Mercurial > repos > iuc > pmids_to_pubtator_matrix

annotate pubmed_by_queries.R @ 0:69714f06f18b draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
author iuc
date Wed, 24 Mar 2021 08:33:56 +0000
parents
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69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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diff changeset
1 #!/usr/bin/env Rscript
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2 #tool: pubmed_by_queries
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3 #
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4 #This tool uses a set of search queries to download a defined number of abstracts or
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5 #PMIDs for search query from PubMed. PubMed's search rules and syntax apply.
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6 #
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7 #Input: Tab-delimited table with search queries in a column starting with "ID_",
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8 #e.g. "ID_gene" if search queries are genes.
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9 #
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10 #Output: Input table with additional columns
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11 #with PMIDs or abstracts (--abstracts) from PubMed.
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12 #
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13 #Usage:
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14 #$pubmed_by_queries.R [-h] [-i INPUT] [-o OUTPUT] [-n NUMBER] [-a] [-k KEY]
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15 #
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16 #optional arguments:
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17 # -h, --help show this help message and exit
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18 # -i INPUT, --input INPUT input file name. add path if file is not in working directory
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19 # -o OUTPUT, --output OUTPUT output file name. [default "pubmed_by_queries_output"]
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20 # -n NUMBER, --number NUMBER number of PMIDs or abstracts to save per ID [default "5"]
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21 # -a, --abstract if abstracts instead of PMIDs should be retrieved use --abstracts
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22 # -k KEY, --key KEY if ncbi API key is available, add it to speed up the download of PubMed data.
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23 # For usage in Galaxy add the API key to the Galaxy user-preferences (User/ Preferences/ Manage Information).
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24
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25 if ("--install_packages" %in% commandArgs()) {
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26 print("Installing packages")
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27 if (!require("argparse")) install.packages("argparse", repo = "http://cran.rstudio.com/") ;
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28 if (!require("easyPubMed")) install.packages("easyPubMed", repo = "http://cran.rstudio.com/") ;
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29 }
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30
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31 suppressPackageStartupMessages(library("argparse"))
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32 suppressPackageStartupMessages(library("easyPubMed"))
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33
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34 parser <- ArgumentParser()
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35 parser$add_argument("-i", "--input",
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36 help = "Input fie name. add path if file is not in working directory")
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37 parser$add_argument("-o", "--output", default = "pubmed_by_queries_output",
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38 help = "Output file name. [default \"%(default)s\"]")
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39 parser$add_argument("-n", "--number", type = "integer", default = 5,
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40 help = "Number of PMIDs (or abstracts) to save per ID. [default \"%(default)s\"]")
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41 parser$add_argument("-a", "--abstract", action = "store_true", default = FALSE,
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42 help = "If abstracts instead of PMIDs should be retrieved use --abstracts ")
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43 parser$add_argument("-k", "--key", type = "character",
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44 help = "If ncbi API key is available, add it to speed up the download of PubMed data. For usage in Galaxy add the API key to the Galaxy user-preferences (User/ Preferences/ Manage Information).")
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45 parser$add_argument("--install_packages", action = "store_true", default = FALSE,
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46 help = "If you want to auto install missing required packages.")
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47 args <- parser$parse_args()
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48
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49 if (!is.null(args$key)) {
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50 if (file.exists(args$key)) {
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51 credentials <- read.table(args$key, quote = "\"", comment.char = "")
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52 args$key <- credentials[1, 1]
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53 }
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54 }
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55
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56 max_web_tries <- 100
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57
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58 data <- read.delim(args$input, stringsAsFactors = FALSE)
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59
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60 id_col_index <- grep("ID_", names(data))
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61
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62
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63 fetch_pmids <- function(data, number, pubmed_search, query, row, max_web_tries) {
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64 my_pubmed_url <- paste("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?",
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65 "db=pubmed&retmax=", number,
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66 "&term=", pubmed_search$OriginalQuery,
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67 "&usehistory=n", sep = "")
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68 # get ids
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69 idxml <- c()
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70 for (i in seq(max_web_tries)) {
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71 tryCatch({
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72 id_connect <- suppressWarnings(url(my_pubmed_url, open = "rb", encoding = "UTF8"))
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73 idxml <- suppressWarnings(readLines(id_connect, warn = FALSE, encoding = "UTF8"))
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74 suppressWarnings(close(id_connect))
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75 break
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76 }, error = function(e) {
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77 print(paste("Error getting URL, sleeping", 2 * i, "seconds."))
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78 print(e)
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79 Sys.sleep(time = 2 * i)
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80 })
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81 }
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82 pmids <- c()
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83 for (i in seq(length(idxml))) {
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84 if (grepl("^<Id>", idxml[i])) {
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85 pmid <- custom_grep(idxml[i], tag = "Id", format = "char")
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86 pmids <- c(pmids, as.character(pmid[1]))
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87 }
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88 }
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diff changeset
89 if (length(pmids) > 0) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
90 data[row, sapply(seq(length(pmids)), function(i) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
91 paste0("PMID_", i)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
92 })] <- pmids
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
93 cat(length(pmids), " PMIDs for ", query, " are added in the table.", "\n")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
94 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
95 return(data)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
96 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
97
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
98
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
99 fetch_abstracts <- function(data, number, query, pubmed_search) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
100 efetch_url <- paste("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?",
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
101 "db=pubmed&WebEnv=", pubmed_search$WebEnv, "&query_key=", pubmed_search$QueryKey,
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
102 "&retstart=", 0, "&retmax=", number,
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
103 "&rettype=", "null", "&retmode=", "xml", sep = "")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
104 api_key <- pubmed_search$APIkey
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
105 if (!is.null(api_key)) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
106 efetch_url <- paste(efetch_url, "&api_key=", api_key, sep = "")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
107 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
108 # initialize
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
109 out_data <- NULL
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
110 try_num <- 1
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
111 t_0 <- Sys.time()
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
112 # Try to fetch results
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
113 while (is.null(out_data)) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
114 # Timing check: kill at 3 min
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
115 if (try_num > 1) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
116 Sys.sleep(time = 2 * try_num)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
117 cat("Problem to receive PubMed data or error is received. Please wait. Try number:",
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
118 try_num, "\n")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
119 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
120 t_1 <- Sys.time()
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
121 if (as.numeric(difftime(t_1, t_0, units = "mins")) > 3) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
122 message("Killing the request! Something is not working. Please, try again later",
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
123 "\n")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
124 return(data)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
125 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
126 # ENTREZ server connect
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
127 out_data <- tryCatch({
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
128 tmp_connect <- suppressWarnings(url(efetch_url,
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
129 open = "rb",
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
130 encoding = "UTF8"))
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
131 suppressWarnings(readLines(tmp_connect,
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
132 warn = FALSE,
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
133 encoding = "UTF8"))
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
134 }, error = function(e) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
135 print(e)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
136 }, finally = {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
137 try(suppressWarnings(close(tmp_connect)),
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
138 silent = TRUE)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
139 })
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
140 # Check if error
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
141 if (!is.null(out_data) &&
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
142 class(out_data) == "character" &&
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
143 grepl("<ERROR>", substr(paste(utils::head(out_data, n = 100),
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
144 collapse = ""), 1, 250))) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
145 out_data <- NULL
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
146 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
147 try_num <- try_num + 1
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
148 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
149 if (is.null(out_data)) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
150 message("Killing the request! Something is not working. Please, try again later",
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
151 "\n")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
152 return(data)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
153 } else {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
154 return(out_data)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
155 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
156 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
157
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
158
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
159 process_xml_abstracts <- function(out_data) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
160 xml_data <- paste(out_data, collapse = "")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
161 # articles to list
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
162 xml_data <- strsplit(xml_data, "<PubmedArticle(>|[[:space:]]+?.*>)")[[1]][-1]
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
163 xml_data <- sapply(xml_data, function(x) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
164 #trim extra stuff at the end of the record
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
165 if (!grepl("</PubmedArticle>$", x))
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
166 x <- sub("(^.*</PubmedArticle>).*$", "\\1", x)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
167 # Rebuid XML structure and proceed
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
168 x <- paste("<PubmedArticle>", x)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
169 gsub("[[:space:]]{2,}", " ", x)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
170 },
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
171 USE.NAMES = FALSE, simplify = TRUE)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
172 #titles
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
173 titles <- sapply(xml_data, function(x) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
174 x <- custom_grep(x, tag = "ArticleTitle", format = "char")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
175 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
176 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
177 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
178 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
179 if (length(x) > 1) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
180 x <- paste(x, collapse = " ", sep = " ")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
181 } else if (length(x) < 1) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
182 x <- NA
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
183 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
184 x
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
185 },
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
186 USE.NAMES = FALSE, simplify = TRUE)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
187 # abstracts
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
188 abstract_text <- sapply(xml_data, function(x) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
189 custom_grep(x, tag = "AbstractText", format = "char")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
190 },
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
191 USE.NAMES = FALSE, simplify = TRUE)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
192 abstracts <- sapply(abstract_text, function(x) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
193 if (length(x) > 1) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
194 x <- paste(x, collapse = " ", sep = " ")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
195 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
196 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
197 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
198 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
199 } else if (length(x) < 1) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
200 x <- NA
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
201 } else {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
202 x <- gsub("</{0,1}i>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
203 x <- gsub("</{0,1}b>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
204 x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
205 x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
206 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
207 x
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
208 },
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
209 USE.NAMES = FALSE, simplify = TRUE)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
210 #add title to abstracts
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
211 if (length(titles) == length(abstracts)) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
212 abstracts <- paste(titles, abstracts)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
213 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
214 return(abstracts)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
215 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
216
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
217
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
218 pubmed_data_in_table <- function(data, row, query, number, key, abstract) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
219 if (is.null(query)) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
220 print(data)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
221 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
222 pubmed_search <- get_pubmed_ids(query, api_key = key)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
223 if (as.numeric(pubmed_search$Count) == 0) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
224 cat("No PubMed result for the following query: ", query, "\n")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
225 return(data)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
226 } else if (abstract == FALSE) { # fetch PMIDs
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
227 data <- fetch_pmids(data, number, pubmed_search, query, row, max_web_tries)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
228 return(data)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
229 } else if (abstract == TRUE) { # fetch abstracts and title text
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
230 out_data <- fetch_abstracts(data, number, query, pubmed_search)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
231 abstracts <- process_xml_abstracts(out_data)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
232 #add abstracts to data frame
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
233 if (length(abstracts) > 0) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
234 data[row, sapply(seq(length(abstracts)),
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
235 function(i) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
236 paste0("ABSTRACT_", i)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
237 })] <- abstracts
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
238 cat(length(abstracts), " abstracts for ", query, " are added in the table.",
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
239 "\n")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
240 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
241 return(data)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
242 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
243 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
244
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
245 for (i in seq(nrow(data))) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
246 data <- tryCatch(pubmed_data_in_table(data = data,
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
247 row = i,
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
248 query = data[i, id_col_index],
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
249 number = args$number,
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
250 key = args$key,
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
251 abstract = args$abstract), error = function(e) {
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
252 print("main error")
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
253 print(e)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
254 Sys.sleep(5)
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
255 })
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
256 }
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
257
69714f06f18b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
258 write.table(data, args$output, append = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)