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annotate ogc_api_processes_wrapper.R @ 0:f6288dd4b77a draft

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
author ecology
date Sat, 04 May 2024 08:42:42 +0000
parents
children bcb6009d5af7
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f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
ecology
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diff changeset
1 library("httr2")
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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2 library("jsonlite")
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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3 library("getopt")
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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5 cat("start generic wrapper service \n")
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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6
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7 getParameters <- function(){
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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8 args <- commandArgs(trailingOnly = TRUE)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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9 con <- file("inputs.json", "r")
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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10 line <- readLines(con, n = 1)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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11 json <- fromJSON(line)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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12 close(con)
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13 return(json$conditional_process)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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14 }
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16 parseResponseBody <- function(body) {
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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17 hex <- c(body)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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18 intValues <- as.integer(hex)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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19 rawVector <- as.raw(intValues)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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20 readableOutput <- rawToChar(rawVector)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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21 jsonObject <- jsonlite::fromJSON(readableOutput)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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22 return(jsonObject)
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23 }
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25 getOutputs <- function(inputs, output, server) {
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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26 url <- paste(paste(server, "/processes/", sep = ""), inputs$select_process, sep = "")
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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27 request <- request(url)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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28 response <- req_perform(request)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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29 responseBody <- parseResponseBody(response$body)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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30 outputs <- list()
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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32 for (x in 1:length(responseBody$outputs)) {
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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33 outputformatName <- paste(names(responseBody$outputs[x]), "_outformat", sep="")
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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34 output_item <- list()
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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35
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36 for (p in names(inputs)) {
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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37 if(p == outputformatName){
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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38 format <- list("mediaType" = inputs[[outputformatName]])
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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39 output_item$format <- format
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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40 }
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41 }
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42 output_item$transmissionMode <- "reference"
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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43 outputs[[x]] <- output_item
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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44 }
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46 names(outputs) <- names(responseBody$outputs)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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47 return(outputs)
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48 }
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49
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50 executeProcess <- function(url, process, requestBodyData, output) {
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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51 url <- paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "")
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52 response <- request(url) %>%
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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53 req_headers(
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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54 "accept" = "/*",
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55 "Prefer" = "respond-async;return=representation",
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56 "Content-Type" = "application/json"
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57 ) %>%
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58 req_body_json(requestBodyData) %>%
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59 req_perform()
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60
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61 cat("\n Process executed")
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62 cat("\n status: ", response$status_code)
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63 cat("\n jobID: ", parseResponseBody(response$body)$jobID, "\n")
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64
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65 jobID <- parseResponseBody(response$body)$jobID
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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67 return(jobID)
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68 }
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70 checkJobStatus <- function(server, jobID) {
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71 response <- request(paste0(server, "jobs/", jobID)) %>%
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72 req_headers(
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73 'accept' = 'application/json'
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74 ) %>%
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75 req_perform()
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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76 jobStatus <- parseResponseBody(response$body)$status
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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77 jobProgress <- parseResponseBody(response$body)$progress
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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78 cat(paste0("\n status: ", jobStatus, ", progress: ", jobProgress))
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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79 return(jobStatus)
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80 }
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81
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82 getStatusCode <- function(server, jobID) {
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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83 url <- paste0(server, "jobs/", jobID)
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
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84 response <- request(url) %>%
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ecology
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diff changeset
85 req_headers(
f6288dd4b77a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 4089d69de9c54df0930f55572e95bf3d22bf5e70
ecology
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86 'accept' = 'application/json'
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87 ) %>%
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88 req_perform()
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89 return(response$status_code)
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90 }
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91
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92 getResult <- function (server, jobID) {
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93 response <- request(paste0(server, "jobs/", jobID, "/results")) %>%
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94 req_headers(
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95 'accept' = 'application/json'
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96 ) %>%
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97 req_perform()
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98 return(response)
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99 }
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100
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101 retrieveResults <- function(server, jobID, outputData) {
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102 status_code <- getStatusCode(server, jobID)
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103 if(status_code == 200){
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104 status <- "running"
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ecology
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105 cat(status)
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106 while(status == "running"){
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107 jobStatus <- checkJobStatus(server, jobID)
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108 if (jobStatus == "successful") {
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109 status <- jobStatus
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ecology
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110 result <- getResult(server, jobID)
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111 if (result$status_code == 200) {
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ecology
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112 resultBody <- parseResponseBody(result$body)
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113 urls <- unname(unlist(lapply(resultBody, function(x) x$href)))
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ecology
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114 urls_with_newline <- paste(urls, collapse = "\n")
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115 sink(paste0(outputData, "_result_urls.txt"))
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ecology
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116 cat(urls_with_newline, "\n")
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117 sink()
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118 }
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119 } else if (jobStatus == "failed") {
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120 status <- jobStatus
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121 }
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122 Sys.sleep(3)
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123 }
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124 cat("\n done \n")
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125 } else if (status_code1 == 400) {
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126 print("A query parameter has an invalid value.")
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127 } else if (status_code1 == 404) {
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128 print("The requested URI was not found.")
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129 } else if (status_code1 == 500) {
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130 print("The requested URI was not found.")
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131 } else {
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132 print(paste("HTTP", status_code1, "Error:", resp1$status_message))
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133 }
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134 }
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135
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136 is_url <- function(x) {
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ecology
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137 grepl("^https?://", x)
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138 }
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139
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140 server <- "https://ospd.geolabs.fr:8300/ogc-api/"
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141
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142 inputParameters <- getParameters()
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143
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144 outputLocation <- inputParameters$outputData
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145
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146 outputs <- getOutputs(inputParameters, outputLocation, server)
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147
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148 for (key in names(inputParameters)) {
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149 print(inputParameters[[key]])
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150 if (is.character(inputParameters[[key]]) && (endsWith(inputParameters[[key]], ".dat") || endsWith(inputParameters[[key]], ".txt"))) {
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151 con <- file(inputParameters[[key]], "r")
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152 url_list <- list()
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153 while (length(line <- readLines(con, n = 1)) > 0) {
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154 if (is_url(line)) {
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155 url_list <- c(url_list, list(list(href = trimws(line))))
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156 }
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157 }
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158 close(con)
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159 inputParameters[[key]] <- url_list
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160 }
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161 }
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162
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163 jsonData <- list(
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164 "inputs" = inputParameters,
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165 "outputs" = outputs
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166 )
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167
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168 jobID <- executeProcess(server, inputParameters$select_process, jsonData, outputLocation)
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169
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170 retrieveResults(server, jobID, outputLocation)