# HG changeset patch
# User ecology
# Date 1717760253 0
# Node ID afede0916f0ac693cb0cb0bb63e26d2e34901e83
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
diff -r 000000000000 -r afede0916f0a crim_project_ogc_api_processes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/crim_project_ogc_api_processes.xml Fri Jun 07 11:37:33 2024 +0000
@@ -0,0 +1,221 @@
+
+ executes remote processes.
+
+ macros.xml
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+ Use the dropdown menu at the top to select the process and then complete the corresponding from, which is different for every process.
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diff -r 000000000000 -r afede0916f0a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jun 07 11:37:33 2024 +0000
@@ -0,0 +1,47 @@
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+ r-base
+ r-getopt
+ r-httr2
+ r-jsonlite
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+ @Manual{httr2, title = {httr2: Perform HTTP Requests and Process the Responses}, author = {Hadley Wickham}, year = {2023}, note = {R package version 1.0.0, https://github.com/r-lib/httr2}, url = {https://httr2.r-lib.org},}
+ 10.48550/arXiv.1403.2805
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+
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+ This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.
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diff -r 000000000000 -r afede0916f0a ogc_api_processes_wrapper.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ogc_api_processes_wrapper.R Fri Jun 07 11:37:33 2024 +0000
@@ -0,0 +1,239 @@
+library("httr2")
+library("jsonlite")
+library("getopt")
+
+cat("start generic wrapper service \n")
+
+getParameters <- function(){
+ con <- file("inputs.json", "r")
+ lines <- readLines(con)
+ close(con)
+
+ json_string <- paste(lines, collapse = "\n")
+ json_data <- fromJSON(json_string)
+ return(json_data$conditional_process)
+}
+
+parseResponseBody <- function(body) {
+ hex <- c(body)
+ intValues <- as.integer(hex)
+ rawVector <- as.raw(intValues)
+ readableOutput <- rawToChar(rawVector)
+ jsonObject <- jsonlite::fromJSON(readableOutput)
+ return(jsonObject)
+}
+
+getOutputs <- function(inputs, output, server) {
+ url <- paste(paste(server, "/processes/", sep = ""), inputs$select_process, sep = "")
+ request <- request(url)
+ response <- req_perform(request)
+ responseBody <- parseResponseBody(response$body)
+ outputs <- list()
+
+ for (x in 1:length(responseBody$outputs)) {
+ outputformatName <- paste(names(responseBody$outputs[x]), "_outformat", sep="")
+ output_item <- list()
+
+ for (p in names(inputs)) {
+ if(p == outputformatName){
+ format <- list("mediaType" = inputs[[outputformatName]])
+ output_item$format <- format
+ }
+ }
+ output_item$transmissionMode <- "reference"
+ outputs[[x]] <- output_item
+ }
+
+ names(outputs) <- names(responseBody$outputs)
+ return(outputs)
+}
+
+executeProcess <- function(url, process, requestBodyData, cookie) {
+ url <- paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "")
+ requestBodyData$inputs$cookie <- NULL
+ requestBodyData$inputs$select_process <- NULL
+
+ requestBodyData$inputs$s3_access_key <- requestBodyData$inputs$user_credentials$s3_access_key
+ requestBodyData$inputs$s3_secret_key <- requestBodyData$inputs$user_credentials$s3_secret_key
+ requestBodyData$inputs$user_credentials <- NULL
+
+ body <- list()
+ body$inputs <- requestBodyData$inputs
+ body$mode <- "async"
+ body$response <- "document"
+
+ response <- request(url) %>%
+ req_headers(
+ "Accept" = "application/json",
+ "Content-Type" = "application/json",
+ "Cookie" = cookie
+ ) %>%
+ req_body_json(body) %>%
+ req_perform()
+
+ cat("\n Process executed")
+ cat("\n status: ", response$status_code)
+ cat("\n jobID: ", parseResponseBody(response$body)$jobID, "\n")
+
+ jobID <- parseResponseBody(response$body)$jobID
+
+ return(jobID)
+}
+
+checkJobStatus <- function(server, process, jobID, cookie) {
+ url <- paste0(server, "processes/", process, "/jobs/", jobID)
+ response <- request(url) %>%
+ req_headers(
+ "Cookie" = cookie
+ ) %>%
+ req_perform()
+ jobStatus <- parseResponseBody(response$body)$status
+ jobProgress <- parseResponseBody(response$body)$progress
+ return(jobStatus)
+}
+
+getStatusCode <- function(server, process, jobID, cookie) {
+ url <- paste0(server, "processes/", process, "/jobs/", jobID)
+ response <- request(url) %>%
+ req_headers(
+ "Cookie" = cookie
+ ) %>%
+ req_perform()
+ status_code <- response$status_code
+ return(status_code)
+}
+
+getResult <- function (server, process, jobID, cookie) {
+ response <- request(paste0(server, "processes/", process, "/jobs/", jobID, "/results")) %>%
+ req_headers(
+ "Cookie" = cookie
+ ) %>%
+ req_perform()
+ return(response)
+}
+
+retrieveResults <- function(server, process, jobID, outputData, cookie) {
+ status_code <- getStatusCode(server, process, jobID, cookie)
+ if(status_code == 200){
+ status <- "running"
+ while(status == "running"){
+ jobStatus <- checkJobStatus(server, process, jobID, cookie)
+ print(jobStatus)
+ if (jobStatus == "succeeded") {
+ status <- jobStatus
+ result <- getResult(server, process, jobID, cookie)
+ if (result$status_code == 200) {
+ resultBody <- parseResponseBody(result$body)
+ urls <- unname(unlist(lapply(resultBody, function(x) x$href)))
+ urls_with_newline <- paste(urls, collapse = "\n")
+ con <- file(outputData, "w")
+ writeLines(urls_with_newline, con = con)
+ close(con)
+ }
+ } else if (jobStatus == "failed") {
+ status <- jobStatus
+ }
+ Sys.sleep(3)
+ }
+ cat("\n done \n")
+ } else if (status_code1 == 400) {
+ print("A query parameter has an invalid value.")
+ } else if (status_code1 == 404) {
+ print("The requested URI was not found.")
+ } else if (status_code1 == 500) {
+ print("The requested URI was not found.")
+ } else {
+ print(paste("HTTP", status_code1, "Error:", resp1$status_message))
+ }
+}
+
+is_url <- function(x) {
+ grepl("^https?://", x)
+}
+
+server <- "https://hirondelle.crim.ca/weaver/"
+
+print("--> Retrieve parameters")
+inputParameters <- getParameters()
+print("--> Parameters retrieved")
+
+args <- commandArgs(trailingOnly = TRUE)
+outputLocation <- args[2]
+
+print("--> Retrieve outputs")
+outputs <- getOutputs(inputParameters, outputLocation, server)
+print("--> Outputs retrieved")
+
+print("--> Parse inputs")
+convertedKeys <- c()
+for (key in names(inputParameters)) {
+ if (is.character(inputParameters[[key]]) && (endsWith(inputParameters[[key]], ".dat") || endsWith(inputParameters[[key]], ".txt"))) {
+ con <- file(inputParameters[[key]], "r")
+ url_list <- list()
+ #while (length(line <- readLines(con, n = 1)) > 0) {
+ # if (is_url(line)) {
+ # url_list <- c(url_list, list(list(href = trimws(line))))
+ # }
+ #}
+ con <- file(inputParameters[[key]], "r")
+ lines <- readLines(con)
+ close(con)
+ json_string <- paste(lines, collapse = "\n")
+ json_data <- fromJSON(json_string)
+
+ inputParameters[[key]] <- json_data
+ convertedKeys <- append(convertedKeys, key)
+ }
+ else if (grepl("_Array_", key)) {
+ keyParts <- strsplit(key, split = "_")[[1]]
+ type <- keyParts[length(keyParts)]
+ values <- inputParameters[[key]]
+ value_list <- strsplit(values, split = ",")
+
+ convertedValues <- c()
+
+ for (value in value_list) {
+ if(type == "integer") {
+ value <- as.integer(value)
+ } else if (type == "numeric") {
+ value <- as.numeric(balue)
+ } else if (type == "character") {
+ value <- as.character(value)
+ }
+ convertedValues <- append(convertedValues, value)
+
+ convertedKey <- ""
+ for (part in keyParts) {
+ if(part == "Array") {
+ break
+ }
+ convertedKey <- paste(convertedKey, paste(part, "_", sep=""), sep="")
+ }
+ convertedKey <- substr(convertedKey, 1, nchar(convertedKey)-1)
+}
+
+ inputParameters[[key]] <- convertedValues
+ convertedKeys <- append(convertedKeys, convertedKey)
+ } else {
+ convertedKeys <- append(convertedKeys, key)
+ }
+}
+
+names(inputParameters) <- convertedKeys
+print("--> Inputs parsed")
+
+print("--> Prepare process execution")
+jsonData <- list(
+ "inputs" = inputParameters,
+ "outputs" = outputs
+)
+
+cookie <- inputParameters$cookie
+
+print("--> Execute process")
+jobID <- executeProcess(server, inputParameters$select_process, jsonData, cookie)
+print("--> Process executed")
+
+print("--> Retrieve results")
+retrieveResults(server, inputParameters$select_process, jobID, outputLocation, cookie)
+print("--> Results retrieved")
\ No newline at end of file
diff -r 000000000000 -r afede0916f0a test-data/crim_test_input.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/crim_test_input.json Fri Jun 07 11:37:33 2024 +0000
@@ -0,0 +1,4 @@
+{
+ "s3_access_key": "1234",
+ "s3_secret_key": "abcd"
+}