diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..adbf6b1 Binary files /dev/null and b/.DS_Store differ diff --git a/.gitignore b/.gitignore index 26fad6f..49422ab 100644 --- a/.gitignore +++ b/.gitignore @@ -34,3 +34,5 @@ vignettes/*.pdf # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html rsconnect/ +.Rproj.user +token.R diff --git a/README.md b/README.md index db97223..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 @@ -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-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 diff --git a/json_files/.json b/json_files/.json new file mode 100644 index 0000000..b46def3 --- /dev/null +++ b/json_files/.json @@ -0,0 +1,14 @@ +{ + "dbid": "r3d100012894", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/117_723A.Godad.2011.json b/json_files/117_723A.Godad.2011.json new file mode 100644 index 0000000..e930a76 --- /dev/null +++ b/json_files/117_723A.Godad.2011.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "tmeZsxjY5oSP1dOcgrJW" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/161_976.Martrat.2014.json b/json_files/161_976.Martrat.2014.json new file mode 100644 index 0000000..0ae1800 --- /dev/null +++ b/json_files/161_976.Martrat.2014.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"orcid": "https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": 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"https://orcid.org/0000-0001-5500-0401", +"objects": [ + { + "type": "dataset", +"id": "annotationId?" +}, +{ + "additionalType": "http://linked.earth/ontology#Dataset", +"dataid": "eEUDNZTrJKRBxHo82oG6" +} +], +"body": "These sites are missing a geo description" +} diff --git a/json_files/Zabieniec.Plociennik.2011.json b/json_files/Zabieniec.Plociennik.2011.json new file mode 100644 index 0000000..d4f42c3 --- /dev/null +++ b/json_files/Zabieniec.Plociennik.2011.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"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..1990679 --- /dev/null +++ b/json_files/brurskardstjorni.Velle.2005.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"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..556bb2e --- /dev/null +++ b/json_files/klotjarnen.Seppa.2009.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"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..cc07e00 --- /dev/null +++ b/json_files/rainbow.Clegg.2011.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"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..0266506 --- /dev/null +++ b/json_files/s53s52.KaislahtiTillman.2010.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"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..90104a4 --- /dev/null +++ b/json_files/sjuuodjijaure.Rosen.2001.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"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..4957134 --- /dev/null +++ b/json_files/vikjordvatnet.Balascio.2012.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"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..5aa0db7 --- /dev/null +++ b/json_files/vuoskkujavri.Bigler.2002.json @@ -0,0 +1,15 @@ +{ + "dbid": "r3d100012894", +"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/src/.DS_Store b/src/.DS_Store new file mode 100644 index 0000000..5008ddf Binary files /dev/null and b/src/.DS_Store differ 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$dataSetName,".json")) + return(json) +} \ No newline at end of file diff --git a/src/createThroughputJson.R b/src/createThroughputJson.R new file mode 100644 index 0000000..c6c0654 --- /dev/null +++ b/src/createThroughputJson.R @@ -0,0 +1,22 @@ +createThroughputJson <- function(lipdObject, additionalType, body, tokenFile){ + + token <- readr::read_file(tokenFile) + + postObject <- list(dbid = "r3d100012894", + orcid = "0000-0001-5500-0401", + additionalType = additionalType, + id = lipdObject$datasetId, + body = body, + token = token) + + postTest <- httr::POST("https://throughputdb.com/api/widget", + body = postObject, + encode = "json") + + if (postTest$status_code == 200) { + message("Success!") + return(httr::content(postTest)$data) + } else { + return(postTest) + } +} 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/workflow.R b/workflow.R new file mode 100644 index 0000000..76944cb --- /dev/null +++ b/workflow.R @@ -0,0 +1,40 @@ + +#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) +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) + +t2 <- tib %>% + group_by(dataSetName) %>% + select(geo_description) %>% + distinct() + +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 = x, + additionalType = additionalType, + body = body, + tokenFile = "token.R") + }) diff --git a/works_in_progress/LIPD-2-CSV.R b/works_in_progress/LIPD-2-CSV.R new file mode 100644 index 0000000..702d6a5 --- /dev/null +++ b/works_in_progress/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/works_in_progress/notes.R b/works_in_progress/notes.R new file mode 100644 index 0000000..d3288b9 --- /dev/null +++ b/works_in_progress/notes.R @@ -0,0 +1,50 @@ +#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/ + + + + + + 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 diff --git a/works_in_progress/trial.R b/works_in_progress/trial.R new file mode 100644 index 0000000..161d769 --- /dev/null +++ b/works_in_progress/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