From 0af49804af1b447ee7d3f5260906f622e85918c3 Mon Sep 17 00:00:00 2001 From: eyackulic <62761629+eyackulic@users.noreply.github.com> Date: Fri, 29 Jan 2021 14:34:07 -0700 Subject: [PATCH 01/10] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index db97223..d3d7c66 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ A short, one paragraph description of the project goes here. This project is an open project, and contributions are welcome from any individual. All contributors to this project are bound by a [code of conduct](CODE_OF_CONDUCT.md). Please review and follow this code of conduct as part of your contribution. - * [Contributor Name1](http://example.com/contributor_url1) [![orcid](https://img.shields.io/badge/orcid-XXXX--XXXX--XXXX--XXXX-brightgreen.svg)](https://orcid.org/XXXX-XXXX-XXXX-XXXX) + * [Ethan Yackulic](http://example.com/contributor_url1) [![orcid](https://img.shields.io/badge/orcid-XXXX--XXXX--XXXX--XXXX-brightgreen.svg)](https://orcid.org/0000-0001-5500-0401) * [Contributor Name2](http://example.com/contributor_url2) [![orcid](https://img.shields.io/badge/orcid-XXXX--XXXX--XXXX--XXXX-brightgreen.svg)](https://orcid.org/XXXX-XXXX-XXXX-XXXX) ### Tips for Contributing From 51482a05706c751e2613fe93eee491b2a4b630db Mon Sep 17 00:00:00 2001 From: eyackulic <62761629+eyackulic@users.noreply.github.com> Date: Fri, 29 Jan 2021 14:36:10 -0700 Subject: [PATCH 02/10] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d3d7c66..a442da8 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ A short, one paragraph description of the project goes here. This project is an open project, and contributions are welcome from any individual. All contributors to this project are bound by a [code of conduct](CODE_OF_CONDUCT.md). Please review and follow this code of conduct as part of your contribution. - * [Ethan Yackulic](http://example.com/contributor_url1) [![orcid](https://img.shields.io/badge/orcid-XXXX--XXXX--XXXX--XXXX-brightgreen.svg)](https://orcid.org/0000-0001-5500-0401) + * [Ethan Yackulic](http://example.com/contributor_url1) [![orcid](https://img.shields.io/badge/orcid-0000--0001--5500--0401-brightgreen.svg)](https://orcid.org/0000-0001-5500-0401) * [Contributor Name2](http://example.com/contributor_url2) [![orcid](https://img.shields.io/badge/orcid-XXXX--XXXX--XXXX--XXXX-brightgreen.svg)](https://orcid.org/XXXX-XXXX-XXXX-XXXX) ### Tips for Contributing From 4aafda7ad4b6519bd7a9391e8b6e7305eaec33ce Mon Sep 17 00:00:00 2001 From: eyackulic <62761629+eyackulic@users.noreply.github.com> Date: Fri, 5 Feb 2021 11:55:15 -0700 Subject: [PATCH 03/10] updated with json files --- .DS_Store | Bin 0 -> 8196 bytes .gitignore | 1 + LIPD-2-CSV.R | 119 ++++++++++++++++++ json_files/117_723A.Godad.2011.json | 15 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a/.gitignore b/.gitignore index 26fad6f..be0b467 100644 --- a/.gitignore +++ b/.gitignore @@ -34,3 +34,4 @@ vignettes/*.pdf # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html rsconnect/ +.Rproj.user diff --git a/LIPD-2-CSV.R b/LIPD-2-CSV.R new file mode 100644 index 0000000..702d6a5 --- /dev/null +++ b/LIPD-2-CSV.R @@ -0,0 +1,119 @@ +remotes::install_github("nickmckay/lipd-utilities",subdir = "R") +remotes::install_github("nickmckay/nuspectral") +remotes::install_github("nickmckay/geoChronR") +install_github("nickmckay/LiPD-Utilities", subdir = "R") + +library(geoChronR) +library(devtools) +library(lipdR) +library(dplyr) + +D=readLipd("~/Desktop/Temp12k1_0_1") +length(D) +#redownload data and rerun + + +e <- D[which(names(D)==naz$dataSetName)] +length(e) +#D=readLipd("~/Desktop/globalHolocene1_0_0") +ts = extractTs(D) +tib <- ts2tibble(ts) + +t2 <- tib%>%group_by(dataSetName)%>%select(geo_description)%>%distinct() +t3 <- t2[!is.na(t2$geo_description),] +naz <- t2[is.na(t2$geo_description),] +da <- subset(D,names(D) %in% naz$dataSetName) + + + +tib[which(is.na(tib$ageUnits)),]%>%select(age) +sel <- tib[which(tib$ageUnits=="unitless"),] +#looking for variables that dont have units +tib[which(is.na(tib$depthUnits)),] +#age units,year, depth units missing +#^start with these + +##level description +##dataset level +tib$dataSetName +t2 <- tib%>%group_by(dataSetName)%>%select(geo_description)%>%distinct() +t3 <- t2[!is.na(t2$geo_description),] +naz <- t2[is.na(t2$geo_description),] + +t2[which(is.na(t2)),] +dim(t2) +tib[which(is.na(tib$geo_description)),] +tib[which(is.na(tib$geo_location)),] +tib[which(is.na(tib$geo_notes)),] +tib[which(is.na(tib$chronDoi)),] + +#geographic metadata easy to visualize/understand + + +#annotations for units should be at #column level +#unique identifier for column +tib$paleoData_TSid + + +##site descriptions missing? +head(sel) + +tib2<-tib[,c(26:38,41:49,301:391)] +as.data.frame(tib2[1,70:106]) +tib%>% select() + +godad <- D$`117_723A.Godad.2011`$pub +D$Deep.Shuman.2016 + + library(rlist) +library(dplyr) +pubz <- D%>% + list.select(pub) + +library(naniar) +head(pubz) +class(tib2) +tibby %>% replace_with_na(replace = list(x = )) +tibby <- data.frame(tib2) + +tibby$pub1_author <- with(tibby, rep(pub1_author, lengths(dataSetName))) +tibby$pub1_author[sapply(tibby$pub1_author, function(x) length(x)==0L)] <- NA +tibby$pub1_author <- gsub("name","",tibby$pub1_author) +tibby$pub1_author <- unlist(tibby$pub1_author) + +tibby$pub2_author <- with(tibby, rep(pub2_author, lengths(dataSetName))) +tibby$pub2_author[sapply(tibby$pub2_author, function(x) length(x)==0L)] <- NA +tibby$pub2_author <- gsub("name","",tibby$pub2_author) +tibby$pub2_author <- unlist(tibby$pub2_author) + +tibby$pub3_author <- with(tibby, rep(pub3_author, lengths(dataSetName))) +tibby$pub3_author[sapply(tibby$pub3_author, function(x) length(x)==0L)] <- NA +tibby$pub3_author <- gsub("name","",tibby$pub3_author) +tibby$pub3_author <- unlist(tibby$pub3_author) + +tibby$pub4_author <- with(tibby, rep(pub4_author, lengths(dataSetName))) +tibby$pub4_author[sapply(tibby$pub4_author, function(x) length(x)==0L)] <- NA +tibby$pub4_author <- gsub("name","",tibby$pub4_author) +tibby$pub4_author <- unlist(tibby$pub4_author) + +tibby$pub5_author <- with(tibby, rep(pub5_author, lengths(dataSetName))) +tibby$pub5_author[sapply(tibby$pub5_author, function(x) length(x)==0L)] <- NA +tibby$pub5_author <- gsub("name","",tibby$pub5_author) +tibby$pub5_author <- unlist(tibby$pub5_author) + +write.csv(tibby,file = "allPubData.csv") + +#plut into database structure -- take a stab at it +#cypher script to pull into neo4j from csv +#work on the ruler with the core photo +#separate routine -- takes pnj +#a nice, plotrgb function +#email Kim about paleo-seminar + + + + +#for(i in 1:length(annot)){ +# a[i] <- rjson::fromJSON(annot[[i]]) +# stack(a) +#} diff --git a/json_files/117_723A.Godad.2011.json b/json_files/117_723A.Godad.2011.json new 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geo description" +} diff --git a/json_files/Zabieniec.Plociennik.2011.json b/json_files/Zabieniec.Plociennik.2011.json new file mode 100644 index 0000000..b92d844 --- /dev/null +++ b/json_files/Zabieniec.Plociennik.2011.json @@ -0,0 +1,15 @@ +{ + "dbid": "lipdRe3Placeholder", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "WWgp2nXnhjbJjfElW7o3" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/brurskardstjorni.Velle.2005.json b/json_files/brurskardstjorni.Velle.2005.json new file mode 100644 index 0000000..632e9f5 --- /dev/null +++ b/json_files/brurskardstjorni.Velle.2005.json @@ -0,0 +1,15 @@ +{ + "dbid": "lipdRe3Placeholder", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "mCgUSWeP4uNUtjBefops" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/klotjarnen.Seppa.2009.json b/json_files/klotjarnen.Seppa.2009.json new file mode 100644 index 0000000..f55222e --- /dev/null +++ b/json_files/klotjarnen.Seppa.2009.json @@ -0,0 +1,15 @@ +{ + "dbid": "lipdRe3Placeholder", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "7QPHJmiK8y5lhLxXxSYk" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/rainbow.Clegg.2011.json b/json_files/rainbow.Clegg.2011.json new file mode 100644 index 0000000..52b6495 --- /dev/null +++ b/json_files/rainbow.Clegg.2011.json @@ -0,0 +1,15 @@ +{ + "dbid": "lipdRe3Placeholder", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "FvAJXMecx1fSF5di3i0E" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/s53s52.KaislahtiTillman.2010.json b/json_files/s53s52.KaislahtiTillman.2010.json new file mode 100644 index 0000000..6d31094 --- /dev/null +++ b/json_files/s53s52.KaislahtiTillman.2010.json @@ -0,0 +1,15 @@ +{ + "dbid": "lipdRe3Placeholder", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "6p7m4YXujrmSNtYTQrFK" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/sjuuodjijaure.Rosen.2001.json b/json_files/sjuuodjijaure.Rosen.2001.json new file mode 100644 index 0000000..4aac755 --- /dev/null +++ b/json_files/sjuuodjijaure.Rosen.2001.json @@ -0,0 +1,15 @@ +{ + "dbid": "lipdRe3Placeholder", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "dOAcAkxAQzeBF0ZXxJE8" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/vikjordvatnet.Balascio.2012.json b/json_files/vikjordvatnet.Balascio.2012.json new file mode 100644 index 0000000..94a4ac6 --- /dev/null +++ b/json_files/vikjordvatnet.Balascio.2012.json @@ -0,0 +1,15 @@ +{ + "dbid": "lipdRe3Placeholder", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "rFrrtgeDpAD9zjpB4xT5" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/vuoskkujavri.Bigler.2002.json b/json_files/vuoskkujavri.Bigler.2002.json new file mode 100644 index 0000000..4633726 --- /dev/null +++ b/json_files/vuoskkujavri.Bigler.2002.json @@ -0,0 +1,15 @@ +{ + "dbid": "lipdRe3Placeholder", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "gU8V0V0IFwoUQy0lRPr0" +} +], +"body": "These sites are missing a geo description" +} diff --git a/notes.R b/notes.R new file mode 100644 index 0000000..c2b8505 --- /dev/null +++ b/notes.R @@ -0,0 +1,16 @@ +#general datasets to annotate for coding, funding, + +#figure out how to add date, modify, access, etc +#HOW TO CREATE OWN ANNOTATIONS IN NEO4J, HOW TO QUERY + +#lets organize all of the annotations from lipd and show connections +#funding metadata + + +#keep a google sheet for metadata -- all of the annotations that we are putting in +#get to working on lipd filies + +http://nickmckay.github.io/LiPD-utilities/r/index.html +https://github.com/nickmckay/LiPD-utilities +http://nickmckay.github.io/GeoChronR/ +https://lipdverse.org/Temp12k/current_version/ \ No newline at end of file diff --git a/src/.DS_Store b/src/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6 GIT binary patch literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0% + pullTsVariable("paleoData_variableName") %>% + setdiff(c("age","depth","year")) + + if(length(variables) > 2){ + variables <- paste(variables,collapse= ", ") %>% + stringr::str_replace(pattern = "(?=[^,]*$)",replacement = " and") + }else if(length(variables) == 2){ + variables <- paste(variables,collapse= ", ") %>% + stringr::str_replace(pattern = ",",replacement = " and") + } + + + if(noLoc){ + descstring <- glue::glue("This dataset is derived from a {L$archiveType} archive, and includes data on {variables}. The data are relevant to the time interval {durstring}.") + }else{ + descstring <- glue::glue("This dataset from {locstring} is derived from a {L$archiveType} archive, and includes data on {variables}. The data are relevant to the time interval {durstring}.") + } + + return(descstring) + +} + diff --git a/streamlined.R b/streamlined.R new file mode 100644 index 0000000..d69cceb --- /dev/null +++ b/streamlined.R @@ -0,0 +1,29 @@ + +#If its got a missing value, post an annotation that says its missing values +#change function to take large set of values +#maybe create for loop that looks first for condition and then creates annotation if ==yes + + +remotes::install_github("nickmckay/lipd-utilities",subdir = "R") +remotes::install_github("nickmckay/nuspectral") +remotes::install_github("nickmckay/geoChronR") +install_github("nickmckay/LiPD-Utilities", subdir = "R") + +library(geoChronR) +library(devtools) +library(lipdR) +library(dplyr) + +D=readLipd("https://lipdverse.org/Temp12k/1_0_2/Temp12k1_0_2.zip") +ts = extractTs(D) +tib <- ts2tibble(ts) + +t2 <- tib%>%group_by(dataSetName)%>%select(geo_description)%>%distinct() +naz <- t2[is.na(t2$geo_description),] +da <- subset(D,names(D) %in% naz$dataSetName) + +output <- list(length=length(da)) +for (i in 1:length(da)) { + output[[i]] <- createThroughputJson(L=da[[i]]) +} + diff --git a/throughput-lipd.Rproj b/throughput-lipd.Rproj new file mode 100644 index 0000000..8e3c2eb --- /dev/null +++ b/throughput-lipd.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX diff --git a/tmp.json b/tmp.json new file mode 100644 index 0000000..e69de29 diff --git a/trial.R b/trial.R new file mode 100644 index 0000000..161d769 --- /dev/null +++ b/trial.R @@ -0,0 +1,31 @@ +createThroughputJson <- function(L){ + + J <- list() + + #static + J[["dbid"]] <- "lipdRe3Placeholder" + J[["orcid"]] <- "https://orcid.org/0000-0001-5500-0401" + + + + #objects + J[["objects"]] <- vector(mode = "list",length = 2) #preallocate empty list + J[["objects"]][[1]][["type"]] <- "dataset" #Does this describe the annotation? + J[["objects"]][[1]][["id"]] <- "annotationId?" #how generate this? + + + J[["objects"]][[2]][["additionalType"]] <- "http://linked.earth/ontology#Dataset" + J[["objects"]][[2]][["dataid"]] <- L[[]]$datasetId + + J[["body"]] <- "These sites are missing a geo description" + + return(J) +} +#write to json +# json <- RJSONIO::toJSON(x = J) + +# writeLines(json, con = "~/Downloads/test.json") + +# return(json) +#} +for i in 1:length(L){ \ No newline at end of file From 14408ab6572e03ea1ca649a4f2ce7fe7fd4bbe53 Mon Sep 17 00:00:00 2001 From: eyackulic <62761629+eyackulic@users.noreply.github.com> Date: Fri, 5 Feb 2021 11:58:27 -0700 Subject: [PATCH 04/10] updates --- .DS_Store | Bin 8196 -> 8196 bytes ...roughput_JSON.R => createThroughputJson.R} | 0 streamlined.R | 10 +++--- tmp.json | 0 workflow.R | 29 ++++++++++++++++++ .../LIPD-2-CSV.R | 0 notes.R => works_in_progress/notes.R | 0 trial.R => works_in_progress/trial.R | 0 8 files changed, 34 insertions(+), 5 deletions(-) rename src/{Throughput_JSON.R => createThroughputJson.R} (100%) delete mode 100644 tmp.json create mode 100644 workflow.R rename LIPD-2-CSV.R => works_in_progress/LIPD-2-CSV.R (100%) rename notes.R => works_in_progress/notes.R (100%) rename trial.R => works_in_progress/trial.R (100%) diff --git a/.DS_Store b/.DS_Store index fd0035b9744cf2e0c19a798dca34674085784fbe..114edf3bd8a164f58e1af0f1da58d7a3b63399b9 100644 GIT binary patch delta 259 zcmZp1XmOa}&nUDpU^hRb&}JTiolKLpg(D{K751tZWGH9IXDDLGW+-NeXUJs81Cj+m zem+AwkW2-N7U!fJ1}Ep|7BC5Ro@VQzj3 Y5n8e7EXY7{>Skx2Bg~uGCH}Gl0G&}i)c^nh delta 262 zcmZp1XmOa}&nUbxU^hRb@Ma!?olMa@3_c8=3;_%-47vQ<2I$-9J-^?8BvB@9JCb%_kQ z3^@#$Kz*qUDVTZ~RswC|m@Fh58p#3Fk;_m3RFehNozIYm>J|oTkV+J{fNaPF+K_{3 RF5_pATOg`8Cx|TJ1_0sZLZ1Kt diff --git a/src/Throughput_JSON.R b/src/createThroughputJson.R similarity index 100% rename from src/Throughput_JSON.R rename to src/createThroughputJson.R diff --git a/streamlined.R b/streamlined.R index d69cceb..8b9cc42 100644 --- a/streamlined.R +++ b/streamlined.R @@ -4,13 +4,13 @@ #maybe create for loop that looks first for condition and then creates annotation if ==yes -remotes::install_github("nickmckay/lipd-utilities",subdir = "R") -remotes::install_github("nickmckay/nuspectral") -remotes::install_github("nickmckay/geoChronR") -install_github("nickmckay/LiPD-Utilities", subdir = "R") +#remotes::install_github("nickmckay/lipd-utilities",subdir = "R") +#remotes::install_github("nickmckay/nuspectral") +#remotes::install_github("nickmckay/geoChronR") +#install_github("nickmckay/LiPD-Utilities", subdir = "R") library(geoChronR) -library(devtools) +#library(devtools) library(lipdR) library(dplyr) diff --git a/tmp.json b/tmp.json deleted file mode 100644 index e69de29..0000000 diff --git a/workflow.R b/workflow.R new file mode 100644 index 0000000..d69cceb --- /dev/null +++ b/workflow.R @@ -0,0 +1,29 @@ + +#If its got a missing value, post an annotation that says its missing values +#change function to take large set of values +#maybe create for loop that looks first for condition and then creates annotation if ==yes + + +remotes::install_github("nickmckay/lipd-utilities",subdir = "R") +remotes::install_github("nickmckay/nuspectral") +remotes::install_github("nickmckay/geoChronR") +install_github("nickmckay/LiPD-Utilities", subdir = "R") + +library(geoChronR) +library(devtools) +library(lipdR) +library(dplyr) + +D=readLipd("https://lipdverse.org/Temp12k/1_0_2/Temp12k1_0_2.zip") +ts = extractTs(D) +tib <- ts2tibble(ts) + +t2 <- tib%>%group_by(dataSetName)%>%select(geo_description)%>%distinct() +naz <- t2[is.na(t2$geo_description),] +da <- subset(D,names(D) %in% naz$dataSetName) + +output <- list(length=length(da)) +for (i in 1:length(da)) { + output[[i]] <- createThroughputJson(L=da[[i]]) +} + diff --git a/LIPD-2-CSV.R b/works_in_progress/LIPD-2-CSV.R similarity index 100% rename from LIPD-2-CSV.R rename to works_in_progress/LIPD-2-CSV.R diff --git a/notes.R b/works_in_progress/notes.R similarity index 100% rename from notes.R rename to works_in_progress/notes.R diff --git a/trial.R b/works_in_progress/trial.R similarity index 100% rename from trial.R rename to works_in_progress/trial.R From 73ec07be942893a305448e07f941cffa6981baaf Mon Sep 17 00:00:00 2001 From: eyackulic <62761629+eyackulic@users.noreply.github.com> Date: Fri, 5 Feb 2021 11:58:57 -0700 Subject: [PATCH 05/10] Delete streamlined.R --- streamlined.R | 29 ----------------------------- 1 file changed, 29 deletions(-) delete mode 100644 streamlined.R diff --git a/streamlined.R b/streamlined.R deleted file mode 100644 index 8b9cc42..0000000 --- a/streamlined.R +++ /dev/null @@ -1,29 +0,0 @@ - -#If its got a missing value, post an annotation that says its missing values -#change function to take large set of values -#maybe create for loop that looks first for condition and then creates annotation if ==yes - - -#remotes::install_github("nickmckay/lipd-utilities",subdir = "R") -#remotes::install_github("nickmckay/nuspectral") -#remotes::install_github("nickmckay/geoChronR") -#install_github("nickmckay/LiPD-Utilities", subdir = "R") - -library(geoChronR) -#library(devtools) -library(lipdR) -library(dplyr) - -D=readLipd("https://lipdverse.org/Temp12k/1_0_2/Temp12k1_0_2.zip") -ts = extractTs(D) -tib <- ts2tibble(ts) - -t2 <- tib%>%group_by(dataSetName)%>%select(geo_description)%>%distinct() -naz <- t2[is.na(t2$geo_description),] -da <- subset(D,names(D) %in% naz$dataSetName) - -output <- list(length=length(da)) -for (i in 1:length(da)) { - output[[i]] <- createThroughputJson(L=da[[i]]) -} - From b0e089a3d079dad18472f74e577207a20b651799 Mon Sep 17 00:00:00 2001 From: eyackulic <62761629+eyackulic@users.noreply.github.com> Date: Fri, 5 Feb 2021 12:16:39 -0700 Subject: [PATCH 06/10] gitignore update --- .DS_Store | Bin 8196 -> 8196 bytes .gitignore | 1 + json_files/117_723A.Godad.2011.json | 2 +- 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.../SouthernCalifornia.Ohlwein.2012.json | 2 +- json_files/Soylegrotta.Lauritzen.1999.json | 2 +- json_files/Spaime.Hammarlund.2004.json | 2 +- json_files/Spannagel.Fohlmeister.2012.json | 2 +- json_files/SprucePond.Shuman.2016.json | 2 +- json_files/StaroselskyMoch.Novenko.2018.json | 2 +- json_files/Starvatn.Andresen.2008.json | 2 +- json_files/Station803.Bringue.2012.json | 2 +- json_files/Stazersee.Heiri.2015.json | 2 +- json_files/Steel.Shuman.2016.json | 2 +- json_files/StellaLake.Reinemann.2009.json | 2 +- json_files/Sutherland.Shuman.2016.json | 2 +- json_files/Svanavatnet.Bjune.2008.json | 2 +- json_files/Svartvatnet-Norway.Seppa.2009.json | 2 +- .../Svartvatnet-Svalbard.Luoto.2018.json | 2 +- json_files/TALDICE.Mezgec.2017.json | 2 +- json_files/TK2.Porinchu.2019.json | 2 +- json_files/TN057-17.Nielsen.2004.json | 2 +- json_files/TN062-0550.Barron.2018.json | 2 +- json_files/TR163_22.Lea.2006.json | 2 +- json_files/TR163_31.Dubois.2009.json | 2 +- json_files/TTR17_434G.Rodrigo-Gamiz.2014.json | 2 +- json_files/TalkinTarn.Langdon.2004.json | 2 +- json_files/TanaLake.Loomis.2015.json | 2 +- json_files/Tanganyika.Tierney.2008.json | 2 +- json_files/TangledUpLake.Anderson.2001.json | 2 +- json_files/TaulMuced.Diaconu.2017.json | 2 +- json_files/TauldintreBrazi.Toth.2015.json | 2 +- json_files/Temje.Nazarova.2013.json | 2 +- json_files/TiancaiLake.Zhang.2017.json | 2 +- json_files/Tiavatnet.Seppa.2009.json | 2 +- json_files/Tibetanus.Hammarlund.2002.json | 2 +- json_files/Tigalmamine.Cheddadi.1998.json | 2 +- json_files/Topptjonna.Paus.2011.json | 2 +- json_files/Tornetrask.Grudd.2002.json | 2 +- json_files/Toskaljavri.Seppa.2002.json | 2 +- .../TourbieredeLanorieHenri.Comtois.1982.json | 2 +- ...TourbieredeLanorieStJean.Comtois.1982.json | 2 +- json_files/Trehorningen.Antonsson.2007.json | 2 +- json_files/Trettetjorn.Bjune.2005.json | 2 +- .../Troll28-03.Klitgard-Kristensen.2001.json | 2 +- json_files/Trout.Irvine.2012.json | 2 +- json_files/Tsuolbmajavri.Korhola.2002.json | 2 +- json_files/Tumbulovaty.Kultti.2004.json | 2 +- json_files/Turkana.Berke.2012.json | 2 +- json_files/TwoYourtsLake.Nazarova.2013.json | 2 +- json_files/UpperFly.Bunbury.2009.json | 2 +- json_files/VM12_107.Schmidt.2012.json | 2 +- json_files/VM21_30.Koutavas.2003.json | 2 +- json_files/VM28_122.Schmidt.2004.json | 2 +- json_files/Valiranta.Kharinei.2015.json | 2 +- json_files/Vatnamyri.Holmes.2011.json | 2 +- json_files/VestreOykjamytjorn.Velle.2005.json | 2 +- json_files/Victoria.Berke.2012.json | 2 +- json_files/Vostok.Vimeux.2002.json | 2 +- json_files/Vuoksjavratje.Berntsson.2014.json | 2 +- .../VuolepNjakajaure.Heinrichs.2006.json | 2 +- json_files/WAISDivide.Cuffey.2016.json | 2 +- json_files/WAISDivide.Fegyveresi.2016.json | 2 +- .../WCA3BGumboLimboFarTail.Willard.2001.json | 2 +- .../WCA3BGumboLimboMarsh.Willard.2001.json | 2 +- json_files/WIND28K.Kiefer.2006.json | 2 +- json_files/Wachel3.Doerfler.1989.json | 2 +- json_files/Waskey.Levy.2004.json | 2 +- json_files/WestOkoboji.VanZant.1979.json | 2 +- json_files/WhitePond.Krause.2019.json | 2 +- json_files/Windy.Chase.2008.json | 2 +- json_files/Wonderkrater.Truc.2013.json | 2 +- json_files/Ximencuo.Herzschuh.2014.json | 2 +- json_files/XingyunLake.Wu.2018.json | 2 +- json_files/Yakumo.Leipe.2013.json | 2 +- json_files/Yanou.Foster.2016.json | 2 +- json_files/Yarnyshnoe.Seppa.2008.json | 2 +- json_files/Zabieniec.Plociennik.2011.json | 2 +- json_files/brurskardstjorni.Velle.2005.json | 2 +- json_files/klotjarnen.Seppa.2009.json | 2 +- json_files/rainbow.Clegg.2011.json | 2 +- json_files/s53s52.KaislahtiTillman.2010.json | 2 +- json_files/sjuuodjijaure.Rosen.2001.json | 2 +- json_files/vikjordvatnet.Balascio.2012.json | 2 +- json_files/vuoskkujavri.Bigler.2002.json | 2 +- src/JSON_Annotation.R | 16 ++++++++++++++++ 623 files changed, 637 insertions(+), 620 deletions(-) create mode 100644 src/JSON_Annotation.R diff --git a/.DS_Store b/.DS_Store index 114edf3bd8a164f58e1af0f1da58d7a3b63399b9..c258c15a847088d7fbf5de3aba67c93a18989139 100644 GIT binary patch delta 51 zcmV-30L=e{K!iZB{SX1kll~BZ3mAKQGcY$dEFdv9lZp`?0hyDi5g!4XlkgE3v)~bD J0<%UGz6kZSF*!LoEFdv5Gn0uC9RZq?rx70ko0IPm7_;9I KX9BZF6uk@j?Gl3k diff --git a/.gitignore b/.gitignore index be0b467..49422ab 100644 --- a/.gitignore +++ b/.gitignore @@ -35,3 +35,4 @@ vignettes/*.pdf # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html rsconnect/ .Rproj.user +token.R diff --git a/json_files/117_723A.Godad.2011.json b/json_files/117_723A.Godad.2011.json index 8e33afe..e930a76 100644 --- a/json_files/117_723A.Godad.2011.json +++ b/json_files/117_723A.Godad.2011.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/161_976.Martrat.2014.json b/json_files/161_976.Martrat.2014.json index aba0271..0ae1800 100644 --- a/json_files/161_976.Martrat.2014.json +++ b/json_files/161_976.Martrat.2014.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/165_1002C.Herbert.2000.json b/json_files/165_1002C.Herbert.2000.json index f60db41..7237aec 100644 --- a/json_files/165_1002C.Herbert.2000.json +++ b/json_files/165_1002C.Herbert.2000.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/2005-804-006.Ledu.2010.json b/json_files/2005-804-006.Ledu.2010.json index 1583e33..357ab71 100644 --- a/json_files/2005-804-006.Ledu.2010.json +++ b/json_files/2005-804-006.Ledu.2010.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/31Lake.Eisner.1995.json b/json_files/31Lake.Eisner.1995.json index 24953a7..6416208 100644 --- a/json_files/31Lake.Eisner.1995.json +++ b/json_files/31Lake.Eisner.1995.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/3MPond.Pellatt.2000.json b/json_files/3MPond.Pellatt.2000.json index 1386c01..a378318 100644 --- a/json_files/3MPond.Pellatt.2000.json +++ b/json_files/3MPond.Pellatt.2000.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/850Lake.Shemesh.2001.json b/json_files/850Lake.Shemesh.2001.json index be07ab2..9fb63c1 100644 --- a/json_files/850Lake.Shemesh.2001.json +++ b/json_files/850Lake.Shemesh.2001.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/893A.Kennet.2007.json b/json_files/893A.Kennet.2007.json index ca0c4de..50d93f8 100644 --- a/json_files/893A.Kennet.2007.json +++ b/json_files/893A.Kennet.2007.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/A7.Sun.2005.json b/json_files/A7.Sun.2005.json index 891d20a..f685c36 100644 --- a/json_files/A7.Sun.2005.json +++ b/json_files/A7.Sun.2005.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/AMP112.vanderBilt.2016.json b/json_files/AMP112.vanderBilt.2016.json index 2215ba4..69819a3 100644 --- a/json_files/AMP112.vanderBilt.2016.json +++ b/json_files/AMP112.vanderBilt.2016.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/Abalone.Cole.1994.json b/json_files/Abalone.Cole.1994.json index 9f909eb..cca63c9 100644 --- a/json_files/Abalone.Cole.1994.json +++ b/json_files/Abalone.Cole.1994.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/AdelaideTarn.Jara.2015.json b/json_files/AdelaideTarn.Jara.2015.json index a57d80d..ce47567 100644 --- a/json_files/AdelaideTarn.Jara.2015.json +++ b/json_files/AdelaideTarn.Jara.2015.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/Agassiz.Lecavalier.2017.json b/json_files/Agassiz.Lecavalier.2017.json index b890a00..20ea7d5 100644 --- a/json_files/Agassiz.Lecavalier.2017.json +++ b/json_files/Agassiz.Lecavalier.2017.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git 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a/json_files/Waskey.Levy.2004.json +++ b/json_files/Waskey.Levy.2004.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/WestOkoboji.VanZant.1979.json b/json_files/WestOkoboji.VanZant.1979.json index a1ddb76..d367eca 100644 --- a/json_files/WestOkoboji.VanZant.1979.json +++ b/json_files/WestOkoboji.VanZant.1979.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/WhitePond.Krause.2019.json b/json_files/WhitePond.Krause.2019.json index 74d4f36..8278012 100644 --- a/json_files/WhitePond.Krause.2019.json +++ b/json_files/WhitePond.Krause.2019.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/Windy.Chase.2008.json b/json_files/Windy.Chase.2008.json index 7fc5758..76c6f75 100644 --- a/json_files/Windy.Chase.2008.json +++ b/json_files/Windy.Chase.2008.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/Wonderkrater.Truc.2013.json b/json_files/Wonderkrater.Truc.2013.json index f9aade8..a0aa285 100644 --- a/json_files/Wonderkrater.Truc.2013.json +++ b/json_files/Wonderkrater.Truc.2013.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/Ximencuo.Herzschuh.2014.json b/json_files/Ximencuo.Herzschuh.2014.json index aed496b..cd29acb 100644 --- a/json_files/Ximencuo.Herzschuh.2014.json +++ b/json_files/Ximencuo.Herzschuh.2014.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/XingyunLake.Wu.2018.json b/json_files/XingyunLake.Wu.2018.json index 2b9f75c..c579cbe 100644 --- a/json_files/XingyunLake.Wu.2018.json +++ b/json_files/XingyunLake.Wu.2018.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/Yakumo.Leipe.2013.json b/json_files/Yakumo.Leipe.2013.json index 2f76644..cfc8129 100644 --- a/json_files/Yakumo.Leipe.2013.json +++ b/json_files/Yakumo.Leipe.2013.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/Yanou.Foster.2016.json b/json_files/Yanou.Foster.2016.json index bb47b7b..c8ef910 100644 --- a/json_files/Yanou.Foster.2016.json +++ b/json_files/Yanou.Foster.2016.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/Yarnyshnoe.Seppa.2008.json b/json_files/Yarnyshnoe.Seppa.2008.json index 2ba4059..1fb6c3b 100644 --- a/json_files/Yarnyshnoe.Seppa.2008.json +++ b/json_files/Yarnyshnoe.Seppa.2008.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/Zabieniec.Plociennik.2011.json b/json_files/Zabieniec.Plociennik.2011.json index b92d844..d4f42c3 100644 --- a/json_files/Zabieniec.Plociennik.2011.json +++ b/json_files/Zabieniec.Plociennik.2011.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/brurskardstjorni.Velle.2005.json b/json_files/brurskardstjorni.Velle.2005.json index 632e9f5..1990679 100644 --- a/json_files/brurskardstjorni.Velle.2005.json +++ b/json_files/brurskardstjorni.Velle.2005.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/klotjarnen.Seppa.2009.json b/json_files/klotjarnen.Seppa.2009.json index f55222e..556bb2e 100644 --- a/json_files/klotjarnen.Seppa.2009.json +++ b/json_files/klotjarnen.Seppa.2009.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/rainbow.Clegg.2011.json b/json_files/rainbow.Clegg.2011.json index 52b6495..cc07e00 100644 --- a/json_files/rainbow.Clegg.2011.json +++ b/json_files/rainbow.Clegg.2011.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/s53s52.KaislahtiTillman.2010.json b/json_files/s53s52.KaislahtiTillman.2010.json index 6d31094..0266506 100644 --- a/json_files/s53s52.KaislahtiTillman.2010.json +++ b/json_files/s53s52.KaislahtiTillman.2010.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/sjuuodjijaure.Rosen.2001.json b/json_files/sjuuodjijaure.Rosen.2001.json index 4aac755..90104a4 100644 --- a/json_files/sjuuodjijaure.Rosen.2001.json +++ b/json_files/sjuuodjijaure.Rosen.2001.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/vikjordvatnet.Balascio.2012.json b/json_files/vikjordvatnet.Balascio.2012.json index 94a4ac6..4957134 100644 --- a/json_files/vikjordvatnet.Balascio.2012.json +++ b/json_files/vikjordvatnet.Balascio.2012.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/json_files/vuoskkujavri.Bigler.2002.json b/json_files/vuoskkujavri.Bigler.2002.json index 4633726..5aa0db7 100644 --- a/json_files/vuoskkujavri.Bigler.2002.json +++ b/json_files/vuoskkujavri.Bigler.2002.json @@ -1,5 +1,5 @@ { - "dbid": "lipdRe3Placeholder", + "dbid": "r3d100012894", "orcid": "https://orcid.org/0000-0001-5500-0401", "objects": [ { diff --git a/src/JSON_Annotation.R b/src/JSON_Annotation.R new file mode 100644 index 0000000..8ea91e3 --- /dev/null +++ b/src/JSON_Annotation.R @@ -0,0 +1,16 @@ +JSONannotation <- function(L){ + J <- list() + + #static + J[["dbid"]] <- "r3d100012894" + J[["orcid"]] <- "0000-0001-5500-0401" + J[["additionalType"] <- "http://linked.earth/ontology#Dataset" + + J[["id"]] <- L$datasetId#L[[i]]$datasetId + + J[["body"]] <- "These sites are missing a geo description" + J[["token"]] <- #secret token + json <- RJSONIO::toJSON(x = J) + writeLines(json, con = paste0("~/Documents/Github/throughput-lipd/json_files/",L$dataSetName,".json")) + return(json) +} \ No newline at end of file From aec20113cd622484fb0e1f4d5eafe239db7bf9ea Mon Sep 17 00:00:00 2001 From: eyackulic <62761629+eyackulic@users.noreply.github.com> Date: Fri, 5 Feb 2021 12:35:52 -0700 Subject: [PATCH 07/10] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index a442da8..a0f6b98 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ [![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) -[![NSF-XXXXXXX](https://img.shields.io/badge/NSF-XXXXXXX-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=XXXXXXX) [![NSF-XXXXXXX](https://img.shields.io/badge/NSF-XXXXXXX-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=XXXXXXX) +[![NSF-1928320](https://img.shields.io/badge/NSF-1928320-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1928320) [![NSF-XXXXXXX](https://img.shields.io/badge/NSF-XXXXXXX-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=XXXXXXX) # Project Name From b349f379280752b607d641aa475c45e7f1713aa7 Mon Sep 17 00:00:00 2001 From: SimonGoring Date: Fri, 5 Feb 2021 12:46:19 -0800 Subject: [PATCH 08/10] Cleaning up code to reflect new API structure. Some stylistic changes, other changes to reflect the changing API endpoint. --- src/createThroughputJson.R | 134 ++++++------------------------------- workflow.R | 25 ++++--- 2 files changed, 35 insertions(+), 124 deletions(-) diff --git a/src/createThroughputJson.R b/src/createThroughputJson.R index 6afb5cb..d028516 100644 --- a/src/createThroughputJson.R +++ b/src/createThroughputJson.R @@ -1,114 +1,22 @@ -createThroughputJson <- function(L){ - J <- list() - - #static - J[["dbid"]] <- "r3d100012894" - J[["orcid"]] <- "https://orcid.org/0000-0001-5500-0401" - - - - #objects - J[["objects"]] <- vector(mode = "list",length = 2) #preallocate empty list - J[["objects"]][[1]][["type"]] <- "dataset" #Does this describe the annotation? - J[["objects"]][[1]][["id"]] <- "annotationId?" #how generate this? - - - #J[["objects"]][[2]][["level"]] <- "dataset" - J[["objects"]][[2]][["additionalType"]] <- "http://linked.earth/ontology#Dataset" - - J[["objects"]][[2]][["dataid"]] <- L$datasetId#L[[i]]$datasetId - - J[["body"]] <- "These sites are missing a geo description" - #J[["body"]] <- createDescription(L) - #for a publication DOI - #J[["body"]] <- L$pub[[1]]$doi - - #write to json - #return(J) -#} - - json <- RJSONIO::toJSON(x = J) - writeLines(json, con = paste0("~/Documents/Github/throughput-lipd/json_files/",L$dataSetName,".json")) - return(json) -} - - -createDescription <- function(L){ - #https://developers.google.com/search/docs/data-types/dataset#dataset - - #current goal. Automate description using 1) Location, 2) Duration 3) variables and 4) archive type - - #location - sn <- L$geo$siteName - gcmd <- L$geo$gcmdLocation - - if(is.null(sn)){ - noLoc <- TRUE - }else{ - noLoc <- FALSE - } - - if(is.null(gcmd)){ - locstring <- sn - }else{ - locstring <- glue::glue("{sn} ({gcmd})") - } - - #duration - ts <- extractTs(L) - ages <- try(pullTsVariable(ts,"age"),silent = TRUE) - years <- try(pullTsVariable(ts,"year"),silent = TRUE) - au <- try(pullTsVariable(ts,"ageUnits"),silent = TRUE) - yu <- try(pullTsVariable(ts,"yearUnits"),silent = TRUE) - - noDur <- FALSE - if(class(ages) != "try-error"){#lets go - if(is.list(ages)){ - young <- min(sapply(ages,min,na.rm = TRUE)) - old <- max(sapply(ages,max,na.rm = TRUE)) - }else{ - young <- min(ages,na.rm = TRUE) - old <- max(ages,na.rm = TRUE) - } - units <- unique(au)[1] - }else if(class(years) != "try-error"){ - if(is.list(years)){ - young <- max(sapply(ages,max,na.rm = TRUE)) - old <- min(sapply(ages,min,na.rm = TRUE)) - }else{ - young <- max(years,na.rm = TRUE) - old <- min(years,na.rm = TRUE) - } - units <- unique(yu)[1] - }else{ - noDur <- TRUE +JSONannotation <- function(lipdObject, additionalType, body, tokenFile){ + + token <- readr::read_file(tokenFile) + + postObject <- list(dbid = "r3d100012894", + orcid = "0000-0001-5500-0401", + additionalType = additionalType, + id = lipdObject$datasetId, + body = body, + token = token) + + postTest <- httr::POST("http://localhost:3000/api/widget", + body = postObject, + encode = "json") + + if (postTest$status_code == 200) { + message("Success!") + return(NULL) + } else { + return(postTest) } - - if(!noDur){ - durstring <- glue::glue("from {round(old)} to {round(young)} ({units})") - } - - #variables - variables <- extractTs(L) %>% - pullTsVariable("paleoData_variableName") %>% - setdiff(c("age","depth","year")) - - if(length(variables) > 2){ - variables <- paste(variables,collapse= ", ") %>% - stringr::str_replace(pattern = "(?=[^,]*$)",replacement = " and") - }else if(length(variables) == 2){ - variables <- paste(variables,collapse= ", ") %>% - stringr::str_replace(pattern = ",",replacement = " and") - } - - - if(noLoc){ - descstring <- glue::glue("This dataset is derived from a {L$archiveType} archive, and includes data on {variables}. The data are relevant to the time interval {durstring}.") - }else{ - descstring <- glue::glue("This dataset from {locstring} is derived from a {L$archiveType} archive, and includes data on {variables}. The data are relevant to the time interval {durstring}.") - } - - return(descstring) - -} - +} \ No newline at end of file diff --git a/workflow.R b/workflow.R index d69cceb..3ef37d7 100644 --- a/workflow.R +++ b/workflow.R @@ -3,7 +3,6 @@ #change function to take large set of values #maybe create for loop that looks first for condition and then creates annotation if ==yes - remotes::install_github("nickmckay/lipd-utilities",subdir = "R") remotes::install_github("nickmckay/nuspectral") remotes::install_github("nickmckay/geoChronR") @@ -13,17 +12,21 @@ library(geoChronR) library(devtools) library(lipdR) library(dplyr) +library(purrr) -D=readLipd("https://lipdverse.org/Temp12k/1_0_2/Temp12k1_0_2.zip") -ts = extractTs(D) -tib <- ts2tibble(ts) +D <- lipdR::readLipd("https://lipdverse.org/Temp12k/1_0_2/Temp12k1_0_2.zip") +ts <- lipdR::extractTs(D) +tib <- lipdR::ts2tibble(ts) -t2 <- tib%>%group_by(dataSetName)%>%select(geo_description)%>%distinct() -naz <- t2[is.na(t2$geo_description),] -da <- subset(D,names(D) %in% naz$dataSetName) +t2 <- tib %>% + group_by(dataSetName) %>% + select(geo_description) %>% + distinct() -output <- list(length=length(da)) -for (i in 1:length(da)) { - output[[i]] <- createThroughputJson(L=da[[i]]) -} +naz <- t2[is.na(t2$geo_description), ] +da <- subset(D, names(D) %in% naz$dataSetName) +output <- da %>% + map(function(x) { + createThroughputJson(L = x) + }) \ No newline at end of file From 0451d0bbfd3944093a109f8f595944e457adf0fb Mon Sep 17 00:00:00 2001 From: eyackulic <62761629+eyackulic@users.noreply.github.com> Date: Wed, 17 Feb 2021 11:11:09 -0700 Subject: [PATCH 09/10] workflow changes --- .DS_Store | Bin 8196 -> 10244 bytes json_files/.json | 14 ++++++++++++++ src/createThroughputJson.R | 10 +++++----- workflow.R | 11 ++++++++--- works_in_progress/notes.R | 36 +++++++++++++++++++++++++++++++++++- 5 files changed, 62 insertions(+), 9 deletions(-) create mode 100644 json_files/.json diff --git a/.DS_Store b/.DS_Store index c258c15a847088d7fbf5de3aba67c93a18989139..adbf6b1aaa61e34bc6db1aaa3d0e42893dbd052c 100644 GIT binary patch literal 10244 zcmeHMTWl0n82$1Buv;(s<%g*c; zTB}tg#)Kzt0e!$rj29lf1RlZ26Y7((35wANFGOEZV)Oxx_@6nmrCqjKA54hMN#^|L zod5sN<(u!!xeNecb4soU@B@IC9wsG`q8x$g*>h9yI3=Ydk^BL|&WEOa>e|#-;t~pvXP~kj$rIJ5ZX= z0k)6dkpV}JacR3!o&5BGjw?Dx4CL;l_cL>n0Y{E;$=w0DJD}4tIwusgTPHuiZ4MaV z(v4jNTm)`LfSuh-?DKjMLQ~G~TObI%r0IcLh=bg!8L_BlM9H2_u?Oj?x^4$bu@8U@ z5wIYVW%pK=T_NlP6$T&$Nl?I?YK`St*0W(hm|%cTJ!5`a4xjnt^XH_V?5K`eKHbitA=r zDvm|8SW1gnN|UBBV=5~$V@X5Px(rjbR72n1Zz+eYOhr>v{X0w}X|>pug(WFvDq9t* zOHC_5s*$QHVXbv0ST*K0C25kZ4Ak)<3a93kFIrMnv$AnrAT(Yi6_?Bx%fuaox^Aia zR3*7RV#X9*R`r42Ayu{p`_ihZMm42JkHi(B7^{Wxq6G`@ysN_J;|4bzGN%2hsCqD^ zT8E`duh(wF?^`VHlBstchRj-#z0w(~hgx6iTkPA(G%ZPmV%c$6?z>m)F$o#36yb)o zVx8D?faoGfCNF6a@Avg;k*J~xlFZv#Bd+!JrTLHrsf`z|7t4J8^pfK=L{s2pO}-Z2 z9@cDo#I!mSiq5)pfpj#q4U2ug?M&As%dA7*%D{=2ZS*PwRUE}iE&w?dgE)+j;TS%FNAMUvgU{mg_yV59H}Fk-8&BbBJd5Y>1H6D2@pHU{ zU*dOo1%JYy@hV>Px#-HUgDkPb+T2^mn(XLxh+BRvHqrJO{w7@eJRUxVf|Cz{tOXE-B68s3i!Zo6A0nWt|T!d9vhifr_ z8*J*fVFzx*KJ3RGxC<5BhXbhM0kklMX*@(kK7vo;QG5!Ywu$^45&1a2g0JFh_&O2# zU3?GUpCI&ycpg8&ar_Fu$)a!jRQlq#)6q9>1cT06=3Ta~_3As{pKqGpR-UnKVsK{5 zM!GwxYlc2RZL+CX2<^~H`-Bi|fo=$8t>{O|V)8ygfURWNM0<-4k~wx3_)C^Y9_;{< z5Sv=Bz5h5qY1J>Iy~iNg8MLz)pj3jS1vRu|P$?}_OIt}Y{r;?)*bZfKO~o)oR!KNO z?S{#l?LD~X0F~071% - map(function(x) { - createThroughputJson(L = x) - }) \ No newline at end of file + purrr::map(function(x) { + createThroughputJson(lipdObject = da,additionalType = additionalType,body = body,tokenFile = token) + }) + +output +token <- readr::read_file("token.R") +additionalType = "http://linked.earth/ontology#Dataset" +body = "These sites are missing a geo description" diff --git a/works_in_progress/notes.R b/works_in_progress/notes.R index c2b8505..d3288b9 100644 --- a/works_in_progress/notes.R +++ b/works_in_progress/notes.R @@ -13,4 +13,38 @@ http://nickmckay.github.io/LiPD-utilities/r/index.html https://github.com/nickmckay/LiPD-utilities http://nickmckay.github.io/GeoChronR/ -https://lipdverse.org/Temp12k/current_version/ \ No newline at end of file +https://lipdverse.org/Temp12k/current_version/ + + + + + + FIND CODE REPOSITORIES THAT ARE NOT CATALOGUED FOR LINKEDEARTH +go through code repositories and see if they are actually using data and can we figure out what datasets + +Use this command in neo4j: + + MATCH (dc:dataCat) +WHERE dc.name CONTAINS("Linked") +WITH dc +MATCH (dc)<-[:Target]-(:ANNOTATION)-[Target]->(cd:codeRepo) +RETURN dc.name, cd.name + + +In prep for all day workshop: + + Morgan is working on typology -- + + Take the result from my search and tag each repo as it pertains to Morgan's typology + +deborah kider + +start finding more linkedearth repos that link to databases + + +https://nickmckay.github.io/LinkedEarth-Neotoma-P418/LE-Neo_UseCase.html +https://github.com/nickmckay/LinkedEarth-Neotoma-P418 +http://nickmckay.github.io/GeoChronR/ +https://github.com/nickmckay/Temperature12k +process/extract file to send to Claire. +i.e. csv files with wavelengths and depth averaged measurements From 92067394bcc27036185e7fbfcb1676e82721ae94 Mon Sep 17 00:00:00 2001 From: Simon Goring Date: Wed, 17 Feb 2021 11:48:43 -0800 Subject: [PATCH 10/10] For pull --- src/createThroughputJson.R | 8 ++++---- workflow.R | 15 +++++++++------ 2 files changed, 13 insertions(+), 10 deletions(-) diff --git a/src/createThroughputJson.R b/src/createThroughputJson.R index 6855978..c6c0654 100644 --- a/src/createThroughputJson.R +++ b/src/createThroughputJson.R @@ -1,21 +1,21 @@ createThroughputJson <- function(lipdObject, additionalType, body, tokenFile){ - token <- readr::read_file("token.R") + token <- readr::read_file(tokenFile) postObject <- list(dbid = "r3d100012894", orcid = "0000-0001-5500-0401", additionalType = additionalType, id = lipdObject$datasetId, body = body, - token = token[1]) + token = token) - postTest <- httr::POST("throughputdb.com", + postTest <- httr::POST("https://throughputdb.com/api/widget", body = postObject, encode = "json") if (postTest$status_code == 200) { message("Success!") - return(NULL) + return(httr::content(postTest)$data) } else { return(postTest) } diff --git a/workflow.R b/workflow.R index 8c4d2e5..76944cb 100644 --- a/workflow.R +++ b/workflow.R @@ -14,6 +14,8 @@ library(lipdR) library(dplyr) library(purrr) +source('src/createThroughputJson.R') + D <- lipdR::readLipd("https://lipdverse.org/Temp12k/1_0_2/Temp12k1_0_2.zip") ts <- lipdR::extractTs(D) tib <- lipdR::ts2tibble(ts) @@ -26,12 +28,13 @@ t2 <- tib %>% naz <- t2[is.na(t2$geo_description), ] da <- subset(D, names(D) %in% naz$dataSetName) +additionalType <- "http://linked.earth/ontology#Dataset" +body <- "These sites are missing a geo description" + output <- da %>% purrr::map(function(x) { - createThroughputJson(lipdObject = da,additionalType = additionalType,body = body,tokenFile = token) + createThroughputJson(lipdObject = x, + additionalType = additionalType, + body = body, + tokenFile = "token.R") }) - -output -token <- readr::read_file("token.R") -additionalType = "http://linked.earth/ontology#Dataset" -body = "These sites are missing a geo description"