Mercurial > repos > ecology > hirondelle_crim
annotate ogc_api_processes_wrapper.R @ 1:52baddd15640 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
author | ecology |
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date | Fri, 06 Sep 2024 10:30:30 +0000 |
parents | afede0916f0a |
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rev | line source |
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afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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1 library("httr2") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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2 library("jsonlite") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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3 library("getopt") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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4 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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5 cat("start generic wrapper service \n") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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6 |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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7 remove_null_values <- function(x) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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8 # Check if the input is a list |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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9 if (is.list(x)) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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10 # Remove NULL values and apply the function recursively to sublists |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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11 x <- lapply(x, remove_null_values) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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12 x <- x[!sapply(x, is.null)] |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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13 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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14 return(x) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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15 } |
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afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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16 |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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17 getParameters <- function() { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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18 con <- file("inputs.json", "r") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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19 lines <- readLines(con) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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20 close(con) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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21 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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22 json_string <- paste(lines, collapse = "\n") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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23 json_data <- fromJSON(json_string) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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24 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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25 # Remove NULL values from json_data |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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26 cleaned_json_data <- remove_null_values(json_data) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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27 return(cleaned_json_data$conditional_process) |
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afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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28 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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29 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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30 parseResponseBody <- function(body) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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31 hex <- c(body) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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32 intValues <- as.integer(hex) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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33 rawVector <- as.raw(intValues) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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34 readableOutput <- rawToChar(rawVector) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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35 jsonObject <- jsonlite::fromJSON(readableOutput) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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36 return(jsonObject) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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37 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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38 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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39 getOutputs <- function(inputs, output, server) { |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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40 url <- |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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41 paste(paste(server, "/processes/", sep = ""), |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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42 inputs$select_process, |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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43 sep = "") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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44 request <- request(url) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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45 response <- req_perform(request) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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46 responseBody <- parseResponseBody(response$body) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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47 outputs <- list() |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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48 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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49 for (x in 1:length(responseBody$outputs)) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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50 outputformatName <- |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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51 paste(names(responseBody$outputs[x]), "_outformat", sep = "") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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52 output_item <- list() |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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53 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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54 for (p in names(inputs)) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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55 if (p == outputformatName) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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56 format <- list("mediaType" = inputs[[outputformatName]]) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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57 output_item$format <- format |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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58 } |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
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59 } |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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60 output_item$transmissionMode <- "reference" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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61 outputs[[x]] <- output_item |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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62 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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63 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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64 names(outputs) <- names(responseBody$outputs) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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65 return(outputs) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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66 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
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67 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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68 executeProcess <- function(url, process, requestBodyData, cookie) { |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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69 url <- |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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70 paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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71 requestBodyData$inputs$cookie <- NULL |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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72 requestBodyData$inputs$select_process <- NULL |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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73 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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74 requestBodyData$inputs$s3_access_key <- |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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75 requestBodyData$inputs$user_credentials$s3_access_key |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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76 requestBodyData$inputs$s3_secret_key <- |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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77 requestBodyData$inputs$user_credentials$s3_secret_key |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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78 requestBodyData$inputs$user_credentials <- NULL |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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0
diff
changeset
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79 if (process == "plot-image") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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80 tmp <- requestBodyData$inputs$color_scale |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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81 color_scale <- gsub("__ob__", "[", tmp) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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0
diff
changeset
|
82 color_scale <- gsub("__cb__", "]", color_scale) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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83 requestBodyData$inputs$color_scale <- color_scale |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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84 #print(requestBodyData$inputs$color_scale) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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0
diff
changeset
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85 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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0
diff
changeset
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86 if (process == "calculate-band") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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87 requestBodyData$inputs$name <- "output" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
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88 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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89 if (process == "reproject-image") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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90 requestBodyData$inputs$output_name <- "output" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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91 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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92 #requestBodyData$inputs$input_image$href <- "https://hirondelle.crim.ca/wpsoutputs/weaver/public/test-data/S2A_MSIL2A_20190701T110621_N0500_R137_T29SPC_20230604T023542_turbidity.tiff" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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93 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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94 body <- list() |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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95 body$inputs <- requestBodyData$inputs |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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96 #print(body$inputs) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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97 body$mode <- "async" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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98 body$response <- "document" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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99 #print(body$inputs) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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100 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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101 response <- request(url) %>% |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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102 req_headers("Accept" = "application/json", |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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103 "Content-Type" = "application/json", |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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104 "Cookie" = cookie) %>% |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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105 req_body_json(body) %>% |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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106 req_perform() |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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107 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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108 cat("\n Process executed") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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109 cat("\n status: ", response$status_code) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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110 cat("\n jobID: ", parseResponseBody(response$body)$jobID, "\n") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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111 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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112 jobID <- parseResponseBody(response$body)$jobID |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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113 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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114 return(jobID) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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115 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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116 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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117 checkJobStatus <- function(server, process, jobID, cookie) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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118 url <- paste0(server, "processes/", process, "/jobs/", jobID) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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119 response <- request(url) %>% |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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120 req_headers("Cookie" = cookie) %>% |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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changeset
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121 req_perform() |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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122 jobStatus <- parseResponseBody(response$body)$status |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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123 jobProgress <- parseResponseBody(response$body)$progress |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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124 return(jobStatus) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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125 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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126 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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127 getStatusCode <- function(server, process, jobID, cookie) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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128 url <- paste0(server, "processes/", process, "/jobs/", jobID) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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129 response <- request(url) %>% |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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130 req_headers("Cookie" = cookie) %>% |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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131 req_perform() |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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132 status_code <- response$status_code |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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133 return(status_code) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
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134 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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135 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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136 getResult <- function (server, process, jobID, cookie) { |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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137 response <- |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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138 request(paste0(server, "processes/", process, "/jobs/", jobID, "/results")) %>% |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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139 req_headers("Cookie" = cookie) %>% |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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140 req_perform() |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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141 return(response) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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142 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
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143 |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
|
144 retrieveResults <- |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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145 function(server, process, jobID, outputData, cookie) { |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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146 status_code <- getStatusCode(server, process, jobID, cookie) |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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147 if (status_code == 200) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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148 status <- "running" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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149 while (status == "running") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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150 jobStatus <- checkJobStatus(server, process, jobID, cookie) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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151 print(jobStatus) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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152 if (jobStatus == "succeeded") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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153 status <- jobStatus |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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154 result <- getResult(server, process, jobID, cookie) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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155 if (result$status_code == 200) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
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156 resultBody <- parseResponseBody(result$body) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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0
diff
changeset
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157 #print(resultBody) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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158 if (process == "select-products-sentinel2") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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159 urls <- unname(unlist(lapply(resultBody, function(x) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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160 x$value))) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
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161 } else if (process == "download-band-sentinel2-product-safe" || |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
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162 process == "calculate-band" || |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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changeset
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163 process == "plot-image" || process == "reproject-image") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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164 urls <- unname(unlist(lapply(resultBody, function(x) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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165 x$href))) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
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166 } |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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167 urls_with_newline <- paste(urls, collapse = "\n") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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168 con <- file(outputData, "w") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
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169 writeLines(urls_with_newline, con = con) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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170 close(con) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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171 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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172 } else if (jobStatus == "failed") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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173 status <- jobStatus |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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174 } |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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175 Sys.sleep(3) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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176 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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177 cat("\n done \n") |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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178 } else if (status_code1 == 400) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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179 print("A query parameter has an invalid value.") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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180 } else if (status_code1 == 404) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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181 print("The requested URI was not found.") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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182 } else if (status_code1 == 500) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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183 print("The requested URI was not found.") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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184 } else { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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185 print(paste("HTTP", status_code1, "Error:", resp1$status_message)) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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186 } |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
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187 } |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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188 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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189 is_url <- function(x) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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190 grepl("^https?://", x) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
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191 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
192 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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193 server <- "https://hirondelle.crim.ca/weaver/" |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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194 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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195 print("--> Retrieve parameters") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
196 inputParameters <- getParameters() |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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197 #print(inputParameters) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
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198 print("--> Parameters retrieved") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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199 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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200 args <- commandArgs(trailingOnly = TRUE) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
201 outputLocation <- args[2] |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
202 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
203 print("--> Retrieve outputs") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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204 outputs <- getOutputs(inputParameters, outputLocation, server) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
205 print("--> Outputs retrieved") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
206 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
207 print("--> Parse inputs") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
208 convertedKeys <- c() |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
209 for (key in names(inputParameters)) { |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
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210 if (is.character(inputParameters[[key]]) && |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
211 (endsWith(inputParameters[[key]], ".dat") || |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
212 endsWith(inputParameters[[key]], ".txt"))) { |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
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213 con <- file(inputParameters[[key]], "r") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
214 url_list <- list() |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
215 #while (length(line <- readLines(con, n = 1)) > 0) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
216 # if (is_url(line)) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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217 # url_list <- c(url_list, list(list(href = trimws(line)))) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
218 # } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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219 #} |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
220 con <- file(inputParameters[[key]], "r") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
221 lines <- readLines(con) |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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222 print("--------------------------------------------------------------------1") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
223 print(length(lines)) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
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changeset
|
224 close(con) |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
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225 if (!length(lines) > 1 && endsWith(lines, ".jp2") && startsWith(lines, "https")) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
|
226 print("--------------------------------------------------------------------2") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
|
227 tmp <- list() |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
|
228 tmp$href <- lines |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
|
229 tmp$type <- "image/jp2" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
|
230 inputParameters[[key]] <- tmp |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
231 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
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232 else if (!length(lines) > 1 && endsWith(lines, ".SAFE") && startsWith(lines, "s3:")) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
|
233 print("--------------------------------------------------------------------3") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
234 json_string <- paste(lines, collapse = "\n") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
235 inputParameters[[key]] <- json_string |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
236 } else if (inputParameters$select_process == "plot-image" || |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
237 inputParameters$select_process == "reproject-image") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
238 print("--------------------------------------------------------------------4") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
239 tmp <- list() |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
240 tmp$href <- lines |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
241 tmp$type <- "image/tiff; application=geotiff" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
242 if (inputParameters$select_process == "reproject-image") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
243 tmp$type <- "image/tiff; subtype=geotiff" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
244 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
245 inputParameters[[key]] <- tmp |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
246 } else { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
247 print("-----------------------------------5") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
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248 json_string <- paste(lines, collapse = "\n") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
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249 json_data <- fromJSON(json_string) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
250 inputParameters[[key]] <- json_data |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
251 } |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
252 convertedKeys <- append(convertedKeys, key) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
253 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
254 else if (grepl("_Array_", key)) { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
255 keyParts <- strsplit(key, split = "_")[[1]] |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
256 type <- keyParts[length(keyParts)] |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
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257 values <- inputParameters[[key]] |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
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258 value_list <- strsplit(values, split = ",") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
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259 convertedValues <- c() |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
260 |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
261 for (value in value_list) { |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
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262 if (type == "integer") { |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
263 value <- as.integer(value) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
264 } else if (type == "numeric") { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
265 value <- as.numeric(balue) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
266 } else if (type == "character") { |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
267 value <- as.character(value) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
268 } |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
269 convertedValues <- append(convertedValues, value) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
270 |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
271 convertedKey <- "" |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
272 for (part in keyParts) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
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273 if (part == "Array") { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
274 break |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
275 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
276 convertedKey <- |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
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277 paste(convertedKey, paste(part, "_", sep = ""), sep = "") |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
278 } |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
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279 convertedKey <- substr(convertedKey, 1, nchar(convertedKey) - 1) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
280 } |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
281 |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
282 inputParameters[[key]] <- convertedValues |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
283 #print("-------------------------") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
284 #print(convertedValues) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
285 #print("-------------------------") |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
286 convertedKeys <- append(convertedKeys, convertedKey) |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
287 } else { |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
|
288 #print("-------------------------") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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289 #print(key) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
|
290 #print(inputParameters[[key]]) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
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291 if (!is.null(inputParameters[[key]])) { |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
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292 convertedKeys <- append(convertedKeys, key) |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
293 } |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
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294 #print("-------------------------") |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
295 |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
296 } |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
297 } |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
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diff
changeset
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298 #print(inputParameters) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
299 names(inputParameters) <- convertedKeys |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
300 #print(inputParameters) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
301 print("--> Inputs parsed") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
302 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
303 print("--> Prepare process execution") |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
304 jsonData <- list("inputs" = inputParameters, |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
305 "outputs" = outputs) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
306 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
307 cookie <- inputParameters$cookie |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
308 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
309 print("--> Execute process") |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
310 jobID <- |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
311 executeProcess(server, inputParameters$select_process, jsonData, cookie) |
0
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
312 print("--> Process executed") |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
313 |
afede0916f0a
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
ecology
parents:
diff
changeset
|
314 print("--> Retrieve results") |
1
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
0
diff
changeset
|
315 retrieveResults(server, |
52baddd15640
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
ecology
parents:
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diff
changeset
|
316 inputParameters$select_process, |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
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317 jobID, |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
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318 outputLocation, |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381
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319 cookie) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
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320 print("--> Results retrieved") |