Mercurial > repos > ecology > otb_mean_shift_smoothing

annotate OTB_MeanShiftSmoothing.R @ 1:dd397752ad21 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit 5e963dcfe6e22e42473987179b70ad490f918cb9
author ecology
date Fri, 12 Apr 2024 18:41:57 +0000
parents 6c6e8b16dba6
children
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6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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1 # Run with Rscript ./OTB_MeanShiftSmoothing.R
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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2 #--file otb_band_math_test_input.txt
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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3 #--fOut float --fOutpos float --processingMemory 1024 --spatialR 5 --rangeR 15
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4 #--thresHold 0.1 --maxIter 100 --rangeRamp 0 --modeSearch False
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5 #--outputType png
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6 #--outputFormat download --outputData test1.png
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7
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8 library("httr2")
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9 library("jsonlite")
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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10 library("getopt")
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11
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12 args <- commandArgs(trailingOnly = TRUE)
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13 option_specification <- matrix(c(
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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14 "file", "i1", 1, "character",
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15 "fOut", "i2", 1, "character",
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16 "fOutpos", "i3", 1, "character",
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17 "processingMemory", "i4", 1, "integer",
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18 "spatialR", "i5", 2, "integer",
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19 "rangeR", "i6", 2, "double",
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20 "thresHold", "i7", 2, "double",
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21 "maxIter", "i8", 2, "integer",
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22 "rangeRamp", "i9", 2, "double",
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23 "modeSearch", "i10", 1, "character",
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24 "outputType", "i11", 1, "character",
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25 "outputFormat", "i12", 1, "character",
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26 "outputData", "o", 1, "character"
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27 ), byrow = TRUE, ncol = 4)
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28 options <- getopt(option_specification)
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29
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30 file <- options$file
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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31 fout <- options$fOut
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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32 foutpos <- options$fOutpos
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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33 processing_memory <- options$processingMemory
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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34 spatialr <- options$spatialR
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35 ranger <- options$rangeR
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36 threshold <- options$thresHold
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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37 maxiter <- options$maxIter
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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38 rangeramp <- options$rangeRamp
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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39 modesearch <- options$modeSearch
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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40 output_type <- paste0("image/", options$outputType)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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41 output_format <- options$outputFormat
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42 output_data <- options$outputData
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43
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44 cat("\n file: ", file)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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45 cat("\n fout: ", fout)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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46 cat("\n foutpos: ", foutpos)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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47 cat("\n processing_memory: ", processing_memory)
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48 cat("\n spatialr: ", spatialr)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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49 cat("\n ranger: ", ranger)
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50 cat("\n threshold: ", threshold)
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51 cat("\n maxiter: ", maxiter)
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52 cat("\n rangeramp: ", rangeramp)
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53 cat("\n modesearch: ", modesearch)
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54 cat("\n output_type: ", output_type)
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55 cat("\n output_format: ", output_format)
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56
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57 base_url <- "https://ospd.geolabs.fr:8300/ogc-api/"
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58 execute <- "processes/OTB.MeanShiftSmoothing/execution"
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59 get_status <- "jobs/"
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60 get_result <- "/results"
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61
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62 file_urls <- readLines(file, warn = FALSE)
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63
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64 il_list <- lapply(file_urls, function(url) {
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65 list("href" = url)
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66 })
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67
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68 json_data <- list(
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69 "inputs" = list(
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70 "in" = il_list,
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71 "fout" = fout,
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72 "foutpos" = foutpos,
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73 "ram" = processing_memory,
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74 "spatialr" = spatialr,
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75 "ranger" = ranger,
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76 "thres" = threshold,
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77 "maxiter" = maxiter,
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78 "rangeramp" = rangeramp,
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79 "modesearch" = modesearch
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80 ),
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81 "outputs" = list(
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82 "fout" = list(
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83 "format" = list(
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84 "mediaType" = output_type
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85 ),
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86 "transmissionMode" = "reference"
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
87 ),
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
88 "foutpos" = list(
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
89 "format" = list(
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
90 "mediaType" = output_type
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
91 ),
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
92 "transmissionMode" = "reference"
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
93 )
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
94 )
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
95 )
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
96
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
97 make_response_body_readable <- function(body) {
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
98 hex <- c(body)
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ecology
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diff changeset
99 int_values <- as.integer(hex)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
100 raw_vector <- as.raw(int_values)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
101 readable_output <- rawToChar(raw_vector)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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102 json_object <- jsonlite::fromJSON(readable_output)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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103 return(json_object)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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104 }
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
parents:
diff changeset
105
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
106 tryCatch({
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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107 # Request 1
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ecology
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108 resp1 <- request(paste0(base_url, execute)) %>%
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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109 req_headers(
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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110 "accept" = "/*",
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ecology
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111 "Prefer" = "respond-async;return=representation",
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ecology
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112 "Content-Type" = "application/json"
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ecology
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113 ) %>%
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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114 req_body_json(json_data) %>%
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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115 req_perform()
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ecology
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116 response <- make_response_body_readable(resp1$body)
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ecology
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117 status_code1 <- resp1$status_code
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ecology
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118 if (status_code1 == 201) {
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ecology
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119 status <- "running"
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ecology
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120 attempt <- 1
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ecology
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diff changeset
121 while (status == "running") {
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ecology
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diff changeset
122 # Request 2
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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123 resp2 <- request(paste0(base_url, get_status, response$jobID)) %>%
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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124 req_headers(
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ecology
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125 "accept" = "application/json"
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ecology
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126 ) %>%
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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127 req_perform()
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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128 status_code2 <- resp2$status_code
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ecology
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diff changeset
129 if (status_code2 == 200) {
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ecology
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130 response2 <- make_response_body_readable(resp2$body)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
131 cat("\n", response2$status)
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ecology
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132 if (response2$status == "successful") {
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ecology
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diff changeset
133 status <- "successful"
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ecology
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diff changeset
134 # Request 3
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ecology
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diff changeset
135 resp3 <- request(paste0(
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
136 base_url,
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
137 get_status, response2$jobID, get_result
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ecology
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diff changeset
138 )) %>%
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
139 req_headers(
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
140 "accept" = "application/json"
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ecology
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diff changeset
141 ) %>%
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ecology
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diff changeset
142 req_perform()
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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143 status_code3 <- resp3$status_code
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
144 if (status_code3 == 200) {
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ecology
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diff changeset
145 response3 <- make_response_body_readable(resp3$body)
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ecology
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146 if (output_format == "download") {
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ecology
parents:
diff changeset
147 options(timeout = 600)
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ecology
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148 download.file(response3$fout$href,
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ecology
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149 destfile = paste0("output1.", options$outputType),
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ecology
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diff changeset
150 mode = "wb"
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ecology
parents:
diff changeset
151 )
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ecology
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diff changeset
152 download.file(response3$foutpos$href,
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ecology
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153 destfile = paste0("output2.", options$outputType),
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ecology
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diff changeset
154 mode = "wb"
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ecology
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diff changeset
155 )
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ecology
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diff changeset
156 } else if (output_format == "getUrl") {
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ecology
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diff changeset
157 writeLines(paste(response3$fout$href, response3$foutpos$href,
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
ecology
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diff changeset
158 sep = "\n"
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ecology
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diff changeset
159 ), con = "output.txt")
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ecology
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diff changeset
160 }
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ecology
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diff changeset
161 } else if (status_code3 == 404) {
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ecology
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diff changeset
162 print("The requested URI was not found.")
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ecology
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diff changeset
163 } else if (status_code3 == 500) {
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ecology
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diff changeset
164 print("A server error occurred.")
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ecology
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diff changeset
165 } else {
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ecology
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166 print(paste("HTTP", status_code3, "Error:", resp3$status_message))
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ecology
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diff changeset
167 }
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ecology
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168 } else if (response2$status == "failed") {
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ecology
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169 status <- "failed"
1
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ecology
parents: 0
diff changeset
170 message("An error occurred. For further details, check OGC Job status
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ecology
parents: 0
diff changeset
171 through https://ospd.geolabs.fr:8300/ogc-api/jobs/", response2$jobID)
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ecology
parents: 0
diff changeset
172 q(status = 1)
0
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ecology
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diff changeset
173 }
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ecology
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diff changeset
174 } else {
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ecology
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175 status <- "failed"
1
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176 print(paste("HTTP", status_code2, "Error:", resp2$status_message, "An error occurred. For further details,
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177 check OGC Job status through https://ospd.geolabs.fr:8300/ogc-api/jobs/", response2$jobID))
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178 q(status = 1)
0
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179 }
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180 Sys.sleep(3)
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181 }
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182 print(status)
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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183 } else if (status_code1 == 400) {
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184 print("A query parameter has an invalid value.")
6c6e8b16dba6 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit bd6f07bf29bad450af2e552f2524f23277edfef5-dirty
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185 } else if (status_code1 == 404) {
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186 print("The requested URI was not found.")
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187 } else if (status_code1 == 500) {
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188 print("The requested URI was not found.")
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189 } else {
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190 print(paste("HTTP", status_code1, "Error:", resp1$status_message))
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191 }
1
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192 }, error = function(e) {
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193 message("An error occurred:", e)
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194 # Exit with code 1
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195 q(status = 1)
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196 })