Retrieve provenance information from the package (Option 1)

Get package from production node of Gulf of Alaska Data Portal (GOA)

library(dataone)
library(datapack)
d1c <- D1Client("PROD", "urn:node:GOA")
## Warning in strptime(x, fmt, tz = "GMT"): unknown timezone 'default/America/Chicago'
pkg <- getDataPackage(d1c, identifier = "urn:uuid:1d23e155-3ef5-47c6-9612-027c80855e8d", lazyLoad=TRUE, limit="0MB", quiet=FALSE)
## Downloading package members for package with metadata identifier: urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171
## Downloaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:3249ada0-afe3-4dd6-875e-0f7928a4c171
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:b4b3cc45-4953-43d3-910a-847528577531
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:44108e76-405d-4d58-b1b3-fb4b55e3fff9
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:66c416af-84e6-4c7e-92a9-4413cf8acd7b
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:c2f47e88-cc2b-47db-a105-101b80e80334
## Skipping metadata object, already downloaded
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:780a5cff-6071-47d1-a52f-8f7a60c24625
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:9490ce50-b7bc-4fe8-89d1-5b00736df835
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:ae595730-172a-43d0-91f8-3173663d7dce
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:5cde46ff-2e8e-4f40-97a1-eb4c4851f22f
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:a8ed4776-1e17-426f-9f54-98073ae35b5f
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:d31ea97c-e061-43f8-af06-62664671f166
## Lazy Loaded object at URL https://goa.nceas.ucsb.edu/goa/d1/mn/v2/object/urn:uuid:5f57c5d3-65f2-4d46-83f5-67f8104c62dd
## Getting resource map with id: urn:uuid:1d23e155-3ef5-47c6-9612-027c80855e8d
saveWidth <- getOption("width")
options(width=120)

Retrieve information for the package

rels <- getRelationships(pkg, condense=T)
rels
##                                 subject                 predicate                               object
## 42                 _r1532118675r23107r1                 foaf:name                     DataONE R Client
## 22                 _r1532118675r23107r2                  rdf:type                     prov:Association
## 16                 _r1532118675r23107r2              prov:hadPlan                       DataDownload.R
## 67                 _r1532118675r23107r3                  rdf:type                     prov:Association
## 43                 _r1532118675r23107r3              prov:hadPlan Total_PAH_and_Al...rocarbons_Clean.R
## 66                 _r1532118675r23107r4                  rdf:type                     prov:Association
## 14                 _r1532118675r23107r4              prov:hadPlan                          hcdbSites.R
## 64                           Alkane.csv       cito:isDocumentedBy                         metadata.xml
## 52                           Alkane.csv                  rdf:type                         provone:Data
## 27                           Alkane.csv       prov:wasGeneratedBy urn:uuid:e4e1e40...af9a-18a2807d7444
## 8                 CollectionMethods.csv       cito:isDocumentedBy                         metadata.xml
## 55                CollectionMethods.csv                  rdf:type                         provone:Data
## 15                CollectionMethods.csv       prov:wasGeneratedBy urn:uuid:e4e1e40...af9a-18a2807d7444
## 7                        DataDownload.R       cito:isDocumentedBy                         metadata.xml
## 62                       DataDownload.R                  rdf:type                      provone:Program
## 56                   hcdbSampleLocs.png       cito:isDocumentedBy                         metadata.xml
## 63                   hcdbSampleLocs.png                  rdf:type                         provone:Data
## 13                   hcdbSampleLocs.png       prov:wasDerivedFrom       Total_Aromatic_Alkanes_PWS.csv
## 2                    hcdbSampleLocs.png       prov:wasGeneratedBy urn:uuid:d248eca...8c8c-59838fa94666
## 23                   hcdbSamplesGOA.png       cito:isDocumentedBy                         metadata.xml
## 54                   hcdbSamplesGOA.png                  rdf:type                         provone:Data
## 4                    hcdbSamplesGOA.png       prov:wasDerivedFrom       Total_Aromatic_Alkanes_PWS.csv
## 69                   hcdbSamplesGOA.png       prov:wasGeneratedBy urn:uuid:d248eca...8c8c-59838fa94666
## 3                           hcdbSites.R       cito:isDocumentedBy                         metadata.xml
## 25                          hcdbSites.R                  rdf:type                      provone:Program
## 28                         metadata.xml            cito:documents                         metadata.xml
## 29                         metadata.xml            cito:documents       Total_Aromatic_Alkanes_PWS.csv
## 30                         metadata.xml            cito:documents                              PAH.csv
## 31                         metadata.xml            cito:documents                           Sample.csv
## 32                         metadata.xml            cito:documents                CollectionMethods.csv
## 33                         metadata.xml            cito:documents                   hcdbSamplesGOA.png
## 34                         metadata.xml            cito:documents                          hcdbSites.R
## 35                         metadata.xml            cito:documents Total_PAH_and_Al...rocarbons_Clean.R
## 36                         metadata.xml            cito:documents                    Non-EVOS_SINs.csv
## 37                         metadata.xml            cito:documents                   hcdbSampleLocs.png
## 38                         metadata.xml            cito:documents                       DataDownload.R
## 39                         metadata.xml            cito:documents                           Alkane.csv
## 10                         metadata.xml       cito:isDocumentedBy                         metadata.xml
## 50                    Non-EVOS_SINs.csv       cito:isDocumentedBy                         metadata.xml
## 9                     Non-EVOS_SINs.csv                  rdf:type                         provone:Data
## 11                              PAH.csv       cito:isDocumentedBy                         metadata.xml
## 12                              PAH.csv                  rdf:type                         provone:Data
## 60                              PAH.csv       prov:wasGeneratedBy urn:uuid:e4e1e40...af9a-18a2807d7444
## 68                           Sample.csv       cito:isDocumentedBy                         metadata.xml
## 17                           Sample.csv                  rdf:type                         provone:Data
## 44                           Sample.csv       prov:wasGeneratedBy urn:uuid:e4e1e40...af9a-18a2807d7444
## 45       Total_Aromatic_Alkanes_PWS.csv       cito:isDocumentedBy                         metadata.xml
## 51       Total_Aromatic_Alkanes_PWS.csv                  rdf:type                         provone:Data
## 18       Total_Aromatic_Alkanes_PWS.csv       prov:wasDerivedFrom                              PAH.csv
## 19       Total_Aromatic_Alkanes_PWS.csv       prov:wasDerivedFrom                           Sample.csv
## 20       Total_Aromatic_Alkanes_PWS.csv       prov:wasDerivedFrom                    Non-EVOS_SINs.csv
## 21       Total_Aromatic_Alkanes_PWS.csv       prov:wasDerivedFrom                           Alkane.csv
## 1        Total_Aromatic_Alkanes_PWS.csv       prov:wasGeneratedBy urn:uuid:a4e3b68...a185-13d4d59d06f9
## 59 Total_PAH_and_Al...rocarbons_Clean.R       cito:isDocumentedBy                         metadata.xml
## 6  Total_PAH_and_Al...rocarbons_Clean.R                  rdf:type                      provone:Program
## 58 urn:uuid:a4e3b68...a185-13d4d59d06f9        dcterms:identifier urn:uuid:a4e3b68...a185-13d4d59d06f9
## 40 urn:uuid:a4e3b68...a185-13d4d59d06f9                  rdf:type                    provone:Execution
## 65 urn:uuid:a4e3b68...a185-13d4d59d06f9 prov:qualifiedAssociation                 _r1532118675r23107r3
## 46 urn:uuid:a4e3b68...a185-13d4d59d06f9                 prov:used                              PAH.csv
## 47 urn:uuid:a4e3b68...a185-13d4d59d06f9                 prov:used                           Sample.csv
## 48 urn:uuid:a4e3b68...a185-13d4d59d06f9                 prov:used                    Non-EVOS_SINs.csv
## 49 urn:uuid:a4e3b68...a185-13d4d59d06f9                 prov:used                           Alkane.csv
## 24 urn:uuid:d248eca...8c8c-59838fa94666        dcterms:identifier urn:uuid:d248eca...8c8c-59838fa94666
## 57 urn:uuid:d248eca...8c8c-59838fa94666                  rdf:type                    provone:Execution
## 26 urn:uuid:d248eca...8c8c-59838fa94666 prov:qualifiedAssociation                 _r1532118675r23107r4
## 41 urn:uuid:d248eca...8c8c-59838fa94666                 prov:used       Total_Aromatic_Alkanes_PWS.csv
## 61 urn:uuid:e4e1e40...af9a-18a2807d7444        dcterms:identifier urn:uuid:e4e1e40...af9a-18a2807d7444
## 53 urn:uuid:e4e1e40...af9a-18a2807d7444                  rdf:type                    provone:Execution
## 5  urn:uuid:e4e1e40...af9a-18a2807d7444 prov:qualifiedAssociation                 _r1532118675r23107r2

Retrieve provenance information from the package

prov <- subset(rels, predicate=="prov:used" | predicate =="prov:wasDerivedFrom" | predicate=="prov:wasGeneratedBy")
prov
##                                 subject           predicate                               object
## 27                           Alkane.csv prov:wasGeneratedBy urn:uuid:e4e1e40...af9a-18a2807d7444
## 15                CollectionMethods.csv prov:wasGeneratedBy urn:uuid:e4e1e40...af9a-18a2807d7444
## 13                   hcdbSampleLocs.png prov:wasDerivedFrom       Total_Aromatic_Alkanes_PWS.csv
## 2                    hcdbSampleLocs.png prov:wasGeneratedBy urn:uuid:d248eca...8c8c-59838fa94666
## 4                    hcdbSamplesGOA.png prov:wasDerivedFrom       Total_Aromatic_Alkanes_PWS.csv
## 69                   hcdbSamplesGOA.png prov:wasGeneratedBy urn:uuid:d248eca...8c8c-59838fa94666
## 60                              PAH.csv prov:wasGeneratedBy urn:uuid:e4e1e40...af9a-18a2807d7444
## 44                           Sample.csv prov:wasGeneratedBy urn:uuid:e4e1e40...af9a-18a2807d7444
## 18       Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                              PAH.csv
## 19       Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                           Sample.csv
## 20       Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                    Non-EVOS_SINs.csv
## 21       Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                           Alkane.csv
## 1        Total_Aromatic_Alkanes_PWS.csv prov:wasGeneratedBy urn:uuid:a4e3b68...a185-13d4d59d06f9
## 46 urn:uuid:a4e3b68...a185-13d4d59d06f9           prov:used                              PAH.csv
## 47 urn:uuid:a4e3b68...a185-13d4d59d06f9           prov:used                           Sample.csv
## 48 urn:uuid:a4e3b68...a185-13d4d59d06f9           prov:used                    Non-EVOS_SINs.csv
## 49 urn:uuid:a4e3b68...a185-13d4d59d06f9           prov:used                           Alkane.csv
## 41 urn:uuid:d248eca...8c8c-59838fa94666           prov:used       Total_Aromatic_Alkanes_PWS.csv

Replace ids with names

  • Create a data frame that contains id->name relationship
provPlan <- subset(rels,predicate == "prov:hadPlan")
provAsso <- subset(rels,predicate == "prov:qualifiedAssociation")
provPlan
##                 subject    predicate                               object
## 16 _r1532118675r23107r2 prov:hadPlan                       DataDownload.R
## 43 _r1532118675r23107r3 prov:hadPlan Total_PAH_and_Al...rocarbons_Clean.R
## 14 _r1532118675r23107r4 prov:hadPlan                          hcdbSites.R
provAsso
##                                 subject                 predicate               object
## 65 urn:uuid:a4e3b68...a185-13d4d59d06f9 prov:qualifiedAssociation _r1532118675r23107r3
## 26 urn:uuid:d248eca...8c8c-59838fa94666 prov:qualifiedAssociation _r1532118675r23107r4
## 5  urn:uuid:e4e1e40...af9a-18a2807d7444 prov:qualifiedAssociation _r1532118675r23107r2
provAsso$object <- provPlan$object[match(provAsso$object, provPlan$subject)]
provAsso
##                                 subject                 predicate                               object
## 65 urn:uuid:a4e3b68...a185-13d4d59d06f9 prov:qualifiedAssociation Total_PAH_and_Al...rocarbons_Clean.R
## 26 urn:uuid:d248eca...8c8c-59838fa94666 prov:qualifiedAssociation                          hcdbSites.R
## 5  urn:uuid:e4e1e40...af9a-18a2807d7444 prov:qualifiedAssociation                       DataDownload.R
  • Replace ids with names in the provenance relationship
indx <- match(prov$subject, provAsso$subject, nomatch = 0)
prov$subject[indx != 0] <- provAsso$object[indx]
indx <- match(prov$object, provAsso$subject, nomatch = 0)
prov$object[indx != 0] <- provAsso$object[indx]
prov
##                                 subject           predicate                               object
## 27                           Alkane.csv prov:wasGeneratedBy                       DataDownload.R
## 15                CollectionMethods.csv prov:wasGeneratedBy                       DataDownload.R
## 13                   hcdbSampleLocs.png prov:wasDerivedFrom       Total_Aromatic_Alkanes_PWS.csv
## 2                    hcdbSampleLocs.png prov:wasGeneratedBy                          hcdbSites.R
## 4                    hcdbSamplesGOA.png prov:wasDerivedFrom       Total_Aromatic_Alkanes_PWS.csv
## 69                   hcdbSamplesGOA.png prov:wasGeneratedBy                          hcdbSites.R
## 60                              PAH.csv prov:wasGeneratedBy                       DataDownload.R
## 44                           Sample.csv prov:wasGeneratedBy                       DataDownload.R
## 18       Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                              PAH.csv
## 19       Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                           Sample.csv
## 20       Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                    Non-EVOS_SINs.csv
## 21       Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                           Alkane.csv
## 1        Total_Aromatic_Alkanes_PWS.csv prov:wasGeneratedBy Total_PAH_and_Al...rocarbons_Clean.R
## 46 Total_PAH_and_Al...rocarbons_Clean.R           prov:used                              PAH.csv
## 47 Total_PAH_and_Al...rocarbons_Clean.R           prov:used                           Sample.csv
## 48 Total_PAH_and_Al...rocarbons_Clean.R           prov:used                    Non-EVOS_SINs.csv
## 49 Total_PAH_and_Al...rocarbons_Clean.R           prov:used                           Alkane.csv
## 41                          hcdbSites.R           prov:used       Total_Aromatic_Alkanes_PWS.csv

Convert data fram columns from factors to chars

prov <- data.frame(lapply(prov, as.character), stringsAsFactors=FALSE)

Create RDF and store into a file

library(rdflib)
provSimp <- subset(prov, predicate=="prov:used" | predicate=="prov:wasGeneratedBy")
provSimp
##                                 subject           predicate                               object
## 1                            Alkane.csv prov:wasGeneratedBy                       DataDownload.R
## 2                 CollectionMethods.csv prov:wasGeneratedBy                       DataDownload.R
## 4                    hcdbSampleLocs.png prov:wasGeneratedBy                          hcdbSites.R
## 6                    hcdbSamplesGOA.png prov:wasGeneratedBy                          hcdbSites.R
## 7                               PAH.csv prov:wasGeneratedBy                       DataDownload.R
## 8                            Sample.csv prov:wasGeneratedBy                       DataDownload.R
## 13       Total_Aromatic_Alkanes_PWS.csv prov:wasGeneratedBy Total_PAH_and_Al...rocarbons_Clean.R
## 14 Total_PAH_and_Al...rocarbons_Clean.R           prov:used                              PAH.csv
## 15 Total_PAH_and_Al...rocarbons_Clean.R           prov:used                           Sample.csv
## 16 Total_PAH_and_Al...rocarbons_Clean.R           prov:used                    Non-EVOS_SINs.csv
## 17 Total_PAH_and_Al...rocarbons_Clean.R           prov:used                           Alkane.csv
## 18                          hcdbSites.R           prov:used       Total_Aromatic_Alkanes_PWS.csv
provSimp <- data.frame(lapply(provSimp, as.character), stringsAsFactors=FALSE)
rdfSimp <- rdf()
for (i in 1:nrow(provSimp)) rdf_add(rdfSimp, provSimp$subject[i], provSimp$predicate[i], provSimp$object[i], subjectType="uri", objectType="uri")
options(rdf_print_format = "rdfxml")
rdf_serialize(rdfSimp, "./results/provSimp.rdfxml")
rdf
## <?xml version="1.0" encoding="utf-8"?>
## <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:base="localhost://">
##   <rdf:Description rdf:about="Total_Aromatic_Alkanes_PWS.csv">
##     <ns0:wasDerivedFrom xmlns:ns0="prov:" rdf:resource="hcdbSamplesGOA.png"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="Total_Aromatic_Alkanes_PWS.csv">
##     <ns0:wasDerivedFrom xmlns:ns0="prov:" rdf:resource="hcdbSampleLocs.png"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="DataDownload.R">
##     <ns0:wasGeneratedBy xmlns:ns0="prov:" rdf:resource="Sample.csv"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="DataDownload.R">
##     <ns0:wasGeneratedBy xmlns:ns0="prov:" rdf:resource="PAH.csv"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="DataDownload.R">
##     <ns0:wasGeneratedBy xmlns:ns0="prov:" rdf:resource="CollectionMethods.csv"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="DataDownload.R">
##     <ns0:wasGeneratedBy xmlns:ns0="prov:" rdf:resource="Alkane.csv"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="Sample.csv">
##     <ns0:used xmlns:ns0="prov:" rdf:resource="Total_PAH_and_Al...rocarbons_Clean.R"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="Non-EVOS_SINs.csv">
##     <ns0:used xmlns:ns0="prov:" rdf:resource="Total_PAH_and_Al...rocarbons_Clean.R"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="Alkane.csv">
##     <ns0:used xmlns:ns0="prov:" rdf:resource="Total_PAH_and_Al...rocarbons_Clean.R"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="Sample.csv">
##     <ns0:wasDerivedFrom xmlns:ns0="prov:" rdf:resource="Total_Aromatic_Alkanes_PWS.csv"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="Alkane.csv">
##     <ns0:wasDerivedFrom xmlns:ns0="prov:" rdf:resource="Total_Aromatic_Alkanes_PWS.csv"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="hcdbSites.R">
##     <ns0:wasGeneratedBy xmlns:ns0="prov:" rdf:resource="hcdbSamplesGOA.png"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="hcdbSites.R">
##     <ns0:wasGeneratedBy xmlns:ns0="prov:" rdf:resource="hcdbSampleLocs.png"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="PAH.csv">
##     <ns0:used xmlns:ns0="prov:" rdf:resource="Total_PAH_and_Al...rocarbons_Clean.R"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="Total_PAH_and_Al...rocarbons_Clean.R">
##     <ns0:wasGeneratedBy xmlns:ns0="prov:" rdf:resource="Total_Aromatic_Alkanes_PWS.csv"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="Non-EVOS_SINs.csv">
##     <ns0:wasDerivedFrom xmlns:ns0="prov:" rdf:resource="Total_Aromatic_Alkanes_PWS.csv"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="PAH.csv">
##     <ns0:wasDerivedFrom xmlns:ns0="prov:" rdf:resource="Total_Aromatic_Alkanes_PWS.csv"/>
##   </rdf:Description>
##   <rdf:Description rdf:about="Total_Aromatic_Alkanes_PWS.csv">
##     <ns0:used xmlns:ns0="prov:" rdf:resource="hcdbSites.R"/>
##   </rdf:Description>
## </rdf:RDF>
system("rapper --output dot ./results/provSimp.rdfxml > ./results/provSimp.dot")
system("dot -Tpdf ./results/provSimp.dot > ./results/provSimp.pdf")
knitr::include_graphics("./results/provSimp.pdf")

Visualize provenance in YesWorkflow (YW)

Capture provenance needed for generating YW comments
provYwDef <- subset(prov, predicate == "prov:wasDerivedFrom")
provYwUsed <- subset(prov, predicate == "prov:used")
provYwDef
##                           subject           predicate                         object
## 3              hcdbSampleLocs.png prov:wasDerivedFrom Total_Aromatic_Alkanes_PWS.csv
## 5              hcdbSamplesGOA.png prov:wasDerivedFrom Total_Aromatic_Alkanes_PWS.csv
## 9  Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                        PAH.csv
## 10 Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                     Sample.csv
## 11 Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom              Non-EVOS_SINs.csv
## 12 Total_Aromatic_Alkanes_PWS.csv prov:wasDerivedFrom                     Alkane.csv
provYwUsed
##                                 subject predicate                         object
## 14 Total_PAH_and_Al...rocarbons_Clean.R prov:used                        PAH.csv
## 15 Total_PAH_and_Al...rocarbons_Clean.R prov:used                     Sample.csv
## 16 Total_PAH_and_Al...rocarbons_Clean.R prov:used              Non-EVOS_SINs.csv
## 17 Total_PAH_and_Al...rocarbons_Clean.R prov:used                     Alkane.csv
## 18                          hcdbSites.R prov:used Total_Aromatic_Alkanes_PWS.csv
Create data frame which shows subject=output, predicate=program, and object=input
provYwDef$predicate <- provYwUsed$subject[match(provYwDef$object, provYwUsed$object, nomatch=0)]
provYwDef
##                           subject                            predicate                         object
## 3              hcdbSampleLocs.png                          hcdbSites.R Total_Aromatic_Alkanes_PWS.csv
## 5              hcdbSamplesGOA.png                          hcdbSites.R Total_Aromatic_Alkanes_PWS.csv
## 9  Total_Aromatic_Alkanes_PWS.csv Total_PAH_and_Al...rocarbons_Clean.R                        PAH.csv
## 10 Total_Aromatic_Alkanes_PWS.csv Total_PAH_and_Al...rocarbons_Clean.R                     Sample.csv
## 11 Total_Aromatic_Alkanes_PWS.csv Total_PAH_and_Al...rocarbons_Clean.R              Non-EVOS_SINs.csv
## 12 Total_Aromatic_Alkanes_PWS.csv Total_PAH_and_Al...rocarbons_Clean.R                     Alkane.csv
Split data frame by the program
ins <- split(provYwDef$object, provYwDef$predicate)
outs <- split(provYwDef$subject, provYwDef$predicate)
ins
## $hcdbSites.R
## [1] "Total_Aromatic_Alkanes_PWS.csv" "Total_Aromatic_Alkanes_PWS.csv"
## 
## $Total_PAH_and_Al...rocarbons_Clean.R
## [1] "PAH.csv"           "Sample.csv"        "Non-EVOS_SINs.csv" "Alkane.csv"
outs
## $hcdbSites.R
## [1] "hcdbSampleLocs.png" "hcdbSamplesGOA.png"
## 
## $Total_PAH_and_Al...rocarbons_Clean.R
## [1] "Total_Aromatic_Alkanes_PWS.csv" "Total_Aromatic_Alkanes_PWS.csv" "Total_Aromatic_Alkanes_PWS.csv"
## [4] "Total_Aromatic_Alkanes_PWS.csv"
Generate YW comments for inputs and outputs for each group
ins <- data.frame(lapply(as.data.frame(ins), as.character), stringsAsFactors = FALSE)
for(i in names(ins)) ins[[i]] <- paste("#@in ", sub("\\..*","",ins[[i]]), " @URI file:", ins[[i]],sep="")
ins
##                                                                hcdbSites.R
## 1 #@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 2 #@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 3 #@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 4 #@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
##             Total_PAH_and_Al...rocarbons_Clean.R
## 1                     #@in PAH @URI file:PAH.csv
## 2               #@in Sample @URI file:Sample.csv
## 3 #@in Non-EVOS_SINs @URI file:Non-EVOS_SINs.csv
## 4               #@in Alkane @URI file:Alkane.csv
outs <- data.frame(lapply(as.data.frame(outs), as.character), stringsAsFactors = FALSE)
for(i in names(outs)) outs[[i]] <- paste("#@out ", sub("\\..*","",outs[[i]]), " @URI file:", outs[[i]],sep="")
outs
##                                         hcdbSites.R
## 1 #@out hcdbSampleLocs @URI file:hcdbSampleLocs.png
## 2 #@out hcdbSamplesGOA @URI file:hcdbSamplesGOA.png
## 3 #@out hcdbSampleLocs @URI file:hcdbSampleLocs.png
## 4 #@out hcdbSamplesGOA @URI file:hcdbSamplesGOA.png
##                                        Total_PAH_and_Al...rocarbons_Clean.R
## 1 #@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 2 #@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 3 #@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 4 #@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
Combine YW comments in each group
inouts <- rbind(ins,outs)
inouts
##                                                                hcdbSites.R
## 1 #@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 2 #@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 3 #@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 4 #@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 5                        #@out hcdbSampleLocs @URI file:hcdbSampleLocs.png
## 6                        #@out hcdbSamplesGOA @URI file:hcdbSamplesGOA.png
## 7                        #@out hcdbSampleLocs @URI file:hcdbSampleLocs.png
## 8                        #@out hcdbSamplesGOA @URI file:hcdbSamplesGOA.png
##                                        Total_PAH_and_Al...rocarbons_Clean.R
## 1                                                #@in PAH @URI file:PAH.csv
## 2                                          #@in Sample @URI file:Sample.csv
## 3                            #@in Non-EVOS_SINs @URI file:Non-EVOS_SINs.csv
## 4                                          #@in Alkane @URI file:Alkane.csv
## 5 #@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 6 #@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 7 #@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
## 8 #@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv
Create file, write comments into the corresponding file, and generate YW
for(i in names(inouts)) {
  filename <- paste("YW",i,sep="")
  name <- paste("test/",filename,sep="")
  file.create(name)
  write(paste("#@begin",sub("\\..*","",i)),file=name,append = TRUE)
  write(unique(ins[[i]]),file=name,append=TRUE)
  write(paste("#@begin",sub("\\..*","",i), "@desc", i),file=name,append = TRUE)
  write(unique(inouts[[i]]),file=name,append=TRUE)
  write(paste("#@end",sub("\\..*","",i)),file=name,append = TRUE)
  write(unique(outs[[i]]),file=name,append=TRUE)
  write(paste("#@end",sub("\\..*","",i)),file=name,append = TRUE)
  system(paste("java -jar /Users/eunjungpark/Documents/dataone/DataONE_2018_Summer_Intern_Project1/transparency/yw_jar/yesworkflow-0.2.1-SNAPSHOT-jar-with-dependencies.jar graph ",name," -c graph.view=combined -c graph.layout=tb > ",sub("\\..*","",name),".gv",sep=""))
  system(paste("dot -Tpdf ",sub("\\..*","",name),".gv > ",sub("\\..*","",name),".pdf", sep=""))
  #system(paste("cat /Users/eunjungpark/Documents/dataone/DataONE_2018_Summer_Intern_Project1/transparency/",sub("\\..*","",name),sep = ""),intern = TRUE)
}
system("cat /Users/eunjungpark/Documents/dataone/DataONE_2018_Summer_Intern_Project1/transparency/test/YWTotal_PAH_and_Al.R",intern = TRUE)
##  [1] "#@begin Total_PAH_and_Al"                                                 
##  [2] "#@in PAH @URI file:PAH.csv"                                               
##  [3] "#@in Sample @URI file:Sample.csv"                                         
##  [4] "#@in Non-EVOS_SINs @URI file:Non-EVOS_SINs.csv"                           
##  [5] "#@in Alkane @URI file:Alkane.csv"                                         
##  [6] "#@begin Total_PAH_and_Al @desc Total_PAH_and_Al...rocarbons_Clean.R"      
##  [7] "#@in PAH @URI file:PAH.csv"                                               
##  [8] "#@in Sample @URI file:Sample.csv"                                         
##  [9] "#@in Non-EVOS_SINs @URI file:Non-EVOS_SINs.csv"                           
## [10] "#@in Alkane @URI file:Alkane.csv"                                         
## [11] "#@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv"
## [12] "#@end Total_PAH_and_Al"                                                   
## [13] "#@out Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv"
## [14] "#@end Total_PAH_and_Al"
system("cat /Users/eunjungpark/Documents/dataone/DataONE_2018_Summer_Intern_Project1/transparency/test/YWhcdbSites.R",intern = TRUE)
##  [1] "#@begin hcdbSites"                                                       
##  [2] "#@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv"
##  [3] "#@begin hcdbSites @desc hcdbSites.R"                                     
##  [4] "#@in Total_Aromatic_Alkanes_PWS @URI file:Total_Aromatic_Alkanes_PWS.csv"
##  [5] "#@out hcdbSampleLocs @URI file:hcdbSampleLocs.png"                       
##  [6] "#@out hcdbSamplesGOA @URI file:hcdbSamplesGOA.png"                       
##  [7] "#@end hcdbSites"                                                         
##  [8] "#@out hcdbSampleLocs @URI file:hcdbSampleLocs.png"                       
##  [9] "#@out hcdbSamplesGOA @URI file:hcdbSamplesGOA.png"                       
## [10] "#@end hcdbSites"
Run, e.g, make.sh (below script block can be stored in a single executable file)
# define base directories
export EXAMPLE_DIR=.
export PROJECT_ROOT=.

# define lcoation of YesWorkflow jar file
export YW_JAR="${PROJECT_ROOT}/yw_jar/yesworkflow-0.2.1-SNAPSHOT-jar-with-dependencies.jar"

# define command for running YesWorkflow
export YW_CMD="java -jar $YW_JAR"

# destination of facts, views and query results
export SCRIPT_DIR=${EXAMPLE_DIR}/scripts
export RESULTS_DIR=${EXAMPLE_DIR}/results

mkdir -p $RESULTS_DIR

# generate workflow using commented script
graph_name="aoos_retro_wf_graph"
$YW_CMD graph "./scripts/aoos.R" \
    -c graph.view=combined \
    -c graph.layout=tb \
      > $RESULTS_DIR/$graph_name.gv
dot -Tpdf $RESULTS_DIR/$graph_name.gv > $RESULTS_DIR/$graph_name.pdf
dot -Tsvg $RESULTS_DIR/$graph_name.gv > $RESULTS_DIR/$graph_name.svg
#system("source ./make.sh")
knitr::include_graphics("./results/aoos_retro_wf_graph.pdf")

Record provenance using recordr (Option2)

source("./setup.R")
## Checking rgeos availability: TRUE
## rgeos version: 0.3-28, (SVN revision 572)
##  GEOS runtime version: 3.6.2-CAPI-1.10.2 4d2925d6 
##  Linking to sp version: 1.3-1 
##  Polygon checking: TRUE
## rgdal: version: 1.3-3, (SVN revision 759)
##  Geospatial Data Abstraction Library extensions to R successfully loaded
##  Loaded GDAL runtime: GDAL 2.3.0, released 2018/05/04
##  Path to GDAL shared files: /usr/local/Cellar/gdal/2.3.0/share/gdal
##  GDAL binary built with GEOS: TRUE 
##  Loaded PROJ.4 runtime: Rel. 5.1.0, June 1st, 2018, [PJ_VERSION: 510]
##  Path to PROJ.4 shared files: (autodetected)
##  Linking to sp version: 1.3-1
## 
## Attaching package: 'raster'
## The following object is masked from 'package:datapack':
## 
##     getData
## The following object is masked from 'package:dataone':
## 
##     getData
## ── Attaching packages ────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
## ✔ ggplot2 3.0.0     ✔ purrr   0.2.5
## ✔ tibble  1.4.2     ✔ dplyr   0.7.6
## ✔ tidyr   0.8.1     ✔ stringr 1.2.0
## ✔ readr   1.1.1     ✔ forcats 0.3.0
## ── Conflicts ───────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ tidyr::extract() masks raster::extract()
## ✖ dplyr::filter()  masks stats::filter()
## ✖ dplyr::lag()     masks stats::lag()
## ✖ dplyr::select()  masks raster::select()
library(recordr)
rc <- new("Recordr")
## A new recordr home directory has been created at:
## 
##  /var/folders/7t/xdmtt00j0w53slb206w9xh100000gn/T//RtmpSAtjQP/recordr
## The recordr package will save run information to this directory, which is under
## the R session temporary directory. Therefore the information that recordr collects
## will be removed by R when the current R session ends.
## 
## If you wish to change the recordr home directory so that information is saved to a
## permanent location please use the "newDir" argument, for example
## 
##  "rc <- new("Recordr", newDir="/Users/bobsmith/recordr")

Record provenance for the first script

record(rc, "./scripts/Total_PAH_and_Alkanes_GoA_Hydrocarbons_Clean.R", tag="total_pah_and_alkanes_goa_hydrocarbons_clean script1")
## 'data.frame':    16960 obs. of  72 variables:
##  $ Funding     : chr  "EVOSTC" "EVOSTC" "EVOSTC" "EVOSTC" ...
##  $ Sin         : int  -600 -600 -557 -557 -900 20120312 20120313 20120310 20120309 20120308 ...
##  $ type        : chr  "QC" "QC" "QC" "QC" ...
##  $ Rep         : int  1 2 1 2 1 1 1 1 1 1 ...
##  $ LAB         : chr  "ABL" "ABL" "ABL" "ABL" ...
##  $ QCbatch     : chr  "20120827MZ" "20120827MZ" "20120827MZ" "20120827MZ" ...
##  $ strMAT      : chr  "sed" "sed" "sed" "sed" ...
##  $ LabSam      : chr  "NISTARO" "NISTARO" "AREF" "BREF" ...
##  $ Vol         : int  NA NA NA NA NA NA NA NA NA NA ...
##  $ Proportion  : num  NA NA NA NA NA NA NA NA NA NA ...
##  $ DryWt       : num  1 1 0.00678 0.00678 1 ...
##  $ WetWt       : num  1 1 0.00678 0.00678 1 ...
##  $ AnalysisType: chr  "QCCALI" "QCCALI" "QCOIL" "QCOIL" ...
##  $ Catno       : chr  "RMB_000" "RMB_000" "RMB_000" "RMB_000" ...
##  $ NaphD8      : num  92.5 92.5 88.7 86.7 108.4 ...
##  $ Acend10     : num  100.6 101.1 94.5 94.2 116.1 ...
##  $ Phend10     : num  101.1 101 94.9 95.2 116.3 ...
##  $ Anthra10    : num  NA NA NA NA NA NA NA NA NA NA ...
##  $ Banth12     : num  NA NA NA NA NA NA NA NA NA NA ...
##  $ Chryd12     : num  104.5 104.8 94.6 93.5 114.3 ...
##  $ Benad12     : num  114 114 115 113 133 ...
##  $ Peryd12     : num  106.5 109.5 89.3 91.8 106.7 ...
##  $ Units       : chr  "ng/g" "ng/g" "ng/g oil" "ng/g oil" ...
##  $ Naph        : num  247 247 124275 136809 0 ...
##  $ Menap2      : num  180 181 477226 487966 0 ...
##  $ MENAP1      : num  160 161 341500 345107 0 ...
##  $ DIMETH      : num  138 137 501639 503703 0 ...
##  $ C2NAPH      : num  412 412 1784545 1737098 0 ...
##  $ TRIMETH     : num  0 0 237407 239645 0 ...
##  $ C3NAPH      : num  0 0 1602999 1701227 0 ...
##  $ C4NAPH      : num  0 0 961949 990175 0 ...
##  $ BIPHENYL    : num  114 114 23663 23529 111 ...
##  $ ACENTHY     : num  138 134 15476 0 0 ...
##  $ ACENTHE     : num  118 118 16798 16649 0 ...
##  $ FLUORENE    : num  106 107 32643 33024 0 ...
##  $ C1FLUOR     : num  0 0 111440 113162 0 ...
##  $ C2FLUOR     : num  0 0 179608 180330 0 ...
##  $ C3FLUOR     : num  0 0 209519 199383 0 ...
##  $ C4FLUOR     : num  0 0 25311 25879 0 ...
##  $ DITHIO      : num  96.1 96.8 48726.8 45625.9 0 ...
##  $ C1DITHIO    : num  0 0 181422 183124 0 ...
##  $ C2DITHIO    : num  0 0 293077 296922 0 ...
##  $ C3DITHIO    : num  0 0 258189 258230 0 ...
##  $ C4DITHIO    : num  0 0 36010 37554 0 ...
##  $ PHENANTH    : num  245 245 97646 99282 0 ...
##  $ MEPHEN1     : num  202 205 97291 97390 0 ...
##  $ C1PHENAN    : num  978 980 470442 477279 0 ...
##  $ C2PHENAN    : num  0 167 733661 734837 0 ...
##  $ C3PHENAN    : num  0 0 502830 539533 0 ...
##  $ C4PHENAN    : num  0 0 230727 228864 0 ...
##  $ ANTHRA      : num  83.7 84.1 3669.9 2878 0 ...
##  $ FLUORANT    : num  190 189 2667 2660 0 ...
##  $ PYRENE      : num  208 208 8622 8475 0 ...
##  $ C1FLUORA    : num  0 0 40463 38925 0 ...
##  $ C2FLUORA    : num  0 0 83041 87831 0 ...
##  $ C3FLUORA    : num  0 0 65452 59747 0 ...
##  $ C4FLUORA    : num  0 0 46432 45956 0 ...
##  $ BENANTH     : num  107 107 4676 3706 0 ...
##  $ CHRYSENE    : num  104 104 11122 11243 0 ...
##  $ C1CHRYS     : num  89 88.6 26538.6 28080.2 0 ...
##  $ C2CHRYS     : num  0 0 53113 47651 0 ...
##  $ C3CHRYS     : num  0 0 22029 21114 0 ...
##  $ C4CHRYS     : num  0 0 7310 8871 0 ...
##  $ BENZOBFL    : num  193 195 834 1026 0 ...
##  $ BENZOKFL    : num  74.5 74.7 130.6 136.6 0 ...
##  $ BENEPY      : num  108 109 2575 3014 0 ...
##  $ BENAPY      : num  112 113 632 883 0 ...
##  $ PERYLENE    : num  103 102 33971 33769 0 ...
##  $ INDENO      : num  117 113 0 0 0 ...
##  $ DIBENZ      : num  111 112 302 350 0 ...
##  $ BENZOP      : num  142 132 1335 1611 0 ...
##  $ comment     : logi  NA NA NA NA NA NA ...
## ----------------------------------------------------------------------------------------------------------------------
## You have loaded plyr after dplyr - this is likely to cause problems.
## If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
## library(plyr); library(dplyr)
## ----------------------------------------------------------------------------------------------------------------------
## 
## Attaching package: 'plyr'
## The following objects are masked from 'package:dplyr':
## 
##     arrange, count, desc, failwith, id, mutate, rename, summarise, summarize
## The following object is masked from 'package:purrr':
## 
##     compact
## 'data.frame':    15955 obs. of  53 variables:
##  $ Funding     : chr  "EVOSTC" "EVOSTC" "EVOSTC" "EVOSTC" ...
##  $ Sin         : int  -902 -902 -902 -902 -902 -902 -902 -902 -902 -902 ...
##  $ type        : chr  "QC" "QC" "QC" "QC" ...
##  $ Rep         : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ LAB         : chr  "ABL" "ABL" "ABL" "ABL" ...
##  $ QCbatch     : chr  "W102390" "L012391" "W101090" "W100990" ...
##  $ strMAT      : chr  "" "" "" "" ...
##  $ LabSam      : chr  "" "" "" "" ...
##  $ Vol         : int  NA NA NA NA NA NA NA NA NA NA ...
##  $ Proportion  : logi  NA NA NA NA NA NA ...
##  $ DryWt       : num  NA NA NA NA NA NA NA NA NA NA ...
##  $ WetWt       : num  1 1 1 1 1 1 1 1 1 1 ...
##  $ AnalysisType: chr  "" "" "" "" ...
##  $ Catno       : chr  "NMFS_000" "NMFS_000" "NMFS_000" "NMFS_000" ...
##  $ C12d26      : num  15.4 40.9 44.4 52.3 56.3 ...
##  $ C16d34      : num  45.2 68.9 77.8 62.3 64.8 ...
##  $ C20d42      : num  79.7 88.6 89.2 79.9 79.1 ...
##  $ C24d50      : num  87.8 92.2 86.9 84.7 82 ...
##  $ C30d64      : num  88.3 96.2 86.1 84.3 70.1 ...
##  $ Units       : chr  "" "" "" "" ...
##  $ C9ALK       : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ C10ALK      : num  5799 9024 9399 9067 9731 ...
##  $ C11ALK      : num  7115 9666 9279 9244 9789 ...
##  $ C12ALK      : num  10957 11305 10176 10265 10754 ...
##  $ C13ALK      : num  15396 12642 10918 10936 11227 ...
##  $ C14ALK      : num  6703 8743 7349 9347 9903 ...
##  $ C15ALK      : num  8123 9500 8664 9265 9797 ...
##  $ C16ALK      : num  11290 11966 10943 10940 11554 ...
##  $ C17ALK      : num  14662 13658 12383 12285 13160 ...
##  $ PRISTANE    : num  15357 14620 12439 12720 13234 ...
##  $ C18ALK      : num  10570 12613 12216 11400 12166 ...
##  $ PHYTANE     : num  51.9 83.7 10.6 31 99.4 ...
##  $ C19ALK      : num  10422 11554 10845 10516 11108 ...
##  $ C20ALK      : num  10096 10536 9709 9759 10198 ...
##  $ C21ALK      : num  10345 10350 9295 9685 10083 ...
##  $ C22ALK      : num  10735 11262 10937 10703 10884 ...
##  $ C23ALK      : num  9798 10094 9605 9596 9805 ...
##  $ C24ALK      : num  10298 10559 9773 9919 10220 ...
##  $ C25ALK      : num  9695 10025 9026 9288 9635 ...
##  $ C26ALK      : num  9627 10042 8828 9123 9512 ...
##  $ C27ALK      : num  4097 4298 3642 3791 4000 ...
##  $ C28ALK      : num  10516 10852 10689 10838 10926 ...
##  $ C29ALK      : num  9499 9863 9407 9448 9671 ...
##  $ C30ALK      : num  10179 10519 9718 9672 10053 ...
##  $ C31ALK      : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ C32ALK      : num  10168 10027 9036 8612 8990 ...
##  $ C33ALK      : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ C34ALK      : num  10776 10199 8883 8425 5148 ...
##  $ C35ALK      : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ C36ALK      : num  0 0 0 0 0 0 0 0 0 0 ...
##  $ TOTALKANES  : num  242657 254894 233495 235218 241905 ...
##  $ UCM         : num  7942 0 0 0 0 ...
##  $ comment     : chr  "" "" "" "" ...
## [1] "urn:uuid:a323e130-4923-4e49-8259-0433e517beea"

Record provenance for the second script

record(rc, "./scripts/hcdbSites.R", tag="hcdbsites script2")
## [1] "urn:uuid:b8470053-48fd-4739-a2a8-3c79ccce1739"

List the records

listRuns(rc)
## Seq   Script                         Tag                  Start Time              End Time                Run Id        
## 2     /Users/eunjun...ts/hcdbSites.R hcdbsites script2    2018-07-20 20:32:02 GMT 2018-07-20 20:32:03 GMT ...79ccce1739 
## 1     /Users/eunjun...arbons_Clean.R total_pah_and_alkane 2018-07-20 20:31:51 GMT 2018-07-20 20:32:01 GMT ...33e517beea

View each record in detail

viewRuns(rc, tag="script1")
## [details]: Run details
## ----------------------
## "/Users/eunjungpark/Documents/data...d_Alkanes_GoA_Hydrocarbons_Clean.R" was executed on 2018-07-20 20:31:51 GMT
## Tag: "total_pah_and_alkanes_goa_hydrocarbons_clean script1"
## Run sequence #: 1
## Publish date: Not published
## Published to: NA
## Published Id: NA
## View at: NA
## Run by user: eunjungpark
## Account subject: NA
## Run Id: urn:uuid:a323e130-4923-4e49-8259-0433e517beea
## Data package Id: urn:uuid:cc1d66f9-8a2e-4502-88fe-b4bca9d825db
## HostId: eunjeong-bag-ui-MacBook-Pro.local
## Operating system: x86_64-apple-darwin13.4.0
## R version: R version 3.3.3 (2017-03-06)
## Dependencies: stats, graphics, grDevices, utils, datasets, methods, base, httr_1.3.1, bit64_0.9-7, jsonlite_1.5, modelr_0.1.2, assertthat_0.2.0, blob_1.1.1, cellranger_1.1.0, yaml_2.1.16, RSQLite_2.0, pillar_1.2.3, backports_1.1.2, lattice_0.20-35, glue_1.2.0, uuid_0.1-2, digest_0.6.15, redland_1.0.17-9, rvest_0.3.2, EML_1.0.3, colorspace_1.3-2, htmltools_0.3.6, plyr_1.8.4, psych_1.8.4, XML_3.98-1.9, pkgconfig_2.0.1, broom_0.4.4, haven_1.1.1, scales_0.5.0, openssl_1.0.1, withr_2.1.2, lazyeval_0.2.1, cli_1.0.0, mnormt_1.5-5, magrittr_1.5, crayon_1.3.4, readxl_1.1.0, memoise_1.1.0, evaluate_0.10.1, nlme_3.1-131, xml2_1.2.0, parsedate_1.1.3, foreign_0.8-70, tools_3.3.3, hash_2.2.6, hms_0.4.2, V8_1.5, munsell_0.5.0, bindrcpp_0.2.2, rlang_0.2.1, grid_3.3.3, jsonld_2.0, rstudioapi_0.7, rappdirs_0.3.1, base64enc_0.1-3, rmarkdown_1.10, gtable_0.2.0, DBI_1.0.0, roxygen2_6.0.1, curl_3.2, reshape2_1.4.3, R6_2.2.2, lubridate_1.7.4, knitr_1.18, bit_1.1-14, bindr_0.1.1, commonmark_1.5, rprojroot_1.3-2, stringi_1.2.3, parallel_3.3.3, Rcpp_0.12.17, tidyselect_0.2.3, recordr_1.0.3.9000, RColorBrewer_1.1-2, forcats_0.3.0, stringr_1.2.0, dplyr_0.7.6, purrr_0.2.5, readr_1.1.1, tidyr_0.8.1, tibble_1.4.2, ggplot2_3.0.0, tidyverse_1.2.1, raster_2.6-7, rgdal_1.3-3, rgeos_0.3-28, maptools_0.9-2, sp_1.3-1, rdflib_0.1.0, datapack_1.3.1, dataone_2.1.1
## Run start time: 2018-07-20 20:31:51 GMT
## Run end time: 2018-07-20 20:32:01 GMT
## Error message from this run: NA
## 
## [used]: 4 items used by this run
## -----------------------------------
## Location                                                     Size (kb)    Modified time      
## /Users/eunjungpark/Documents...612_027c80855e8d/data/PAH.csv 5525560      2018-06-11 14:21:24
## /Users/eunjungpark/Documents..._027c80855e8d/data/Alkane.csv 3932743      2018-06-11 14:21:24
## /Users/eunjungpark/Documents..._027c80855e8d/data/Sample.csv 1500015      2018-06-11 14:21:24
## /Users/eunjungpark/Documents...855e8d/data/Non-EVOS_SINs.csv 3545         2018-06-11 14:21:24
## 
## [generated]: 1 items generated by this run
## -----------------------------------------
## Location                                                     Size (kb)    Modified time      
## /Users/eunjungpark/Documents...otal_Aromatic_Alkanes_PWS.csv 2795130      2018-07-20 20:32:01
viewRuns(rc, tag="script2")
## [details]: Run details
## ----------------------
## "/Users/eunjungpark/Documents/data...1/transparency/scripts/hcdbSites.R" was executed on 2018-07-20 20:32:02 GMT
## Tag: "hcdbsites script2"
## Run sequence #: 2
## Publish date: Not published
## Published to: NA
## Published Id: NA
## View at: NA
## Run by user: eunjungpark
## Account subject: NA
## Run Id: urn:uuid:b8470053-48fd-4739-a2a8-3c79ccce1739
## Data package Id: urn:uuid:cfa0a1d4-3506-444a-9d3f-6d9206a60d3a
## HostId: eunjeong-bag-ui-MacBook-Pro.local
## Operating system: x86_64-apple-darwin13.4.0
## R version: R version 3.3.3 (2017-03-06)
## Dependencies: stats, graphics, grDevices, utils, datasets, methods, base, httr_1.3.1, bit64_0.9-7, jsonlite_1.5, modelr_0.1.2, assertthat_0.2.0, blob_1.1.1, cellranger_1.1.0, yaml_2.1.16, RSQLite_2.0, pillar_1.2.3, backports_1.1.2, lattice_0.20-35, glue_1.2.0, uuid_0.1-2, digest_0.6.15, redland_1.0.17-9, rvest_0.3.2, EML_1.0.3, colorspace_1.3-2, htmltools_0.3.6, psych_1.8.4, XML_3.98-1.9, pkgconfig_2.0.1, broom_0.4.4, haven_1.1.1, scales_0.5.0, openssl_1.0.1, withr_2.1.2, lazyeval_0.2.1, cli_1.0.0, mnormt_1.5-5, magrittr_1.5, crayon_1.3.4, readxl_1.1.0, memoise_1.1.0, evaluate_0.10.1, nlme_3.1-131, xml2_1.2.0, parsedate_1.1.3, foreign_0.8-70, tools_3.3.3, hash_2.2.6, hms_0.4.2, V8_1.5, munsell_0.5.0, bindrcpp_0.2.2, rlang_0.2.1, grid_3.3.3, jsonld_2.0, rstudioapi_0.7, rappdirs_0.3.1, base64enc_0.1-3, rmarkdown_1.10, gtable_0.2.0, DBI_1.0.0, roxygen2_6.0.1, curl_3.2, reshape2_1.4.3, R6_2.2.2, lubridate_1.7.4, knitr_1.18, bit_1.1-14, bindr_0.1.1, commonmark_1.5, rprojroot_1.3-2, stringi_1.2.3, parallel_3.3.3, Rcpp_0.12.17, tidyselect_0.2.3, plyr_1.8.4, png_0.1-7, recordr_1.0.3.9000, RColorBrewer_1.1-2, forcats_0.3.0, stringr_1.2.0, dplyr_0.7.6, purrr_0.2.5, readr_1.1.1, tidyr_0.8.1, tibble_1.4.2, ggplot2_3.0.0, tidyverse_1.2.1, raster_2.6-7, rgdal_1.3-3, rgeos_0.3-28, maptools_0.9-2, sp_1.3-1, rdflib_0.1.0, datapack_1.3.1, dataone_2.1.1
## Run start time: 2018-07-20 20:32:02 GMT
## Run end time: 2018-07-20 20:32:03 GMT
## Error message from this run: cannot coerce type 'closure' to vector of type 'character'
## 
## [used]: 1 items used by this run
## -----------------------------------
## Location                                                     Size (kb)    Modified time      
## /Users/eunjungpark/Documents...otal_Aromatic_Alkanes_PWS.csv 2954215      2018-06-25 19:21:25
## 
## [generated]: 0 items generated by this run