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planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit b3d67b03e9bde6f6b1e2a48b8d5664129d3c57d5
author ecology
date Mon, 18 Aug 2025 10:12:19 +0000
parents aec309f44d47
children
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0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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1 library("httr2")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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2 library("jsonlite")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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3 library("getopt")
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5 cat("START GENERIC WRAPPER SERVICE \n")
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7 remove_null_values <- function(x) {
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8 if (is.list(x)) {
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9 x <- lapply(x, remove_null_values)
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10 x <- x[!sapply(x, is.null)]
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11 }
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12 return(x)
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13 }
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15 getParameters <- function() {
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16 con <- file("inputs.json", "r")
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17 lines <- readLines(con)
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18 close(con)
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20 json_string <- paste(lines, collapse = "\n")
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21 json_data <- fromJSON(json_string)
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23 cleaned_json_data <- remove_null_values(json_data)
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24 return(cleaned_json_data$conditional_process)
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25 }
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27 parseResponseBody <- function(body) {
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28 hex <- c(body)
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29 intValues <- as.integer(hex)
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30 rawVector <- as.raw(intValues)
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31 readableOutput <- rawToChar(rawVector)
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32 jsonObject <- jsonlite::fromJSON(readableOutput)
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33 return(jsonObject)
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34 }
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36 executeProcess <- function(url, process, requestBodyData) {
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37 url <-
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38 paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "")
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39 requestBodyData$inputs$select_process <- NULL
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41 body <- list()
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42 body$inputs <- requestBodyData$inputs
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44 response <- request(url) %>%
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45 req_headers("Content-Type" = "application/json",
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46 "Prefer" = "respond-async") %>%
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47 req_body_json(body) %>%
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48 req_perform()
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50 cat("\n 3.1: Process executed")
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51 cat("\n 3.1: Status code: ", response$status_code)
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52 jobId <- parseResponseBody(response$body)$jobID
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53 cat("\n 3.1: Job ID: ", jobId, "\n")
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54
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55 return(jobId)
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56 }
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57
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58 checkJobStatus <- function(server, process, jobID) {
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59 url <- paste0(server, "jobs/", jobID)
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60 response <- request(url) %>%
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61 req_perform()
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62 jobStatus <- parseResponseBody(response$body)$status
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63 jobProgress <- parseResponseBody(response$body)$progress
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64 return(jobStatus)
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65 }
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66
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67 getStatusCode <- function(url) {
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68 response <- request(url) %>%
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69 req_perform()
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70 status_code <- response$status_code
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71 return(status_code)
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72 }
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73
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74 getResult <- function (server, process, jobID) {
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75 response <-
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76 request(paste0(server, "jobs/", jobID, "/results?f=json")) %>%
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77 req_perform()
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78 return(response)
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79 }
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81 findHref <- function(obj) {
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82 hrefs <- c()
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83 if (is.list(obj)) {
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84 for (name in names(obj)) {
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85 element <- obj[[name]]
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86 if (is.list(element)) {
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87 hrefs <- c(hrefs, findHref(element))
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88 } else if (name == "href") {
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89 hrefs <- c(hrefs, element)
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90 }
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91 }
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92 }
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93 return(hrefs)
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94 }
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95
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96 retrieveResults <- function(server, process, jobID, outputData) {
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97 url <- paste0(server, "jobs/", jobID)
c805cb663bac planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 176da50f4af1ff7f4e0e325984c8edd27fe93926
ecology
parents: 2
diff changeset
98 cat(" 4.1: Job URL: ", url)
c805cb663bac planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 176da50f4af1ff7f4e0e325984c8edd27fe93926
ecology
parents: 2
diff changeset
99 status_code <- getStatusCode(url)
c805cb663bac planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 176da50f4af1ff7f4e0e325984c8edd27fe93926
ecology
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diff changeset
100 cat("\n 4.2: Status code: ", status_code, "\n")
0
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101
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ecology
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diff changeset
102 if (status_code == 200) {
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ecology
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103 status <- "running"
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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104
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ecology
parents:
diff changeset
105 while (status == "running") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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parents:
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106 jobStatus <- checkJobStatus(server, process, jobID)
7
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107 cat(" 4.3: Job status: ", jobStatus, "\n")
0
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ecology
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108
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109 if (jobStatus == "successful") {
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ecology
parents:
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110 status <- jobStatus
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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111 result <- getResult(server, process, jobID)
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ecology
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112
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113 if (result$status_code == 200) {
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114 resultBody <- parseResponseBody(result$body)
7
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115 cat("\n 4.4 Outputs: \n")
0
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ecology
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116 print(resultBody)
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ecology
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117 hrefs <- findHref(resultBody)
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118
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119 if (length(hrefs) > 0) {
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120 urls_with_newline <- paste(hrefs, collapse = "\n")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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121 con <- file(outputData, "w")
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ecology
parents:
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122 writeLines(urls_with_newline, con = con)
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ecology
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123 close(con)
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124 } else {
7
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125 stop(paste0("Job failed. No hrefs found. See details at: ", server, "jobs/", jobID))
0
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126 }
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127 }
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128 } else if (jobStatus == "failed") {
7
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129 stop(paste0("Job failed. See details at: ", server, "jobs/", jobID))
0
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130 }
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ecology
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diff changeset
131 Sys.sleep(3)
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132 }
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133
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134 } else if (status_code1 == 400) {
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135 print("A query parameter has an invalid value.")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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136 } else if (status_code1 == 404) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
137 print("The requested URI was not found.")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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138 } else if (status_code1 == 500) {
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ecology
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139 print("The requested URI was not found.")
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ecology
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diff changeset
140 } else {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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141 print(paste("HTTP", status_code1, "Error:", resp1$status_message))
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142 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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143 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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144
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ecology
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145 saveResult <- function(href, outputData) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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146 con <- file(outputData, "w")
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ecology
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147 writeLines(href, con = con)
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ecology
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148 close(con)
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ecology
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149 }
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150
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ecology
parents:
diff changeset
151 is_url <- function(x) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
152 grepl("^https?://", x)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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153 }
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154
2
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ecology
parents: 1
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155 server <- "https://aquainfra.ogc.igb-berlin.de/pygeoapi/"
0
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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156
7
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ecology
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diff changeset
157 cat("\n1: START RETRIEVING PARAMETERS\n\n")
0
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
158 inputParameters <- getParameters()
7
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diff changeset
159 print(inputParameters)
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ecology
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diff changeset
160 cat("1: END RETRIEVING PARAMETERS\n")
0
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
161
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162 args <- commandArgs(trailingOnly = TRUE)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
163 outputLocation <- args[2]
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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164
7
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diff changeset
165 cat("\n2: START PARSING INPUTS\n\n")
0
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ecology
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diff changeset
166 convertedKeys <- c()
1
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parents: 0
diff changeset
167
0
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diff changeset
168 for (key in names(inputParameters)) {
8
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parents: 7
diff changeset
169 value_no_spaces <- gsub(" ", "", inputParameters[[key]])
aec309f44d47 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit d6d779f958b5d3347769bdc83c885950ae975a42
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parents: 7
diff changeset
170 if (value_no_spaces == "") {
aec309f44d47 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit d6d779f958b5d3347769bdc83c885950ae975a42
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diff changeset
171 inputParameters[[key]] <- NULL
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parents: 7
diff changeset
172 }
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173
0
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ecology
parents:
diff changeset
174 if (is.character(inputParameters[[key]]) &&
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
175 (endsWith(inputParameters[[key]], ".dat") ||
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
176 endsWith(inputParameters[[key]], ".txt"))) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
177 con <- file(inputParameters[[key]], "r")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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178 url_list <- list()
1
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diff changeset
179
0
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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diff changeset
180 con <- file(inputParameters[[key]], "r")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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181 lines <- readLines(con)
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ecology
parents:
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182 close(con)
1
84557c0b3eef planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 3989415663771a85b3a0be6c02308994ac4adc85
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parents: 0
diff changeset
183
7
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diff changeset
184 json_string <- paste(lines, collapse = ",")
1
84557c0b3eef planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 3989415663771a85b3a0be6c02308994ac4adc85
ecology
parents: 0
diff changeset
185 inputParameters[[key]] <- json_string
84557c0b3eef planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 3989415663771a85b3a0be6c02308994ac4adc85
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186
0
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diff changeset
187 convertedKeys <- append(convertedKeys, key)
8
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parents: 7
diff changeset
188 } else if (
aec309f44d47 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit d6d779f958b5d3347769bdc83c885950ae975a42
ecology
parents: 7
diff changeset
189 grepl("_object", key) &&
aec309f44d47 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit d6d779f958b5d3347769bdc83c885950ae975a42
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diff changeset
190 !is.null(inputParameters[[key]]) &&
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ecology
parents: 7
diff changeset
191 !is.na(inputParameters[[key]]) &&
aec309f44d47 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit d6d779f958b5d3347769bdc83c885950ae975a42
ecology
parents: 7
diff changeset
192 gsub(" ", "", inputParameters[[key]]) != ""
aec309f44d47 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit d6d779f958b5d3347769bdc83c885950ae975a42
ecology
parents: 7
diff changeset
193 ) {
aec309f44d47 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit d6d779f958b5d3347769bdc83c885950ae975a42
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194 decoded_value <- gsub("__oc__", "{", inputParameters[[key]])
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195 decoded_value <- gsub("__cc__", "}", decoded_value)
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196 decoded_value <- gsub("__ob__", "[", decoded_value)
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197 decoded_value <- gsub("__cb__", "]", decoded_value)
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198 decoded_value <- gsub("__dq__", "\"", decoded_value) # Optional: sometimes used for quotes
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199 decoded_value <- gsub("__cn__", ":", decoded_value) # Optional: used for colon in older versions
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200
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201 parsed_json <- fromJSON(decoded_value)
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202 convertedKey <- gsub("_object", "", key)
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203 convertedKeys <- append(convertedKeys, convertedKey)
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204 #json_string <- toJSON(parsed_json, auto_unbox = FALSE)
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205 inputParameters[[key]] <- parsed_json
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206 } else if (grepl("_array", key)) {
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207 keyParts <- strsplit(key, split = "_")[[1]]
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208 type <- keyParts[length(keyParts)]
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209 values <- inputParameters[[key]]
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210 if (is.character(values) && grepl(",", values)) {
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211 value_list <- unlist(strsplit(values, split = ","))
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212 } else if (is.character(values)) {
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213 value_list <- c(values)
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214 }
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215
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216 convertedValues <- c()
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217
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218 for (value in value_list) {
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219 value <- as.character(value)
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220 value <- gsub(" ", "", value)
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221 #if(type == "integer") {
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222 # value <- as.integer(value)
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223 #} else if (type == "numeric") {
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224 # value <- as.numeric(balue)
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225 #} else if (type == "character") {
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226 # value <- as.character(value)
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227 # value <- gsub(" ", "", value)
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228 #}
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229 convertedValues <- append(convertedValues, value)
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230 convertedKey <- ""
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231 for (part in keyParts) {
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232 if(part == "array") {
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233 break
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234 }
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235 convertedKey <- paste(convertedKey, paste(part, "_", sep=""), sep="")
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236 }
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237 convertedKey <- substr(convertedKey, 1, nchar(convertedKey)-1)
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238 }
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239 inputParameters[[key]] <- convertedValues
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240 convertedKeys <- append(convertedKeys, convertedKey)
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241 }
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242 else {
0
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243 if (!is.null(inputParameters[[key]])) {
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244 convertedKeys <- append(convertedKeys, key)
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245 }
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246 }
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247 }
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248 names(inputParameters) <- convertedKeys
0
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249 print(inputParameters)
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250 cat("2: END PARSING INPUTSs\n")
0
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251
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252 cat("\n3: START EXECUTING PROCESS\n")
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253 jsonData <- list("inputs" = inputParameters)
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254 jobId <- executeProcess(server, inputParameters$select_process, jsonData)
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255 cat("\n3: END EXECUTING PROCESS\n")
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256
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257 cat("\n4: START RETRIEVING RESULTS\n\n")
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258 retrieveResults(server, inputParameters$select_process, jobId, outputLocation)
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259 cat("4: END RETRIEVING RESULTS\n")
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260
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261 cat("\n5: DONE.")