/2012-12-13-BEW-r-client-testing

The Sci Meta and the two data objects create:

http://mn-stage-ucsb-1.test.dataone.org/knb/d1/mn/object/bew_r_test.20121214_16281355520484.0
http://mn-stage-ucsb-1.test.dataone.org/knb/d1/mn/object/bew_r_test.20121214_16281355520484.1
http://mn-stage-ucsb-1.test.dataone.org/knb/d1/mn/object/bew_r_test.20121214_16281355520484.2

But the Package doesn't:
http://mn-stage-ucsb-1.test.dataone.org/knb/d1/mn/object/bew_r_test.20121214_16281355520484
------------------

R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Loading required package: utils
Loading required package: rJava
[R.app GUI 1.53 (6335) i386-apple-darwin9.8.0]

[History restored from /Users/wb5/.Rapp.history]

[Workspace restored from /Users/wb5/Progs/DataONE/r-demo/.RData]

> setwd("/Users/wb5/Progs/DataONE/r-demo")
> source("BEW_demo1.R", echo=TRUE, verbose=FALSE, keep.source=TRUE)

> ################## R Script for running the demonstration
> #### Remember to get an updated client certificate before starting
> # Set up for submit .... [TRUNCATED]

> # Discard all current data to make sure we have a clean slate
> rm(list=ls())

> # Set up the output
> cur_time <- format(Sys.time(), "%Y%m%d_%H%M%s")

> con <- file(paste("BEW_demo1_",cur_time,".log", sep="") )

> sink(con, append=TRUE, split=TRUE)

> #sink(con, append=TRUE, type="message")
>
> # Change the default timeout for the Reserve operation to 60 seconds to deal with the reserve timeout i .... [TRUNCATED]

> d1.config$setProperty("D1Client.CNode.reserveIdentifier.timeout", .jnew("java/lang/Integer","60000"))

> # mn.nodeid <- "urn:node:mnStageORC1"
> mn.nodeid <- "urn:node:mnStageUCSB1"

> # mn.nodeid <- "urn:node:mnStageUNM1"
> cn.env <- "STAGING"

> d1.client <- D1Client(cn.env, mn.nodeid)

> formatid.csv <- "text/csv"

> formatid.eml <- "eml://ecoinformatics.org/eml-2.1.0"

> require(emdbook)
Loading required package: emdbook
Loading required package: MASS
Loading required package: lattice

> print(paste("************* Using CN=",cn.env," and MN=",mn.nodeid,sep="") )
[1] "************* Using CN=STAGING and MN=urn:node:mnStageUCSB1"

> #Create some identifiers
> id.obj_pkg <- paste("bew_r_test", cur_time, sep=".")

> id.obj_scimeta <- paste("bew_r_test", cur_time, "0", sep=".")

> id.obj_pred <- paste("bew_r_test", cur_time, "1", sep=".")

> id.obj_sub1 <- paste("bew_r_test", cur_time, "2", sep=".")

> print(paste("************* Package ID   = ",id.obj_pkg,sep="") )
[1] "************* Package ID   = bew_r_test.20121214_16281355520484"

> print(paste("************* Sci Meta ID = ",id.obj_scimeta,sep="") )
[1] "************* Sci Meta ID = bew_r_test.20121214_16281355520484.0"

> print(paste("************* Data Obj1 ID = ",id.obj_pred,sep="") )
[1] "************* Data Obj1 ID = bew_r_test.20121214_16281355520484.1"

> print(paste("************* Data Obj2 ID = ",id.obj_sub1,sep="") )
[1] "************* Data Obj2 ID = bew_r_test.20121214_16281355520484.2"

> # Start by creating the underlying data package
> demo1.package <- new("DataPackage",packageId=id.obj_pkg)
[1] "@@ DataPackage-class.R initialize"
[1] "@@ DataPackage-class.R - (missing jDataPackage)..."
[1] "@@ DataPackage-class.R - (have packageId)..."

> #Load up a Science Metadata object and create a DataONE object to hold it, and add it to the package
> md_filename <- "/Users/wb5/Progs/DataONE/r-de ..." ... [TRUNCATED]

> finfo <- file.info(md_filename)

> md_text <- readChar(md_filename,finfo$size)

> demo1.scimeta <- new("D1Object", id.obj_scimeta, md_text,formatid.eml, mn.nodeid)
[1] "@@ D1Object-class:R initialize as character"

> setPublicAccess(demo1.scimeta)
[1] "setPublicAccess: got policy editor"

> addData(demo1.package, demo1.scimeta)

> # Get the data object from the emdbook collection and then create a DataONE object to hold it and add
> # it to the package. It's necessary to conv .... [TRUNCATED]

> SeedPred.text <- convert.csv(d1.client,SeedPred)
checkServerTrusted - RSA
INFO [main] (ObjectFormatCache.java:196) - refreshing objectFormatCache from cn: null
INFO [main] (CertificateManager.java:645) - Entering getSSLSocketFactory
INFO [main] (CertificateManager.java:854) - Using client certificate location: /tmp/x509up_u852569749
INFO [main] (CertificateManager.java:720) - creating custom TrustManager
INFO [main] (CertificateManager.java:279) - loading into client truststore:
INFO [main] (CertificateManager.java:286) - 0 alias CN=DataONE Root CA,DC=dataone,DC=org
INFO [main] (CertificateManager.java:286) - 1 alias CN=DataONE Production CA,DC=dataone,DC=org
INFO [main] (CertificateManager.java:286) - 2 alias CN=CILogon Basic CA 1,O=CILogon,C=US,DC=cilogon,DC=org
INFO [main] (CertificateManager.java:286) - 3 alias CN=CILogon OpenID CA 1,O=CILogon,C=US,DC=cilogon,DC=org
INFO [main] (CertificateManager.java:286) - 4 alias CN=CILogon Silver CA 1,O=CILogon,C=US,DC=cilogon,DC=org
INFO [main] (CertificateManager.java:286) - 5 alias CN=RapidSSL CA,O=GeoTrust\, Inc.,C=US
INFO [main] (CertificateManager.java:673) - using allow-all hostname verifier
INFO [main] (RestClient.java:270) - rest call info: GET https://cn-stage.test.dataone.org/cn/v1/formats
INFO [main] (ExceptionHandler.java:94) - response httpCode: 200
INFO [main] (ObjectFormatCache.java:209) - successful cache refresh from cn.listFormats()

> demo1.SeedPred <- new("D1Object", id.obj_pred, SeedPred.text, formatid.csv, mn.nodeid)
[1] "@@ D1Object-class:R initialize as character"
INFO [main] (CertificateManager.java:854) - Using client certificate location: /tmp/x509up_u852569749

> setPublicAccess(demo1.SeedPred)
[1] "setPublicAccess: got policy editor"

> addData(demo1.package,demo1.SeedPred)

> #Create a subset of the SeedPred, just to have a second data object in this collection
> SeedPred.sub1 <- SeedPred[SeedPred$species == "uva" ,]

> SeedPred.sub1.text <- convert.csv(d1.client,SeedPred.sub1)

> demo1.sub1 <- new("D1Object", id.obj_sub1, SeedPred.sub1.text, formatid.csv, mn.nodeid)
[1] "@@ D1Object-class:R initialize as character"

> setPublicAccess(demo1.sub1)
[1] "setPublicAccess: got policy editor"

> addData(demo1.package,demo1.sub1)

> # Now add the relationship that says that the metadata object describes the data object
> insertRelationship(demo1.package, id.obj_scimeta, c(id.obj .... [TRUNCATED]

> # Now put the Package into the DataONE member node
> # create(d1.client, demo1.package)
>
> # Restore output to defaults
> sink()

> #sink(type="message")
>
Warning messages:
1: In write.csv(df, file = con, row.names = FALSE, col.names = TRUE, :
attempt to set 'col.names' ignored
2: In write.csv(df, file = con, row.names = FALSE, col.names = TRUE, :
attempt to set 'col.names' ignored
INFO [main] (CertificateManager.java:854) - Using client certificate location: /tmp/x509up_u852569749
> create(d1.client, demo1.package)
[1] "====> create(D1Client,DataPackage"
[1] "    * building the resource map for the 3 members..."
[1] "@@ D1Object-class:R initialize as character"
[1] "setPublicAccess: got policy editor"
[1] "    * next member to create: bew_r_test.20121214_16281355520484.2"
[1] "@@ D1Object-class:R initialize as something else"
[1] "@@ D1Object-class:R initialize with jobjRef"
[1] "--> create(D1Client, D1Object)"
[1] "    * The object is not null."
[1] "    * The sysmeta is not null."
INFO [main] (CertificateManager.java:854) - Using client certificate location: /tmp/x509up_u852569749
[1] "@@ D1Client-methods 41:"
[1] "    * Created."
[1] "      - created pid: bew_r_test.20121214_16281355520484.2"
[1] "<-- create(D1Client, D1Object)"
[1] "    * next member to create: bew_r_test.20121214_16281355520484.1"
[1] "@@ D1Object-class:R initialize as something else"
[1] "@@ D1Object-class:R initialize with jobjRef"
[1] "--> create(D1Client, D1Object)"
[1] "    * The object is not null."
[1] "    * The sysmeta is not null."
checkServerTrusted - RSA
checkServerTrusted - RSA
[1] "@@ D1Client-methods 41:"
[1] "    * Created."
[1] "      - created pid: bew_r_test.20121214_16281355520484.1"
[1] "<-- create(D1Client, D1Object)"
[1] "    * next member to create: bew_r_test.20121214_16281355520484.0"
[1] "@@ D1Object-class:R initialize as something else"
[1] "@@ D1Object-class:R initialize with jobjRef"
[1] "--> create(D1Client, D1Object)"
[1] "    * The object is not null."
[1] "    * The sysmeta is not null."
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
org.dataone.service.exceptions.ServiceFailure: class java.net.SocketTimeoutException: Read timed out
INFO [main] (CertificateManager.java:645) - Entering getSSLSocketFactory
INFO [main] (CertificateManager.java:854) - Using client certificate location: /tmp/x509up_u852569749
INFO [main] (CertificateManager.java:720) - creating custom TrustManager
INFO [main] (CertificateManager.java:673) - using allow-all hostname verifier
INFO [main] (RestClient.java:270) - rest call info: GET https://cn-stage.test.dataone.org/cn/v1/node
INFO [main] (ExceptionHandler.java:94) - response httpCode: 200
INFO [main] (SimpleMultipartEntity.java:217) - temp outputFile is: /tmp/mmp.output.6121459766923456226.tmp
INFO [main] (SimpleMultipartEntity.java:217) - temp outputFile is: /tmp/mmp.output.1089559976503603960.tmp
INFO [main] (CertificateManager.java:645) - Entering getSSLSocketFactory
INFO [main] (CertificateManager.java:854) - Using client certificate location: /tmp/x509up_u852569749
INFO [main] (CertificateManager.java:720) - creating custom TrustManager
INFO [main] (CertificateManager.java:673) - using allow-all hostname verifier
checkServerTrusted - RSA
INFO [main] (RestClient.java:306) - rest call info: POST https://mn-stage-ucsb-1.test.dataone.org/knb/d1/mn/v1/object; MMP message has: ParamPart:pid = bew_r_test.20121214_16281355520484.2; FilePart:object = /tmp/mmp.output.6121459766923456226.tmp (57723 bytes); FilePart:sysmeta = /tmp/mmp.output.1089559976503603960.tmp (858 bytes);
INFO [main] (ExceptionHandler.java:94) - response httpCode: 200
INFO [main] (CNode.java:276) -   CNode nodelist refresh: new cached time: Dec 14, 2012 4:28:21 PM
INFO [main] (CertificateManager.java:645) - Entering getSSLSocketFactory
INFO [main] (CertificateManager.java:854) - Using client certificate location: /tmp/x509up_u852569749
INFO [main] (CertificateManager.java:720) - creating custom TrustManager
INFO [main] (CertificateManager.java:673) - using allow-all hostname verifier
INFO [main] (RestClient.java:270) - rest call info: GET https://cn-stage.test.dataone.org/cn/v1/node
INFO [main] (ExceptionHandler.java:94) - response httpCode: 200
INFO [main] (SimpleMultipartEntity.java:217) - temp outputFile is: /tmp/mmp.output.4083510636917632970.tmp
INFO [main] (SimpleMultipartEntity.java:217) - temp outputFile is: /tmp/mmp.output.8168115522126552515.tmp
INFO [main] (CertificateManager.java:645) - Entering getSSLSocketFactory
INFO [main] (CertificateManager.java:854) - Using client certificate location: /tmp/x509up_u852569749
INFO [main] (CertificateManager.java:720) - creating custom TrustManager
INFO [main] (CertificateManager.java:673) - using allow-all hostname verifier
checkServerTrusted - RSA
checkServerTrusted - RSA
INFO [main] (RestClient.java:306) - rest call info: POST https://mn-stage-ucsb-1.test.dataone.org/knb/d1/mn/v1/object; MMP message has: ParamPart:pid = bew_r_test.20121214_16281355520484.1; FilePart:object = /tmp/mmp.output.4083510636917632970.tmp (458599 bytes); FilePart:sysmeta = /tmp/mmp.output.8168115522126552515.tmp (859 bytes);
INFO [main] (ExceptionHandler.java:94) - response httpCode: 200
INFO [main] (SimpleMultipartEntity.java:217) - temp outputFile is: /tmp/mmp.output.8259165652239365400.tmp
INFO [main] (SimpleMultipartEntity.java:217) - temp outputFile is: /tmp/mmp.output.6498790447844519435.tmp
INFO [main] (CertificateManager.java:645) - Entering getSSLSocketFactory
INFO [main] (CertificateManager.java:854) - Using client certificate location: /tmp/x509up_u852569749
INFO [main] (CertificateManager.java:720) - creating custom TrustManager
INFO [main] (CertificateManager.java:673) - using allow-all hostname verifier
INFO [main] (RestClient.java:306) - rest call info: POST https://mn-stage-ucsb-1.test.dataone.org/knb/d1/mn/v1/object; MMP message has: ParamPart:pid = bew_r_test.20121214_16281355520484.0; FilePart:object = /tmp/mmp.output.8259165652239365400.tmp (2483 bytes); FilePart:sysmeta = /tmp/mmp.output.6498790447844519435.tmp (883 bytes);
>