @@ -1,71 +0,0 @@ -package org.gcube.dataaccess.algorithms.test; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class TestListSchemas { - - public static void main(String[] args) throws Exception { - System.out.println("TEST 1"); - List trans = null; - trans = TransducerersFactory.getTransducerers(testConfigLocal()); - trans.get(0).init(); - - Regressor.process(trans.get(0)); - trans.get(0).getOutput(); - - trans = null; - } - - private static AlgorithmConfiguration testConfigLocal() { - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTDBSCHEMA"); - - //A test with a database postgres - config.setParam("ResourceName", "GP DB"); - - - - - //connection's parameters for a database postgres - -//// config.setParam("databaseName", "aquamapsdb"); - config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("userName", "postgres"); -// config.setParam("password", "d4science2"); -// config.setParam("driverName", "org.postgresql.Driver"); -// config.setParam("URL", -// "jdbc:postgresql://geoserver-dev.d4science-ii.research-infrastructures.eu:5432/aquamapsdb"); - - - // config.setParam("DatabaseName", "mysql"); - - - - - // Another test with database postgres - -// config.setParam("ResourceName", "TabularData Database"); - -// config.setParam("DatabaseName", "tabulardata"); - -// config.setParam("userName", "tabulardataadmin"); -// config.setParam("password", "gcube2010"); -// config.setParam("driverName", "org.postgresql.Driver"); -// config.setParam("URL", -// "jdbc:postgresql://node7.d.d4science.research-infrastructures.eu:5432/tabulardata"); - - - config.setGcubeScope("/gcube"); -// config.setGcubeScope("/d4science.research-infrastructures.eu"); - return config; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/TestListTables.java b/src/main/java/org/gcube/dataaccess/algorithms/test/TestListTables.java deleted file mode 100644 index 195838a..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/TestListTables.java +++ /dev/null @@ -1,56 +0,0 @@ -package org.gcube.dataaccess.algorithms.test; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class TestListTables { - - - public static void main(String[] args) throws Exception { - System.out.println("TEST 1"); - List trans = null; - trans = TransducerersFactory.getTransducerers(testConfigLocal()); - trans.get(0).init(); - - - Regressor.process(trans.get(0)); - trans.get(0).getOutput(); - - trans = null; - } - - private static AlgorithmConfiguration testConfigLocal() { - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTTABLES"); - - //A test with a database postgres - config.setParam("ResourceName", "GP DB"); - - //connection's parameters for a database postgres - - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - -// config.setParam("userName", "postgres"); -// config.setParam("password", "d4science2"); -// config.setParam("driverName", "org.postgresql.Driver"); -// config.setParam("URL", -// "jdbc:postgresql://geoserver-dev.d4science-ii.research-infrastructures.eu:5432/aquamapsdb"); - - - //a test with a database mysql - - - - config.setGcubeScope("/gcube"); - return config; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/TestSubmitQuery.java b/src/main/java/org/gcube/dataaccess/algorithms/test/TestSubmitQuery.java deleted file mode 100644 index ce8ab1a..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/TestSubmitQuery.java +++ /dev/null @@ -1,92 +0,0 @@ -package org.gcube.dataaccess.algorithms.test; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class TestSubmitQuery { - - public static void main(String[] args) throws Exception { - System.out.println("TEST 1"); - - List trans = null; - trans = TransducerersFactory.getTransducerers(testConfigLocal()); - trans.get(0).init(); - - Regressor.process(trans.get(0)); - trans.get(0).getOutput(); - - trans = null; - } - - private static AlgorithmConfiguration testConfigLocal() { - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - -// // //A test with a database postgres -// config.setParam("ResourceName", "GP DB"); -// -// //connection's parameters for a database postgres -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName","area" ); -// config.setParam("Query","select * from area limit 3" ); - - - // // config.setParam("TableName", "Divisions"); - // config.setParam("TableName", "all_world"); - // config.setParam("Query", "select * from all_world"); - - // config.setParam("userName", "postgres"); - // config.setParam("password", "d4science2"); - // config.setParam("driverName", "org.postgresql.Driver"); - // config.setParam("URL", - // "jdbc:postgresql://geoserver-dev.d4science-ii.research-infrastructures.eu:5432/aquamapsdb"); - // config.setParam("dialect", - // "org.hibernate.dialect.PostgreSQLDialect"); - - - // a test with a database mysql -// config.setParam("ResourceName", "CatalogOfLife2010"); -// config.setParam("DatabaseName", "col2oct2010"); -// config.setParam("TableName", "common_names"); -//// config.setParam("Query", "select record_id, name_code from common_names limit 3"); -//// config.setParam("Query", "select record_id as a, name_code as b from common_names limit 3"); -// -//// config.setParam("Query", "select name_code, record_id from common_names limit 3"); -// -// config.setParam("Query", "select record_id, name_code from common_names limit 3"); - - config.setParam("ResourceName", "StatisticalManagerDataBase"); - config.setParam("DatabaseName", "testdb"); - config.setParam("Query", "select count (*)from (select csquarecode from hcaf_d)"); - - - -// // a test with postgis -// config.setParam("ResourceName", "Geoserver database "); -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); -// -// config.setParam("TableName", "Divisions"); -// config.setParam("Query", "select gid, area from \"Divisions\" limit 30"); -// -//// config.setParam("Query", "select the_geom from Divisions limit 30"); -// -//// config.setParam("Query", "select text(the_geom) from Divisions limit 30"); -// -// config.setParam("Query", "EXPLAIN ANALYZE select gid from \"Divisions\" limit 30"); - - config.setGcubeScope("/gcube/devsec"); - - // config.setGcubeScope("/gcube"); - return config; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/TestTableDetails.java b/src/main/java/org/gcube/dataaccess/algorithms/test/TestTableDetails.java deleted file mode 100644 index 6350762..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/TestTableDetails.java +++ /dev/null @@ -1,106 +0,0 @@ -package org.gcube.dataaccess.algorithms.test; - -import java.util.List; - -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class TestTableDetails { - - - public static void main(String[] args) throws Exception { - System.out.println("TEST 1"); - List trans = null; - trans = TransducerersFactory.getTransducerers(testConfigLocal()); - trans.get(0).init(); - - - Regressor.process(trans.get(0)); - trans.get(0).getOutput(); - - trans = null; - } - - - private static AlgorithmConfiguration testConfigLocal() { - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTTABLEDETAILS"); - -// //A test with a database postgres -// config.setParam("ResourceName", "GP DB"); -// -// //connection's parameters for a database postgres -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); -//// config.setParam("TableName", "Divisions"); -// -//// config.setParam("TableName", "all_world"); -// -// config.setParam("TableName", "biodiversity_lme"); - - -// -// config.setParam("userName", "postgres"); -// config.setParam("password", "d4science2"); -// config.setParam("driverName", "org.postgresql.Driver"); -// config.setParam("URL", -// "jdbc:postgresql://geoserver-dev.d4science-ii.research-infrastructures.eu:5432/aquamapsdb"); -// config.setParam("dialect", "org.hibernate.dialect.PostgreSQLDialect"); - - -// //A test with a database postgres -// config.setParam("ResourceName", "StatisticalManagerDataBase"); -// -// //connection's parameters for a database postgres -// config.setParam("DatabaseName", "testdb"); -// config.setParam("SchemaName", "public"); -//// config.setParam("TableName", "Divisions"); -// -//// config.setParam("TableName", "all_world"); -// -// config.setParam("TableName", "hcaf_d"); -//// -//// config.setParam("userName", "utente"); -//// config.setParam("password", "d4science"); -//// config.setParam("driverName", "org.postgresql.Driver"); -//// config.setParam("URL", -//// "jdbc:postgresql://geoserver-dev.d4science-ii.research-infrastructures.eu:5432/aquamapsdb"); -//// config.setParam("dialect", "org.hibernate.dialect.PostgreSQLDialect"); - - - - - -// //a test with a database mysql -// config.setParam("ResourceName", "CatalogOfLife2010"); -// config.setParam("DatabaseName", "col2oct2010"); -// config.setParam("TableName", "Common_names"); - - - //a test with postgis - config.setParam("ResourceName", "Geoserver database "); - -// config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("DatabaseName", "aquamapsdb"); - - config.setParam("SchemaName", "public"); - config.setParam("TableName", "divisions"); - - - - - - - config.setGcubeScope("/gcube/devsec"); - return config; - - } - - - - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionListDBInfo.java b/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionListDBInfo.java deleted file mode 100644 index d17652b..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionListDBInfo.java +++ /dev/null @@ -1,88 +0,0 @@ -package org.gcube.dataaccess.algorithms.test.regressiontest; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class RegressionListDBInfo { - -// static String[] algorithms = { "Postgres", "NullInputValue"}; - - // static AlgorithmConfiguration[] configs = { testPostgres1(), - // testPostgres2(), testPostgis(), Mysql(), NullInputValue(), - // Postgres3() }; - -// static AlgorithmConfiguration[] configs = { testPostgres1(), NullInputValue()}; - static String[] algorithms = { "Postgres"}; - static AlgorithmConfiguration[] configs = { testPostgres1()}; - - public static void main(String[] args) throws Exception { - - // System.out.println("TEST 1"); - - for (int i = 0; i < algorithms.length; i++) { - AnalysisLogger.getLogger().debug("Executing:" + algorithms[i]); - - // ComputationalAgent trans = new WPSProcess(wps, algorithms[i]); - - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - - // trans.setConfiguration(configs[i]); - // trans.init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - - // Print Result - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - - } - - private static AlgorithmConfiguration testPostgres1() { - - System.out.println("TEST 1: Postgres"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTDBINFO"); - - // A test with a database postgres -// config.setParam("ResourceName", "GP DB"); - -// config.setParam("ResourceName", "AquaMaps Service DataBase"); - -// config.setParam("ResourceName", "StatisticalManagerDataBase"); - config.setParam("ResourceName", "TabularData Database"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue() { - - System.out.println("TEST 2: NullInputValue"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTDBINFO"); - - // A test with a database postgres -// config.setParam("ResourceName", "GP DB"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionListNames.java b/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionListNames.java deleted file mode 100644 index 7ec2b8d..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionListNames.java +++ /dev/null @@ -1,75 +0,0 @@ -package org.gcube.dataaccess.algorithms.test.regressiontest; - -import java.util.LinkedHashMap; -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class RegressionListNames { - - static String[] algorithms = { "Postgres1", "Postgres2", "Postgis", - "Mysql", "NullInputValue" }; - - static AlgorithmConfiguration config; - - public static void main(String[] args) throws Exception { - - System.out.println("TEST 1"); - -// for (int i = 0; i < algorithms.length; i++) { - AnalysisLogger.getLogger().debug("Executing:" + "test"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTDBNAMES"); - config.setGcubeScope("/gcube"); - - - List trans = null; - trans = TransducerersFactory.getTransducerers(config); - trans.get(0).init(); - - // trans.setConfiguration(configs[i]); - // trans.init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - AnalysisLogger.getLogger().debug("ST:" + st); - - -// // Print Result -// PrimitiveType obj= (PrimitiveType)st; -// Object result=(Object) (obj.getContent()); -// LinkedHashMap map=new LinkedHashMap(); -// -// map= (LinkedHashMap) result; -// -// for(int j=0;j trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - - // trans.setConfiguration(configs[i]); - // trans.init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - - // Print Result - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - - } - - - private static AlgorithmConfiguration testPostgres1() { - - System.out.println("TEST 1: Postgres table without rows"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTDBSCHEMA"); - - // A test with a database postgres -// config.setParam("ResourceName", "GP DB"); -// config.setParam("DatabaseName", "aquamapsdb"); - - -// config.setParam("ResourceName", "StatisticalManagerDataBase"); -// config.setParam("DatabaseName", "testdb"); - -// config.setParam("ResourceName", "CatalogOfLife2010"); -// config.setParam("DatabaseName", "col2oct2010"); - -// config.setParam("ResourceName", "StatisticalManagerDataBase"); -// config.setParam("DatabaseName", "testdb"); - - config.setParam("ResourceName", "TimeSeriesDatabase"); - config.setParam("DatabaseName", "timeseries"); - -// config.setParam("ResourceName", "Geoserver database "); -// config.setParam("DatabaseName", "aquamapsdb"); - - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - - private static AlgorithmConfiguration NullInputValue1() { - - System.out.println("TEST 2: NullInputValue1"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTDBSCHEMA"); - - // A test with a database postgres -// config.setParam("ResourceName", "GP DB"); - config.setParam("DatabaseName", "aquamapsdb"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue2() { - - System.out.println("TEST 3: NullInputValue2"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTDBSCHEMA"); - - // A test with a database postgres - config.setParam("ResourceName", "GP DB"); -// config.setParam("DatabaseName", "aquamapsdb"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionListTables.java b/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionListTables.java deleted file mode 100644 index 82632bb..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionListTables.java +++ /dev/null @@ -1,165 +0,0 @@ -package org.gcube.dataaccess.algorithms.test.regressiontest; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class RegressionListTables { - -// static String[] algorithms = { "Postgres1", "Mysql", "NullInputValue1", "NullInputValue2", "NullInputValue3" }; - -// static AlgorithmConfiguration[] configs = { testPostgres1(),Mysql(), NullInputValue1(), NullInputValue2(), NullInputValue3()}; - - - static String[] algorithms = { "Postgres1"}; - static AlgorithmConfiguration[] configs = { Mysql()}; - - public static void main(String[] args) throws Exception { - - // System.out.println("TEST 1"); - - for (int i = 0; i < algorithms.length; i++) { - AnalysisLogger.getLogger().debug("Executing:" + algorithms[i]); - - // ComputationalAgent trans = new WPSProcess(wps, algorithms[i]); - - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - - // trans.setConfiguration(configs[i]); - // trans.init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - - // Print Result - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - - } - - private static AlgorithmConfiguration testPostgres1() { - - System.out.println("TEST 1: Postgres table without rows"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTTABLES"); - - // A test with a database postgres -// config.setParam("ResourceName", "GP DB"); -// -// config.setParam("DatabaseName", "aquamapsdb"); - - config.setParam("ResourceName", "StatisticalManagerDataBase"); - config.setParam("DatabaseName", "testdb"); - config.setParam("SchemaName", "public"); -// config.setParam("SchemaName", "aquamapsvre"); - - -// config.setParam("ResourceName", "CatalogOfLife2010"); -// config.setParam("DatabaseName", "col2oct2010"); -//// config.setParam("SchemaName", ""); - - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration Mysql() { - - System.out.println("TEST 2: Mysql"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTTABLES"); - - // a test with a database mysql - config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("DatabaseName", "col2oct2010"); - config.setParam("SchemaName", ""); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue1() { - - System.out.println("TEST 3: Postgis NullInputValue1"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTTABLES"); - - // a test with postgis -// config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - - private static AlgorithmConfiguration NullInputValue2() { - - System.out.println("TEST 4: Postgis NullInputValue2"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTTABLES"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); -// config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue3() { - - System.out.println("TEST 5: Postgis NullInputValue3"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTTABLES"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); - - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - - - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionRandomSampleOnTable.java b/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionRandomSampleOnTable.java deleted file mode 100644 index 519f610..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionRandomSampleOnTable.java +++ /dev/null @@ -1,273 +0,0 @@ -package org.gcube.dataaccess.algorithms.test.regressiontest; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class RegressionRandomSampleOnTable { - - // static AlgorithmConfiguration[] configs = { testPostgres1(), - // testPostgis(), testMysql1(),testMysql2(), NullInputValue1(), - // NullInputValue2(), NullInputValue3(), NullInputValue4()}; - - // static String[] algorithms = { "Postgres1", "Postgis", "Mysql1", - // "Mysql2", "NullInputValue1", "NullInputValue2", "NullInputValue3", - // "NullInputValue4"}; - - static AlgorithmConfiguration[] configs = { testMysql1() }; - static String[] algorithms = { "Postgres1" }; - - public static void main(String[] args) throws Exception { - - // System.out.println("TEST 1"); - - for (int i = 0; i < algorithms.length; i++) { - AnalysisLogger.getLogger().debug("Executing:" + algorithms[i]); - - // ComputationalAgent trans = new WPSProcess(wps, algorithms[i]); - - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - - // trans.setConfiguration(configs[i]); - // trans.init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - - // Print Result - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - - } - - // Posgresql database - - private static AlgorithmConfiguration testPostgres1() { - - System.out.println("TEST 1: Postgres table without rows"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("RANDOMSAMPLEONTABLE"); - - // A test with a database postgres - // config.setParam("ResourceName", "GP DB"); - // - // config.setParam("DatabaseName", "aquamapsdb"); - // config.setParam("SchemaName", "public"); - // config.setParam("TableName", "area"); // it has not rows - -// config.setParam("ResourceName", "StatisticalManagerDataBase"); -// config.setParam("DatabaseName", "testdb"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "hcaf_d"); - // // config.setParam("TableName", - // "hspec_id_3f4c79fa_442e_42ba_9344_1b3e64dc3326"); - - // config.setParam("TableName", - // "hspec_id_c8e87e16_a0b4_4f9b_b48e_f1cf60ab104c"); - // // config.setParam("TableName", - // "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - // // config.setParam("TableName", "bionymoutlevfaked2csvpreprcsv"); - // - // // config.setParam("TableName", - // "timeseries_id08b3abb9_c7b0_4b82_8117_64b69055416f"); - // // config.setParam("TableName", - // "occurrence_species_idaf35d737_fb3e_43a7_b13a_611dfa97b064"); - // config.setParam("TableName", - // "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); - - // config.setParam("ResourceName", "AquaMaps Service DataBase"); - // config.setParam("DatabaseName", "aquamapsorgupdated"); - // config.setParam("SchemaName", "public"); - // // - // // - // // - // // config.setParam("TableName", "hspec2012_07_11_12_33_05_526"); - // - // // config.setParam("TableName", "custom2013_12_04_15_27_16_493_cet"); - // - // config.setParam("TableName", "hspec_suitable_peng_test_tbsp_1"); - -// config.setParam("ResourceName", "AquaMaps Service DataBase"); -// config.setParam("DatabaseName", "aquamapsorgupdated"); -// config.setParam("SchemaName", "public"); -//// config.setParam("TableName", "hspec_suitable_peng_test_tbsp_1"); -// config.setParam("TableName", "hspen"); - -// config.setParam("ResourceName", "Geoserver database "); -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "SeaVoX_sea_areas_polygons_v14"); - - // Obis - config.setParam("ResourceName", "Obis2Repository"); - config.setParam("DatabaseName", "obis"); -// config.setParam("SchemaName", "calc"); -// config.setParam("TableName", "map1d"); - config.setParam("SchemaName", "newd20110525"); - config.setParam("TableName", "edc"); - - // config.setParam("Query", "select * from area limit 3"); - - // config.setParam("Query", - // "select text(the_geom) from \"Divisions\" limit 1"); - - // config.setParam("TableName", "all_world"); - // config.setParam("TableName", "biodiversity_lme"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration testPostgis() { - - System.out.println("TEST 2: Postgis"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("RANDOMSAMPLEONTABLE"); - - // A test with a database postgres - config.setParam("ResourceName", "GP DB"); - - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration testMysql1() { - - System.out.println("TEST 3: Mysql1"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("RANDOMSAMPLEONTABLE"); - - // A test with a database mysql - config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("DatabaseName", "col2oct2010"); - config.setParam("TableName", "common_names"); - // config.setParam("TableName", "Common_names"); // mysql is not case - // sensitive -// config.setParam("TableName", "databases"); -// config.setParam("TableName", "simple_search"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration testMysql2() { - - System.out.println("TEST 4: Mysql2"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("RANDOMSAMPLEONTABLE"); - - // A test with a database mysql - config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("DatabaseName", "col2oct2010"); - config.setParam("TableName", "example"); // the table does not exist - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue1() { - - System.out.println("TEST 5: Postgis NullInputValue1"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("RANDOMSAMPLEONTABLE"); - - // a test with postgis - // config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue2() { - System.out.println("TEST 6: Postgis NullInputValue2"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("RANDOMSAMPLEONTABLE"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - // config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue3() { - - System.out.println("TEST 7: Postgis NullInputValue3"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("RANDOMSAMPLEONTABLE"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - // config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue4() { - System.out.println("TEST 8: Postgis NullInputValue4"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("RANDOMSAMPLEONTABLE"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - // config.setParam("TableName", "Divisions"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionSampleOnTable.java b/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionSampleOnTable.java deleted file mode 100644 index d5f1848..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionSampleOnTable.java +++ /dev/null @@ -1,266 +0,0 @@ -package org.gcube.dataaccess.algorithms.test.regressiontest; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class RegressionSampleOnTable { - -// static AlgorithmConfiguration[] configs = { testPostgres1(), testPostgis(), testMysql1(),testMysql2(), NullInputValue1(), NullInputValue2(), NullInputValue3(), NullInputValue4()}; - -// static String[] algorithms = { "Postgres1", "Postgis", "Mysql1", "Mysql2", "NullInputValue1", "NullInputValue2", "NullInputValue3", "NullInputValue4"}; - - static AlgorithmConfiguration[] configs = { testMysql1()}; - - static String[] algorithms = { "Postgres1"}; - - public static void main(String[] args) throws Exception { - - // System.out.println("TEST 1"); - - for (int i = 0; i < algorithms.length; i++) { - AnalysisLogger.getLogger().debug("Executing:" + algorithms[i]); - - // ComputationalAgent trans = new WPSProcess(wps, algorithms[i]); - - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - - // trans.setConfiguration(configs[i]); - // trans.init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - - // Print Result - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - - } - - private static AlgorithmConfiguration testPostgres1() { - - System.out.println("TEST 1: Postgres table without rows"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SAMPLEONTABLE"); - - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); -// config.setParam("TableName", "biodiversity"); - - config.setParam("TableName", "SeaVoX_sea_areas_polygons_v14"); -// config.setParam("TableName", ""); - - // A test with a database postgres Geoserver -// config.setParam("ResourceName", "GP DB"); -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); -//// config.setParam("TableName", "area"); // it has not rows -// config.setParam("TableName", "Divisions"); - -// config.setParam("Query", "select * from area limit 3"); - -// config.setParam("Query", "select text(the_geom) from \"Divisions\" limit 1"); - - // config.setParam("TableName", "all_world"); - // config.setParam("TableName", "biodiversity_lme"); - - -// config.setParam("ResourceName", "DionysusDB"); -// config.setParam("DatabaseName", "World"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableNamefcatalog", "countrylanguage"); //mysql is not case sensitive - -// config.setParam("ResourceName", "AquaMaps Service DataBase"); -// config.setParam("DatabaseName", "aquamapsorgupdated"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "speciesoccursum"); -//// config.setParam("TableName", "hspec2012_07_11_12_33_05_526"); -// config.setParam("TableName", "hspen"); - - //Statistical -// config.setParam("ResourceName", "StatisticalManagerDataBase"); -// config.setParam("DatabaseName", "testdb"); -// config.setParam("SchemaName", "public"); -//// config.setParam("TableName", "hspec_id_3f4c79fa_442e_42ba_9344_1b3e64dc3326"); -//// config.setParam("TableName", "taxamatchinput"); -//// config.setParam("TableName", "Divisions"); -// config.setParam("TableName", "hcaf_d"); - - //Obis -// config.setParam("ResourceName", "Obis2Repository"); -// config.setParam("DatabaseName", "obis"); -// config.setParam("SchemaName", "calc"); -// config.setParam("TableName", "map1d"); - - //Obis -// config.setParam("ResourceName", "Obis2Repository"); -// config.setParam("DatabaseName", "obis"); -// config.setParam("SchemaName", "newd20110525"); -//// config.setParam("TableName", "map1d"); -// config.setParam("TableName", "edc"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration testPostgis() { - - System.out.println("TEST 2: Postgis"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SAMPLEONTABLE"); - - // A test with a database postgres -// config.setParam("ResourceName", "GP DB"); - -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "Divisions"); - - config.setParam("ResourceName", "StatisticalManagerDataBase"); - config.setParam("DatabaseName", "testdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "hcaf_d"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration testMysql1() { - - System.out.println("TEST 3: Mysql1"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SAMPLEONTABLE"); - - // A test with a database mysql - config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("DatabaseName", "col2oct2010"); -// config.setParam("TableName", "Common_names"); //mysql is not case sensitive -// config.setParam("TableName", "databases"); -// config.setParam("TableName", "families"); - config.setParam("TableName", "common_names"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - -private static AlgorithmConfiguration testMysql2() { - - System.out.println("TEST 4: Mysql2"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SAMPLEONTABLE"); - - // A test with a database mysql - config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("DatabaseName", "col2oct2010"); - config.setParam("TableName", "example"); //the table does not exist - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - private static AlgorithmConfiguration NullInputValue1() { - - System.out.println("TEST 5: Postgis NullInputValue1"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SAMPLEONTABLE"); - - // a test with postgis -// config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue2() { - System.out.println("TEST 6: Postgis NullInputValue2"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SAMPLEONTABLE"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); -// config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - private static AlgorithmConfiguration NullInputValue3() { - - System.out.println("TEST 7: Postgis NullInputValue3"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SAMPLEONTABLE"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - private static AlgorithmConfiguration NullInputValue4() { - System.out.println("TEST 8: Postgis NullInputValue4"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SAMPLEONTABLE"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); -// config.setParam("TableName", "Divisions"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionSmartSampleOnTable.java b/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionSmartSampleOnTable.java deleted file mode 100644 index 15d9dd4..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionSmartSampleOnTable.java +++ /dev/null @@ -1,305 +0,0 @@ -package org.gcube.dataaccess.algorithms.test.regressiontest; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class RegressionSmartSampleOnTable { - -//static AlgorithmConfiguration[] configs = { testPostgres1(), testPostgis(), testMysql1(),testMysql2(), NullInputValue1(), NullInputValue2(), NullInputValue3(), NullInputValue4()}; - -// static String[] algorithms = { "Postgres1", "Postgis", "Mysql1", "Mysql2", "NullInputValue1", "NullInputValue2", "NullInputValue3", "NullInputValue4"}; - - static AlgorithmConfiguration[] configs = { testMysql1()}; - static String[] algorithms = { "Postgres1"}; - - public static void main(String[] args) throws Exception { - - // System.out.println("TEST 1"); - - for (int i = 0; i < algorithms.length; i++) { - AnalysisLogger.getLogger().debug("Executing:" + algorithms[i]); - - // ComputationalAgent trans = new WPSProcess(wps, algorithms[i]); - - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - - // trans.setConfiguration(configs[i]); - // trans.init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - - // Print Result - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - - } - - private static AlgorithmConfiguration testPostgres1() { - - System.out.println("TEST 1: Postgres table without rows"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SMARTSAMPLEONTABLE"); - -// // A test with a database postgres -// config.setParam("ResourceName", "GP DB"); -// -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "area"); // it has not rows - -// config.setParam("Query", "select * from area limit 3"); - -// config.setParam("Query", "select text(the_geom) from \"Divisions\" limit 1"); - - // config.setParam("TableName", "all_world"); - // config.setParam("TableName", "biodiversity_lme"); - - -// config.setParam("ResourceName", "StatisticalManagerDataBase"); -// config.setParam("DatabaseName", "testdb"); -// config.setParam("SchemaName", "public"); -//// config.setParam("TableName", "hspec_id_3f4c79fa_442e_42ba_9344_1b3e64dc3326"); -// -//// config.setParam("TableName", "hcaf_d"); -// -// config.setParam("TableName", "hspec_id_c8e87e16_a0b4_4f9b_b48e_f1cf60ab104c"); - -// config.setParam("TableName", "hcaf_d"); - -// config.setParam("TableName", "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728"); -// config.setParam("TableName", "bionymoutlevfaked2csvpreprcsv"); - -// config.setParam("TableName", "timeseries_id08b3abb9_c7b0_4b82_8117_64b69055416f"); -// config.setParam("TableName", "occurrence_species_idaf35d737_fb3e_43a7_b13a_611dfa97b064"); - -// config.setParam("TableName", "processedoccurrences_id_e3b82f7f_6bd6_493a_bd2c_552cd486004a"); -// config.setParam("TableName", "hspen_mini_100"); -// config.setParam("TableName", "hspec_id_c8e87e16_a0b4_4f9b_b48e_f1cf60ab104c"); - -// config.setParam("TableName", "hspec_id_3f4c79fa_442e_42ba_9344_1b3e64dc3326"); - - -// config.setParam("ResourceName", "AquaMaps Service DataBase"); -// config.setParam("DatabaseName", "aquamapsorgupdated"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "hspec_suitable_peng_test_tbsp_1"); - -// config.setParam("ResourceName", "AquaMaps Service DataBase"); -// config.setParam("DatabaseName", "aquamapsorgupdated"); -// config.setParam("SchemaName", "public"); -//// config.setParam("TableName", "hspec2012_07_11_12_33_05_526"); -// config.setParam("TableName", "hspen"); - -// config.setParam("ResourceName", "Geoserver database "); -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "SeaVoX_sea_areas_polygons_v14"); - - -////// config.setParam("TableName", "hspec2012_07_11_12_33_05_483"); -// config.setParam("TableName", "hspec_suitable_peng_test_tbsp_1"); -//// config.setParam("TableName", "hspec_suitable_executor_1"); -// config.setParam("TableName", "custom2013_12_04_15_27_16_493_cet"); -// config.setParam("TableName", "hspec2012_07_11_12_33_05_483"); - - - -// config.setParam("ResourceName", "AquaMaps Service DataBase"); -// config.setParam("DatabaseName", "aquamapsorgupdated"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "hspec2012_07_11_12_33_05_526"); - -//// //statistical -// config.setParam("ResourceName", "StatisticalManagerDataBase"); -// config.setParam("DatabaseName", "testdb"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "hcaf_d"); -////// config.setParam("TableName", "hspec_id_3f4c79fa_442e_42ba_9344_1b3e64dc3326"); - - //Obis - config.setParam("ResourceName", "Obis2Repository"); - config.setParam("DatabaseName", "obis"); - config.setParam("SchemaName", "newd20110525"); -// config.setParam("TableName", "map1d"); - config.setParam("TableName", "_positions1"); -// config.setParam("TableName", "map1d"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - } - - private static AlgorithmConfiguration testPostgis() { - - System.out.println("TEST 2: Postgis"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SMARTSAMPLEONTABLE"); - - // A test with a database postgres - config.setParam("ResourceName", "GP DB"); - - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration testMysql1() { - - System.out.println("TEST 3: Mysql1"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SMARTSAMPLEONTABLE"); - - // A test with a database mysql - config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("DatabaseName", "col2oct2010"); - config.setParam("TableName", "common_names"); //mysql is not case sensitive -// config.setParam("TableName", "databases"); -// config.setParam("TableName", "simple_search"); -// config.setParam("TableName", "scientific_names"); - - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - -private static AlgorithmConfiguration testMysql2() { - - System.out.println("TEST 4: Mysql2"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SMARTSAMPLEONTABLE"); - - // A test with a database mysql - config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("DatabaseName", "col2oct2010"); - config.setParam("TableName", "example"); //the table does not exist - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } -//private static AlgorithmConfiguration testMysql3() { //dati sbagliati -// -// System.out.println("TEST 4.1: Mysql3"); -// -// AlgorithmConfiguration config = Regressor.getConfig(); -// -// config.setAgent("SMARTSAMPLEONTABLE"); -// -// // A test with a database mysql -// config.setParam("ResourceName", "CatalogOfLife2010"); -// config.setParam("DatabaseName", "aquamaps"); -// config.setParam("TableName", "hcaf_d"); -// -// config.setGcubeScope("/gcube/devsec"); -// -// return config; -// -//} - - private static AlgorithmConfiguration NullInputValue1() { - - System.out.println("TEST 5: Postgis NullInputValue1"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SMARTSAMPLEONTABLE"); - - // a test with postgis -// config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue2() { - System.out.println("TEST 6: Postgis NullInputValue2"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SMARTSAMPLEONTABLE"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); -// config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - private static AlgorithmConfiguration NullInputValue3() { - - System.out.println("TEST 7: Postgis NullInputValue3"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SMARTSAMPLEONTABLE"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - private static AlgorithmConfiguration NullInputValue4() { - System.out.println("TEST 8: Postgis NullInputValue4"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("SMARTSAMPLEONTABLE"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); -// config.setParam("TableName", "Divisions"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionSubmitQuery.java b/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionSubmitQuery.java deleted file mode 100644 index 14d3a0b..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionSubmitQuery.java +++ /dev/null @@ -1,373 +0,0 @@ -package org.gcube.dataaccess.algorithms.test.regressiontest; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; - -public class RegressionSubmitQuery { - -// static String[] algorithms = { "Postgres1", "Mysql", "Postgres3", "Postgres4", "NullInputValue1", "NullInputValue2", "NullInputValue3", "NullInputValue4", "NullInputValue5", "Postgis"}; - -// static AlgorithmConfiguration[] configs = { testPostgres1(), -// testPostgres2(), testPostgis(), Mysql(), NullInputValue(), -// Postgres3() }; - -// static AlgorithmConfiguration[] configs = { testPostgres1(), Mysql(), Postgres3(), Postgres4(), NullInputValue1(), NullInputValue2(), NullInputValue3(), NullInputValue4(), NullInputValue5(), Postgis()}; - - static String[] algorithms = {"Postgres1"}; - static AlgorithmConfiguration[] configs = { testPostgres1() }; - - public static void main(String[] args) throws Exception { - - // System.out.println("TEST 1"); - - for (int i = 0; i < algorithms.length; i++) { - AnalysisLogger.getLogger().debug("Executing:" + algorithms[i]); - - // ComputationalAgent trans = new WPSProcess(wps, algorithms[i]); - - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - - // trans.setConfiguration(configs[i]); - // trans.init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - - // Print Result - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - - } - - private static AlgorithmConfiguration testPostgres1() { - - System.out.println("TEST 1: Postgres table without rows"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - -// // A test with a database postgres -// config.setParam("ResourceName", "StatisticalManagerDataBase"); -// config.setParam("DatabaseName", "testdb"); -////// config.setParam("", "TRUE"); -// config.setParam("Read-Only Query", "true"); -// config.setParam("Apply Smart Correction", "FALSE"); -// config.setParam("Language", "NONE"); -//// config.setParam("Query", "DELETE from test_gsay_03217cfda4244870b4d11f9e0eca58fe"); -// config.setParam("Query", "select * from hcaf_d limit 20"); - -// config.setParam("Apply Smart Correction", "TRUE"); -// config.setParam("Language", "POSTGRES"); - - - -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "hcaf_d"); - - -// -// -// config.setParam("Query", "select * from hcaf_d limit 1"); -// config.setParam("Query", "select * from hspen limit 6"); - -// config.setParam("Query", "select * from bionymfaked18csvpreprcsv limit 2"); - -// config.setParam("Query", "select count (*)from (select csquarecode from hcaf_d)"); - -// config.setParam("Query", "select csquarecode,months,sum(effort) as effort, sum(total_yft_catch) as total_yft_catch from (select csquarecode,to_char(time,'MM') months,sum(effort) as effort,sum(total_yft_catch) as total_yft_catch from timeseries_idacdbb646_7500_4920_8e0d_aa38cc99a4a6 group by csquarecode,time order by time ASC) as a group by csquarecode,months order by csquarecode"); - -// config.setParam("Query", "select csquarecode, total_yft_catch from timeseries_idacdbb646_7500_4920_8e0d_aa38cc99a4a6 limit 3"); - -// config.setParam("ResourceName", "DionysusDB"); -// config.setParam("DatabaseName", "World"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "countrylanguage"); //mysql is not case sensitive -//// config.setParam("Query", "select * from countrylanguage limit 10"); -// config.setParam("Query", "SELECT * FROM information_schema.COLUMNS WHERE table_name ='countrylanguage' and table_schema='public'"); - -// config.setParam("ResourceName", "GP DB"); -// -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("", "TRUE"); -// config.setParam("SchemaName", "public"); -// config.setParam("TableName", "Divisions"); -// config.setParam("Query","select gid, area, perimeter, nafo_, nafo_id, zone from \"Divisions\" limit 100"); - -// config.setParam("TableName", "area"); // it has not rows - -// config.setParam("Query", "select * from area limit 3"); -// config.setParam("Query", "select gid, area, perimeter, CAST(the_geom as text) from \"Divisions\" limit 10"); - -// config.setParam("Query", "select text(the_geom) from \"Divisions\" limit 1"); - -// config.setParam("Query", "select perimeter,zone from \"Divisions\" where gid='7'"); - -// config.setParam("Query", "select area, CAST(perimeter as text) from \"Divisions\" order by random() limit 2"); - - // config.setParam("TableName", "all_world"); - // config.setParam("TableName", "biodiversity_lme"); - -// //Obis -// config.setParam("ResourceName", "Obis2Repository"); -// config.setParam("DatabaseName", "obis"); -// config.setParam("Read-Only Query", "trie"); -// config.setParam("Apply Smart Correction", "FALSE"); -// config.setParam("Language", "NONE"); -//// config.setParam("Query", "select id from fmap.randomdrs limit 1"); -//// config.setParam("Query", "select lifestage from randomdrs"); -// config.setParam("Query", "select * from newd20110525."+"\""+"edc"+ "\""+" where id='76864082'"); - - -// config.setParam("ResourceName", "AquaMaps Service DataBase"); -// config.setParam("DatabaseName", "aquamapsorgupdated"); -// config.setParam("Read-Only Query", "TRUE"); -// config.setParam("Apply Smart Correction", "FALSE"); -// config.setParam("Language", "NONE"); -//// config.setParam("Query", "select id from fmap.randomdrs limit 1"); -//// config.setParam("Query", "select * from (select * from maxminlat_hspen2012_02_28_17_45_49_572 as a join maxminlat_hspen2011_09_23_15_31_47_530 as b on a.maxclat=b.maxclat limit 2"); -// -//// config.setParam("Query", "select * from maxminlat_hspen2012_02_28_17_45_49_572 as a join maxminlat_hspen2011_09_23_15_31_47_530 as b on a.maxclat=b.maxclat limit 2"); -// -//// config.setParam("Query", "select * from hcaf_d_2018_linear_01341919234605 as a join hcaf_d_2024_linear_11341919235343 as b on a.csquarecode = b.csquarecode limit 1"); -// -// config.setParam("Query", "select * from hcaf_d_2018_linear_01341919234605 as a, hcaf_d_2024_linear_11341919235343 as b where a.csquarecode = b.csquarecode limit 1"); -// - - - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("Read-Only Query", "true"); - config.setParam("Apply Smart Correction", "FALSE"); - config.setParam("Language", "NONE"); - config.setParam("Query", "select st_astext(the_geom) from" +"\""+"SeaVoX_sea_areas_polygons_v14"+"\""+"limit 1"); -// config.setParam("Query", "select * from public.depthmean limit 10"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration Mysql() { - - System.out.println("TEST 2: Mysql"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - -// // a test with postgis -// config.setParam("ResourceName", "Geoserver database "); -// config.setParam("SchemaName", "public"); -// config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("TableName", "Divisions"); - - - - //a test with a database mysql - config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("DatabaseName", "col2oct2010"); - config.setParam("TableName", "Common_names"); //mysql is not case sensitive -// config.setParam("Query", "select * from common_names limit 10"); - config.setParam("Read-Only Query", "TRUE"); - config.setParam("Apply Smart Correction", "FALSE"); - config.setParam("Language", "NONE"); - -// config.setParam("Query", "select a.name_code as uno, b.name_code as due from common_names as a join distribution as b on a.name_code=b.name_code limit 2"); - config.setParam("Query", "select * from common_names as a join distribution as b on a.name_code=b.name_code"); - // config.setParam("TableName", "specialists"); - -// config.setParam("Query", "select * from specialists limit 3"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration Postgres3() { - - System.out.println("TEST 3: Postgis"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); //postgres is case sensitive - config.setParam("Query", "select the_geom from Divisions limit 3"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration Postgres4() { - - System.out.println("TEST 4: Postgis filter query"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); //postgres is case sensitive -// config.setParam("Query", "select the_geom from Divisions limit 30"); - config.setParam("Query", "EXPLAIN ANALYZE select gid from Divisions limit 3"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue1() { - - System.out.println("TEST 5: Postgis NullInputValue1"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - - // a test with postgis -// config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - config.setParam("Query", "EXPLAIN ANALYZE select gid from Divisions limit 3"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue2() { - - System.out.println("TEST 5: Postgis NullInputValue2"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); -// config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - config.setParam("Query", "EXPLAIN ANALYZE select gid from Divisions limit 3"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue3() { - - System.out.println("TEST 5: Postgis NullInputValue3"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); -// config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - config.setParam("Query", "EXPLAIN ANALYZE select gid from Divisions limit 3"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue4() { - - System.out.println("TEST 5: Postgis NullInputValue4"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); -// config.setParam("TableName", "Divisions"); - config.setParam("Query", "EXPLAIN ANALYZE select gid from Divisions limit 3"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue5() { - - System.out.println("TEST 6: Postgis NullInputValue5"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); -// config.setParam("Query", "EXPLAIN ANALYZE select gid from Divisions limit 3"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration Postgis() { - - System.out.println("TEST 7: Postgis"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTSUBMITQUERY"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); //postgres is case sensitive - config.setParam("Query", "select * from \"Divisions\" limit 1"); - - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - - -} diff --git a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionTableDetails.java b/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionTableDetails.java deleted file mode 100644 index 66d7901..0000000 --- a/src/main/java/org/gcube/dataaccess/algorithms/test/regressiontest/RegressionTableDetails.java +++ /dev/null @@ -1,227 +0,0 @@ -package org.gcube.dataaccess.algorithms.test.regressiontest; - -import java.util.List; - -import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger; -import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration; -import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType; -import org.gcube.dataanalysis.ecoengine.test.regression.Regressor; -import org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent; -import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory; - -public class RegressionTableDetails { - - // static String[] algorithms = { "Postgres1", "Postgres2", "Postgis", - // "Mysql", "NullInputValue", "Postgres3" }; - - // static AlgorithmConfiguration[] configs = { testPostgres1(), - // testPostgres2(), testPostgis(), Mysql(), NullInputValue(), Postgres3()}; - - static String[] algorithms = { "Postgres1" }; - static AlgorithmConfiguration[] configs = { testPostgis() }; - - public static void main(String[] args) throws Exception { - - // System.out.println("TEST 1"); - - for (int i = 0; i < algorithms.length; i++) { - AnalysisLogger.getLogger().debug("Executing:" + algorithms[i]); - - // ComputationalAgent trans = new WPSProcess(wps, algorithms[i]); - - List trans = null; - trans = TransducerersFactory.getTransducerers(configs[i]); - trans.get(0).init(); - - // trans.setConfiguration(configs[i]); - // trans.init(); - Regressor.process(trans.get(0)); - StatisticalType st = trans.get(0).getOutput(); - - // Print Result - AnalysisLogger.getLogger().debug("ST:" + st); - trans = null; - } - - } - - private static AlgorithmConfiguration testPostgres1() { - - System.out.println("TEST 1: Postgres"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("GETTABLEDETAILS"); - - // A test with a database postgres - // config.setParam("ResourceName", "GP DB"); - // - // config.setParam("DatabaseName", "aquamapsdb"); - // config.setParam("SchemaName", "public"); - // config.setParam("TableName", "Divisions"); - - // config.setParam("TableName", "all_world"); - // config.setParam("TableName", "biodiversity_lme"); - - // StatisticalManager - // config.setParam("ResourceName", "StatisticalManagerDataBase"); - // config.setParam("DatabaseName", "testdb"); - // // config.setParam("SchemaName", "publicd"); - // - // config.setParam("SchemaName", "public"); - // - // config.setParam("TableName", "hcaf_d"); - - // config.setParam("TableName", - // "hspec_id_c8e87e16_a0b4_4f9b_b48e_f1cf60ab104c"); - - // // config.setParam("TableName", - // "timeseries_id08b3abb9_c7b0_4b82_8117_64b69055416f"); - // // config.setParam("TableName", - // "occurrence_species_idaf35d737_fb3e_43a7_b13a_611dfa97b064"); - // // config.setParam("TableName", - // "occcluster_id_15271993_5129_4eda_92a2_fe8d22737007"); - // config.setParam("TableName", - // "hspec_id_3f4c79fa_442e_42ba_9344_1b3e64dc3326"); - - //AquaMaps - config.setParam("ResourceName", "AquaMaps Service DataBase"); - config.setParam("DatabaseName", "aquamapsorgupdated"); - config.setParam("SchemaName", "public"); -// config.setParam("TableName", "geometry_columns"); - config.setParam("TableName", "source_generation_requests"); - // //// config.setParam("TableName", "hspec2012_07_11_12_33_05_483"); - // config.setParam("TableName", "hspec_suitable_peng_test_tbsp_1"); - - // Obis -// config.setParam("ResourceName", "Obis2Repository"); -// config.setParam("DatabaseName", "obis"); -// config.setParam("SchemaName", "calc"); -// config.setParam("TableName", "map1d"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration testPostgres2() { - - System.out.println("TEST 2: Postgres"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("TableDetails"); - - // A test with a database postgres - config.setParam("ResourceName", "GP DB"); - - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "area"); // it has not rows - - // config.setParam("TableName", "all_world"); - // config.setParam("TableName", "biodiversity_lme"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration testPostgis() { - - System.out.println("TEST 3: Postgis"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("GETTABLEDETAILS"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - // config.setParam("TableName", "Divisions"); -// config.setParam("TableName", "ContinentalMargins"); - -// config.setParam("TableName", "SeaVoX_sea_areas_polygons_v14"); - config.setParam("TableName", "laldrovandiaoleosa20130718230308233cest "); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration Mysql() { - - System.out.println("TEST 4: Mysql"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("GETTABLEDETAILS"); - - // // a test with postgis - // config.setParam("ResourceName", "Geoserver database "); - // config.setParam("SchemaName", "public"); - // config.setParam("DatabaseName", "aquamapsdb"); - // config.setParam("TableName", "Divisions"); - - // a test with a database mysql -// config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("ResourceName", "CatalogOfLife2010"); - config.setParam("DatabaseName", "col2oct2010"); - // config.setParam("TableName", "Common_names"); //mysql is not case - // sensitive - - config.setParam("TableName", "databases"); - - // config.setParam("Query", "select * from common_names limit 3"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration NullInputValue() { - - System.out.println("TEST 5: Postgis NullInputValue"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTTABLEDETAILS"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - // config.setParam("SchemaName", "public"); - config.setParam("TableName", "Divisions"); - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - - private static AlgorithmConfiguration Postgres3() { - - System.out.println("TEST 6: Postgres"); - - AlgorithmConfiguration config = Regressor.getConfig(); - - config.setAgent("LISTTABLEDETAILS"); - - // a test with postgis - config.setParam("ResourceName", "Geoserver database "); - config.setParam("DatabaseName", "aquamapsdb"); - config.setParam("SchemaName", "public"); - config.setParam("TableName", "divisions"); // postgres is case sensitive - - config.setGcubeScope("/gcube/devsec"); - - return config; - - } - -}