-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
update chart to accept named arguments in cmd line invocation of R sc…
…ript
- Loading branch information
1 parent
066ab39
commit 2c68825
Showing
6 changed files
with
63 additions
and
47 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,74 +1,85 @@ | ||
| # search.R | ||
| #!/usr/bin/env Rscript | ||
| suppressPackageStartupMessages(library(dplyr)) | ||
| library(tidyr) | ||
| library(scythe) | ||
| library(dataone) | ||
| library(jsonlite) | ||
| suppressPackageStartupMessages(library(lubridate)) | ||
| library(optparse) | ||
|
|
||
| sources <- c("plos", "xdd", "scopus", "springer") | ||
| nodes <- commandArgs(trailingOnly = TRUE) | ||
| main <- function(){ | ||
|
|
||
| option_list <- list( | ||
| make_option(c("-r", "--rows"), type="integer", default=100000, | ||
| help="Number of rows to return from query [default %default]"), | ||
| make_option(c("-n", "--nodes"), type="character", help="Comma separated list of nodes to query") | ||
| ) | ||
|
|
||
| # parse command-line arguments | ||
| parser <- OptionParser(option_list=option_list) | ||
| opts <- parse_args(parser) | ||
|
|
||
| num_rows <- opts$rows | ||
| nodes <- strsplit(opts$nodes, ",", fixed = TRUE)[[1]] | ||
|
|
||
| sources <- c("plos", "xdd", "scopus", "springer") | ||
|
|
||
| dois <- c() | ||
| for (node in nodes){ | ||
| message(paste("Gathering DOIs for: ", node)) | ||
| node_dois <- get_node_dois(node, num_rows) | ||
| dois <- c(dois, node_dois) | ||
| } | ||
| dois_unique <- unique(dois) | ||
|
|
||
| # set up file to write to | ||
| today <- format(Sys.Date(), "%Y%m%d") | ||
| fp <- paste0("scythe-citations-", today, ".csv") | ||
|
|
||
| message("Beginning citations search.") | ||
| found_citations <- citation_search(dois_unique, sources) | ||
|
|
||
| if (is.null(found_citations) || nrow(found_citations) == 0){ | ||
| writeLines("No citations found.", fp) | ||
| } else { | ||
| existing_citations <- get_metrics_citations() | ||
| new_citations <- anti_join(found_citations, existing_citations, by = c("dataset_id" = "target_id", "article_id" = "source_id")) | ||
| if (nrow(new_citations) > 0) { | ||
| write.csv(new_citations, fp, row_names = FALSE) | ||
| } else { | ||
| writeLines("No new citations found.", fp) | ||
| } | ||
| } | ||
| } | ||
|
|
||
| get_node_dois <- function(node_id) { | ||
| get_node_dois <- function(node_id, num_rows) { | ||
| mn <- getMNode(CNode("PROD"), node_id) | ||
| queryParamList <- list(q="id:doi* OR seriesId:doi*", | ||
| fl="id, seriesId", | ||
| start ="0", | ||
| rows = "10") | ||
| rows = num_rows) | ||
| result <- query(mn, solrQuery=queryParamList, as="data.frame", parse=FALSE) | ||
| pids <- c(result$id, result$seriesId) | ||
| dois <- grep("doi:", pids, value = TRUE) | ||
| return(dois) | ||
| } | ||
|
|
||
| get_metrics_citations <- function(from = as.POSIXct("2000-01-01"), to = as.POSIXct(Sys.Date())){ | ||
|
|
||
| from <- as.Date(from); to <- as.Date(to) | ||
| from_q <- paste(stringr::str_pad(month(from), 2, side = "left", pad = "0"), | ||
| stringr::str_pad(day(from), 2, side = "left", pad = "0"), | ||
| stringr::str_pad(year(from), 2, side = "left", pad = "0"), | ||
| sep = "/") | ||
|
|
||
| to_q <- paste(stringr::str_pad(month(to), 2, side = "left", pad = "0"), | ||
| stringr::str_pad(day(to), 2, side = "left", pad = "0"), | ||
| stringr::str_pad(year(to), 2, side = "left", pad = "0"), | ||
| sep = "/") | ||
|
|
||
| d <- fromJSON(paste0('https://logproc-stage-ucsb-1.test.dataone.org/metrics?q={%22metricsPage%22:{%22total%22:0,%22start%22:0,%22count%22:0},%22metrics%22:[%22citations%22],%22filterBy%22:[{%22filterType%22:%22repository%22,%22values%22:[%22urn:node:ARCTIC%22],%22interpretAs%22:%22list%22},{%22filterType%22:%22month%22,%22values%22:[%22', from_q,'%22,%22', to_q, '%22],%22interpretAs%22:%22range%22}],%22groupBy%22:[%22month%22]}')) | ||
|
|
||
| output_json <- d$resultDetails$citations # pulls citation info | ||
| output_df <- as.data.frame(do.call(rbind, output_json), row.names = FALSE) # binds nested cit info into dataframe | ||
|
|
||
| output_df <- output_df %>% | ||
| unnest_longer(target_id) %>% | ||
| unnest_longer(source_id) | ||
|
|
||
| return(output_df) | ||
| } | ||
|
|
||
| dois <- c() | ||
| for (node in nodes){ | ||
| message(paste("Gathering DOIs for: ", node)) | ||
| node_dois <- get_node_dois(node) | ||
| dois <- c(dois, node_dois) | ||
| } | ||
| dois_unique <- unique(dois) | ||
|
|
||
| # set up file to write to | ||
| today <- format(Sys.Date(), "%Y%m%d") | ||
| fp <- paste0("scythe-citations-", today, ".csv") | ||
|
|
||
| message("Beginning citations search.") | ||
| found_citations <- citation_search(dois_unique, sources) | ||
|
|
||
| if (is.null(found_citations) || nrow(found_citations) == 0){ | ||
| writeLines("No citations found.", fp) | ||
| } else { | ||
| existing_citations <- get_metrics_citations() | ||
| new_citations <- anti_join(found_citations, existing_citations, by = c("dataset_id" = "target_id", "article_id" = "source_id")) | ||
| if (nrow(new_citations) > 0) { | ||
| write.csv(new_citations, fp, row_names = FALSE) | ||
| } else { | ||
| writeLines("No new citations found.", fp) | ||
| } | ||
| } | ||
| main() |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters