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annotate aquainfra_ogc_api_processes.R @ 2:af00a67d3649 draft

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planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 22bb5ef944236a3e6c5d4e9ffb31e99b700031e6
author ecology
date Tue, 04 Feb 2025 07:10:11 +0000
parents 1ff618d89af4
children
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1 library("httr2")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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2 library("jsonlite")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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3 library("getopt")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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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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19
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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$conditional_process)
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25 }
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27 parseResponseBody <- function(body) {
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28 hex <- c(body)
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29 intValues <- as.integer(hex)
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30 rawVector <- as.raw(intValues)
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31 readableOutput <- rawToChar(rawVector)
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32 jsonObject <- jsonlite::fromJSON(readableOutput)
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33 return(jsonObject)
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34 }
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36 getOutputs <- function(inputs, output, server) {
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37 url <-
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38 paste(paste(server, "processes/", sep = ""),
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39 inputs$select_process,
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40 sep = "")
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41 print(url)
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42 request <- request(url)
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43 response <- req_perform(request)
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44 responseBody <- parseResponseBody(response$body)
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45 outputs <- list()
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47 for (x in 1:length(responseBody$outputs)) {
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48 outputformatName <-
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49 paste(names(responseBody$outputs[x]), "_outformat", sep = "")
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50 output_item <- list()
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51
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52 for (p in names(inputs)) {
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53 if (p == outputformatName) {
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54 format <- list("mediaType" = inputs[[outputformatName]])
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55 output_item$format <- format
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56 }
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57 }
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58 output_item$transmissionMode <- "reference"
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59 outputs[[x]] <- output_item
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60 }
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61
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62 names(outputs) <- names(responseBody$outputs)
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63 return(outputs)
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64 }
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65
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66 executeProcess <- function(url, process, requestBodyData) {
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67 url <-
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68 paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "")
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69 requestBodyData$inputs$select_process <- NULL
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70
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71 body <- list()
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72 body$inputs <- requestBodyData$inputs
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73
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74 response <- request(url) %>%
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75 req_headers("Content-Type" = "application/json",
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76 "Prefer" = "respond-async") %>%
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77 req_body_json(body) %>%
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78 req_perform()
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79
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80 cat("\n Process executed")
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81 cat("\n status: ", response$status_code)
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82 jobId <- parseResponseBody(response$body)$jobID
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83
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84 return(jobId)
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85 }
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86
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87 checkJobStatus <- function(server, process, jobID) {
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88 url <- paste0(server, "jobs/", jobID)
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89 response <- request(url) %>%
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90 req_perform()
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91 jobStatus <- parseResponseBody(response$body)$status
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92 jobProgress <- parseResponseBody(response$body)$progress
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93 return(jobStatus)
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94 }
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95
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ecology
parents:
diff changeset
96 getStatusCode <- function(server, process, jobID) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
97 url <- paste0(server, "jobs/", jobID)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
98 print(url)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
99 response <- request(url) %>%
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
100 req_perform()
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
101 status_code <- response$status_code
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
102 return(status_code)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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103 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
104
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ecology
parents:
diff changeset
105 getResult <- function (server, process, jobID) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
106 response <-
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
107 request(paste0(server, "jobs/", jobID, "/results?f=json")) %>%
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
108 req_perform()
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
109 return(response)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
110 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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111
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ecology
parents:
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112 findHref <- function(obj) {
1
1ff618d89af4 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 3989415663771a85b3a0be6c02308994ac4adc85
ecology
parents: 0
diff changeset
113 hrefs <- c()
0
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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114 if (is.list(obj)) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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115 for (name in names(obj)) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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116 element <- obj[[name]]
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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117 if (is.list(element)) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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118 hrefs <- c(hrefs, findHref(element))
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ecology
parents:
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119 } else if (name == "href") {
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ecology
parents:
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120 hrefs <- c(hrefs, element)
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ecology
parents:
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121 }
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ecology
parents:
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122 }
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ecology
parents:
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123 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
124 return(hrefs)
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ecology
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125 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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126
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ecology
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127 retrieveResults <- function(server, process, jobID, outputData) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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128 status_code <- getStatusCode(server, process, jobID)
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ecology
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129 print(status_code)
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ecology
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130
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ecology
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131 if (status_code == 200) {
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ecology
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132 status <- "running"
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ecology
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133
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ecology
parents:
diff changeset
134 while (status == "running") {
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ecology
parents:
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135 jobStatus <- checkJobStatus(server, process, jobID)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
136 print(jobStatus)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
137
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ecology
parents:
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138 if (jobStatus == "successful") {
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ecology
parents:
diff changeset
139 status <- jobStatus
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
140 result <- getResult(server, process, jobID)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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141
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ecology
parents:
diff changeset
142 if (result$status_code == 200) {
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ecology
parents:
diff changeset
143 resultBody <- parseResponseBody(result$body)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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144 print(resultBody)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
145 hrefs <- findHref(resultBody)
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ecology
parents:
diff changeset
146
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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147 if (length(hrefs) > 0) {
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ecology
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148 urls_with_newline <- paste(hrefs, collapse = "\n")
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ecology
parents:
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149 print(urls_with_newline)
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ecology
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diff changeset
150 con <- file(outputData, "w")
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ecology
parents:
diff changeset
151 writeLines(urls_with_newline, con = con)
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ecology
parents:
diff changeset
152 close(con)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
153 } else {
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ecology
parents:
diff changeset
154 print("No hrefs found.")
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ecology
parents:
diff changeset
155 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
156 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
157 } else if (jobStatus == "failed") {
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ecology
parents:
diff changeset
158 status <- jobStatus
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
159 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
160 Sys.sleep(3)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
161 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
162
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ecology
parents:
diff changeset
163 cat("\n done \n")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
164
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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165 } else if (status_code1 == 400) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
166 print("A query parameter has an invalid value.")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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167 } else if (status_code1 == 404) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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168 print("The requested URI was not found.")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
169 } else if (status_code1 == 500) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
170 print("The requested URI was not found.")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
171 } else {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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172 print(paste("HTTP", status_code1, "Error:", resp1$status_message))
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
173 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
174 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
175
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ecology
parents:
diff changeset
176 saveResult <- function(href, outputData) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
177 con <- file(outputData, "w")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
178 writeLines(href, con = con)
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ecology
parents:
diff changeset
179 close(con)
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ecology
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180 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
181
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
182 is_url <- function(x) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
183 grepl("^https?://", x)
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ecology
parents:
diff changeset
184 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
185
2
af00a67d3649 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 22bb5ef944236a3e6c5d4e9ffb31e99b700031e6
ecology
parents: 1
diff changeset
186 server <- "https://aquainfra.ogc.igb-berlin.de/pygeoapi/"
0
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
187
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
188 print("--> Retrieve parameters")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
189 inputParameters <- getParameters()
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
190 print("--> Parameters retrieved")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
191
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
192 args <- commandArgs(trailingOnly = TRUE)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
193 outputLocation <- args[2]
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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194
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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195 print("--> Retrieve outputs")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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196 outputs <- getOutputs(inputParameters, outputLocation, server)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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197 print("--> Outputs retrieved")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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198
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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199 print("--> Parse inputs")
1
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ecology
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200
0
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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201 convertedKeys <- c()
1
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ecology
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202
0
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
203 for (key in names(inputParameters)) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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204 if (is.character(inputParameters[[key]]) &&
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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205 (endsWith(inputParameters[[key]], ".dat") ||
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
206 endsWith(inputParameters[[key]], ".txt"))) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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207 con <- file(inputParameters[[key]], "r")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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208 url_list <- list()
1
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ecology
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209
0
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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210 con <- file(inputParameters[[key]], "r")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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211 lines <- readLines(con)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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212 print(length(lines))
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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213 close(con)
1
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ecology
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214
1ff618d89af4 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 3989415663771a85b3a0be6c02308994ac4adc85
ecology
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diff changeset
215 json_string <- paste(lines, collapse = "\n")
1ff618d89af4 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 3989415663771a85b3a0be6c02308994ac4adc85
ecology
parents: 0
diff changeset
216 inputParameters[[key]] <- json_string
1ff618d89af4 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 3989415663771a85b3a0be6c02308994ac4adc85
ecology
parents: 0
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217
0
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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218 convertedKeys <- append(convertedKeys, key)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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219 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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220 else if (grepl("_Array_", key)) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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221 keyParts <- strsplit(key, split = "_")[[1]]
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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222 type <- keyParts[length(keyParts)]
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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223 values <- inputParameters[[key]]
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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224 value_list <- strsplit(values, split = ",")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
225 convertedValues <- c()
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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226
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
227 for (value in value_list) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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228 if (type == "integer") {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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229 value <- as.integer(value)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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230 } else if (type == "numeric") {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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231 value <- as.numeric(value)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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232 } else if (type == "character") {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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233 value <- as.character(value)
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ecology
parents:
diff changeset
234 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
235 convertedValues <- append(convertedValues, value)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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236
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ecology
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237 convertedKey <- ""
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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238 for (part in keyParts) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
239 if (part == "Array") {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
240 break
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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241 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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242 convertedKey <-
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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243 paste(convertedKey, paste(part, "_", sep = ""), sep = "")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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244 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
245 convertedKey <- substr(convertedKey, 1, nchar(convertedKey) - 1)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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246 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
247
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
248 inputParameters[[key]] <- convertedValues
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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249 convertedKeys <- append(convertedKeys, convertedKey)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
250 } else {
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ecology
parents:
diff changeset
251 if (!is.null(inputParameters[[key]])) {
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
252 convertedKeys <- append(convertedKeys, key)
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ecology
parents:
diff changeset
253 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
254 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
255 }
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
256 print(inputParameters)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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257 names(inputParameters) <- convertedKeys
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
258 print("--> Inputs parsed")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
259
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
260 print("--> Prepare process execution")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
261 jsonData <- list("inputs" = inputParameters,
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
262 "outputs" = outputs)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
263
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
264 print("--> Execute process")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
265 jobId <- executeProcess(server, inputParameters$select_process, jsonData)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
266 print("--> Process executed")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
267
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
268 print("--> Retrieve results")
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
269 retrieveResults(server, inputParameters$select_process, jobId, outputLocation)
0077885b6f1d planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
270 print("--> Results retrieved")