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annotate aquainfra_ogc_api_processes.R @ 0:0117fab93b87 draft

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planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
author ecology
date Mon, 14 Oct 2024 12:22:48 +0000
parents
children 84557c0b3eef
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0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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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")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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4
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5 cat("start generic wrapper service \n")
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6
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7 remove_null_values <- function(x) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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8 # Check if the input is a list
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9 if (is.list(x)) {
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10 # Remove NULL values and apply the function recursively to sublists
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11 x <- lapply(x, remove_null_values)
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12 x <- x[!sapply(x, is.null)]
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13 }
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14 return(x)
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15 }
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17 getParameters <- function() {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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18 con <- file("inputs.json", "r")
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19 lines <- readLines(con)
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20 close(con)
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21
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22 json_string <- paste(lines, collapse = "\n")
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23 json_data <- fromJSON(json_string)
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24
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25 # Remove NULL values from json_data
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26 cleaned_json_data <- remove_null_values(json_data)
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27 return(cleaned_json_data$conditional_process)
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28 }
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29
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30 parseResponseBody <- function(body) {
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31 hex <- c(body)
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32 intValues <- as.integer(hex)
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33 rawVector <- as.raw(intValues)
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34 readableOutput <- rawToChar(rawVector)
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35 jsonObject <- jsonlite::fromJSON(readableOutput)
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36 return(jsonObject)
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37 }
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38
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39 getOutputs <- function(inputs, output, server) {
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40 url <-
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41 paste(paste(server, "/processes/", sep = ""),
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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42 inputs$select_process,
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43 sep = "")
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44 request <- request(url)
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45 response <- req_perform(request)
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46 responseBody <- parseResponseBody(response$body)
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47 outputs <- list()
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48
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49 for (x in 1:length(responseBody$outputs)) {
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50 outputformatName <-
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51 paste(names(responseBody$outputs[x]), "_outformat", sep = "")
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52 output_item <- list()
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53
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54 for (p in names(inputs)) {
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55 if (p == outputformatName) {
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56 format <- list("mediaType" = inputs[[outputformatName]])
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57 output_item$format <- format
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58 }
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59 }
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60 output_item$transmissionMode <- "reference"
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61 outputs[[x]] <- output_item
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62 }
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63
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64 names(outputs) <- names(responseBody$outputs)
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65 return(outputs)
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66 }
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67
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68 executeProcess <- function(url, process, requestBodyData) {
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69 url <-
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70 paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "")
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71 requestBodyData$inputs$select_process <- NULL
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72
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73 body <- list()
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74 body$inputs <- requestBodyData$inputs
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75
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76 response <- request(url) %>%
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77 req_headers("Content-Type" = "application/json",
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78 "Prefer" = "respond-async") %>%
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79 req_body_json(body) %>%
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80 req_perform()
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81
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82 cat("\n Process executed")
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83 cat("\n status: ", response$status_code)
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84 #if ( process == "barplot-trend-results") {
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85 # process = "batplot-trend-results"
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86 #}
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87 #href <- parseResponseBody(response$body)$outputs[[gsub("-", "_", process)]]$href
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88 jobId <- parseResponseBody(response$body)$jobID
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89
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90 return(jobId)
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91 }
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92
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93 checkJobStatus <- function(server, process, jobID) {
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94 url <- paste0(server, "jobs/", jobID)
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95 response <- request(url) %>%
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96 req_perform()
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97 jobStatus <- parseResponseBody(response$body)$status
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
98 jobProgress <- parseResponseBody(response$body)$progress
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
99 return(jobStatus)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
100 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
101
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
102 getStatusCode <- function(server, process, jobID) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
103 url <- paste0(server, "jobs/", jobID)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
104 print(url)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
105 response <- request(url) %>%
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
106 req_perform()
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
107 status_code <- response$status_code
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
108 return(status_code)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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109 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
110
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ecology
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diff changeset
111 getResult <- function (server, process, jobID) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
112 response <-
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
113 request(paste0(server, "jobs/", jobID, "/results?f=json")) %>%
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
114 req_perform()
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
115 return(response)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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116 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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117
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ecology
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118 # Recursive function to search for href in a nested list
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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119 findHref <- function(obj) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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120 hrefs <- c() # Initialize an empty vector to store hrefs
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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121
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ecology
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122 if (is.list(obj)) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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123 # If the object is a list, loop through its elements
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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124 for (name in names(obj)) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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125 element <- obj[[name]]
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ecology
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126
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ecology
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127 if (is.list(element)) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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128 # Recursively search if the element is another list
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ecology
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129 hrefs <- c(hrefs, findHref(element))
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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130 } else if (name == "href") {
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ecology
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131 # If the element has a name "href", capture its value
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ecology
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132 hrefs <- c(hrefs, element)
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ecology
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133 }
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ecology
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134 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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135 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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136 return(hrefs)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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137 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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138
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ecology
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139 retrieveResults <- function(server, process, jobID, outputData) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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140 status_code <- getStatusCode(server, process, jobID)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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141 print(status_code)
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ecology
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142
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ecology
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143 if (status_code == 200) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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144 status <- "running"
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ecology
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145
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ecology
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146 while (status == "running") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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147 jobStatus <- checkJobStatus(server, process, jobID)
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ecology
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148 print(jobStatus)
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ecology
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149
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ecology
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150 if (jobStatus == "successful") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
151 status <- jobStatus
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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152 result <- getResult(server, process, jobID)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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153
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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154 if (result$status_code == 200) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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155 resultBody <- parseResponseBody(result$body)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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156 print(resultBody)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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157
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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158 # Call the recursive function to find all hrefs
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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159 hrefs <- findHref(resultBody)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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160
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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161 if (length(hrefs) > 0) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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162 # Collapse the URLs with a newline
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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163 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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164 print(urls_with_newline)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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165
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ecology
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166 # Write the URLs to a file
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ecology
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167 con <- file(outputData, "w")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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168 writeLines(urls_with_newline, con = con)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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169 close(con)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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170 } else {
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171 print("No hrefs found.")
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ecology
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172 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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173 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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174 } else if (jobStatus == "failed") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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175 status <- jobStatus
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
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176 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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177 Sys.sleep(3)
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ecology
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178 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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179
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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180 cat("\n done \n")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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181
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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182 } else if (status_code1 == 400) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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183 print("A query parameter has an invalid value.")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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184 } 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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185 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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186 } else if (status_code1 == 500) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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187 print("The requested URI was not found.")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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188 } else {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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189 print(paste("HTTP", status_code1, "Error:", resp1$status_message))
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ecology
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190 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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191 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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192
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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193
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ecology
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194
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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195 saveResult <- function(href, outputData) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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196 con <- file(outputData, "w")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
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diff changeset
197 writeLines(href, con = con)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
198 close(con)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
199 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
200
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
201 is_url <- function(x) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
202 grepl("^https?://", x)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
203 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
204
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
205 server <- "https://aqua.igb-berlin.de/pygeoapi-dev/"
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
206
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
207 print("--> Retrieve parameters")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
208 inputParameters <- getParameters()
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
209 #print(inputParameters)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
210 print("--> Parameters retrieved")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
211
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
212 args <- commandArgs(trailingOnly = TRUE)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
213 outputLocation <- args[2]
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
214
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
215 print("--> Retrieve outputs")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
216 outputs <- getOutputs(inputParameters, outputLocation, server)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
217 print("--> Outputs retrieved")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
218
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
219 print("--> Parse inputs")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
220 convertedKeys <- c()
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
221 for (key in names(inputParameters)) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
222 if (is.character(inputParameters[[key]]) &&
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
223 (endsWith(inputParameters[[key]], ".dat") ||
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
224 endsWith(inputParameters[[key]], ".txt"))) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
225 con <- file(inputParameters[[key]], "r")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
226 url_list <- list()
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
227 #while (length(line <- readLines(con, n = 1)) > 0) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
228 # if (is_url(line)) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
229 # url_list <- c(url_list, list(list(href = trimws(line))))
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
230 # }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
231 #}
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
232 con <- file(inputParameters[[key]], "r")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
233 lines <- readLines(con)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
234 print("--------------------------------------------------------------------1")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
235 print(length(lines))
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
236 close(con)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
237 if (!length(lines) > 1 && endsWith(lines, ".jp2") && startsWith(lines, "https")) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
238 print("--------------------------------------------------------------------2")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
239 tmp <- list()
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
240 tmp$href <- lines
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
241 tmp$type <- "image/jp2"
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
242 inputParameters[[key]] <- tmp
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
243 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
244 else if (!length(lines) > 1 && endsWith(lines, ".zip") && startsWith(lines, "https")) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
245 print("--------------------------------------------------------------------3")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
246 json_string <- paste(lines, collapse = "\n")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
247 inputParameters[[key]] <- json_string
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
248 } else if (!length(lines) > 1 && (endsWith(lines, ".xlsx") || endsWith(lines, ".csv") || grepl("f=csv", lines)) && startsWith(lines, "https")) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
249 print("--------------------------------------------------------------------4")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
250 json_string <- paste(lines, collapse = "\n")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
251 inputParameters[[key]] <- json_string
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
252 } else if (inputParameters$select_process == "plot-image" ||
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
253 inputParameters$select_process == "reproject-image") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
254 print("--------------------------------------------------------------------5")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
255 tmp <- list()
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
256 tmp$href <- lines
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
257 tmp$type <- "image/tiff; application=geotiff"
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
258 if (inputParameters$select_process == "reproject-image") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
259 tmp$type <- "image/tiff; subtype=geotiff"
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
260 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
261 inputParameters[[key]] <- tmp
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
262 } else {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
263 print("-----------------------------------6")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
264 json_string <- paste(lines, collapse = "\n")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
265 json_data <- fromJSON(json_string)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
266 inputParameters[[key]] <- json_data
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
267 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
268 convertedKeys <- append(convertedKeys, key)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
269 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
270 else if (grepl("_Array_", key)) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
271 keyParts <- strsplit(key, split = "_")[[1]]
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
272 type <- keyParts[length(keyParts)]
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
273 values <- inputParameters[[key]]
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
274 value_list <- strsplit(values, split = ",")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
275 convertedValues <- c()
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
276
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
277 for (value in value_list) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
278 if (type == "integer") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
279 value <- as.integer(value)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
280 } else if (type == "numeric") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
281 value <- as.numeric(value)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
282 } else if (type == "character") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
283 value <- as.character(value)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
284 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
285 convertedValues <- append(convertedValues, value)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
286
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
287 convertedKey <- ""
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
288 for (part in keyParts) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
289 if (part == "Array") {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
290 break
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
291 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
292 convertedKey <-
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
293 paste(convertedKey, paste(part, "_", sep = ""), sep = "")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
294 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
295 convertedKey <- substr(convertedKey, 1, nchar(convertedKey) - 1)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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296 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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297
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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298 inputParameters[[key]] <- convertedValues
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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299 print("-------------------------")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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300 print(convertedValues)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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301 print("-------------------------")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
302 convertedKeys <- append(convertedKeys, convertedKey)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
303 } else {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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304 print("-------------------------")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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305 print(key)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
306 print(inputParameters[[key]])
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
307 if (!is.null(inputParameters[[key]])) {
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
308 convertedKeys <- append(convertedKeys, key)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
309 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
310 print("-------------------------")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
311
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
312 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
313 }
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
314 print(inputParameters)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
315 names(inputParameters) <- convertedKeys
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
316 #print(inputParameters)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
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317 print("--> Inputs parsed")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
318
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
319 print("--> Prepare process execution")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
320 jsonData <- list("inputs" = inputParameters,
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
321 "outputs" = outputs)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
322
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
323 print("--> Execute process")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
324 jobId <- executeProcess(server, inputParameters$select_process, jsonData)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
325 print("--> Process executed")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
326
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
327 print("--> Retrieve results")
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
328 retrieveResults(server, inputParameters$select_process, jobId, outputLocation)
0117fab93b87 planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 6db8e8425f0525fc2e5df8cb43beb3b14024d0ab
ecology
parents:
diff changeset
329 print("--> Results retrieved")