# HG changeset patch # User ecology # Date 1725618622 0 # Node ID 92ca20fdb7902c706f53973d1d1147efe2ee0202 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 8b4b58222af2c77abd41dd8f17862a24ca7d3381 diff -r 000000000000 -r 92ca20fdb790 crim_project_ogc_api_processes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crim_project_ogc_api_processes.xml Fri Sep 06 10:30:22 2024 +0000 @@ -0,0 +1,121 @@ + + executes remote processes. + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Use the dropdown menu at the top to select the process and then complete the corresponding from, which is different for every process. + + \ No newline at end of file diff -r 000000000000 -r 92ca20fdb790 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 06 10:30:22 2024 +0000 @@ -0,0 +1,47 @@ + + + + r-base + r-getopt + r-httr2 + r-jsonlite + + + + + + + + + + + + + + + + + + @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 + + + + 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. + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r 92ca20fdb790 ogc_api_processes_wrapper.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ogc_api_processes_wrapper.R Fri Sep 06 10:30:22 2024 +0000 @@ -0,0 +1,320 @@ +library("httr2") +library("jsonlite") +library("getopt") + +cat("start generic wrapper service \n") + +remove_null_values <- function(x) { + # Check if the input is a list + if (is.list(x)) { + # Remove NULL values and apply the function recursively to sublists + x <- lapply(x, remove_null_values) + x <- x[!sapply(x, is.null)] + } + return(x) +} + +getParameters <- function() { + con <- file("inputs.json", "r") + lines <- readLines(con) + close(con) + + json_string <- paste(lines, collapse = "\n") + json_data <- fromJSON(json_string) + + # Remove NULL values from json_data + cleaned_json_data <- remove_null_values(json_data) + return(cleaned_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 + if (process == "plot-image") { + tmp <- requestBodyData$inputs$color_scale + color_scale <- gsub("__ob__", "[", tmp) + color_scale <- gsub("__cb__", "]", color_scale) + requestBodyData$inputs$color_scale <- color_scale + #print(requestBodyData$inputs$color_scale) + } + if (process == "calculate-band") { + requestBodyData$inputs$name <- "output" + } + if (process == "reproject-image") { + requestBodyData$inputs$output_name <- "output" + } + #requestBodyData$inputs$input_image$href <- "https://hirondelle.crim.ca/wpsoutputs/weaver/public/test-data/S2A_MSIL2A_20190701T110621_N0500_R137_T29SPC_20230604T023542_turbidity.tiff" + + body <- list() + body$inputs <- requestBodyData$inputs + #print(body$inputs) + body$mode <- "async" + body$response <- "document" + #print(body$inputs) + + response <- request(url) %>% + req_headers("Accept" = "application/json", + "Content-Type" = "application/json", + "Cookie" = cookie) %>% + req_body_json(body) %>% + req_perform() + + cat("\n Process executed") + cat("\n status: ", response$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$body) + #print(resultBody) + if (process == "select-products-sentinel2") { + urls <- unname(unlist(lapply(resultBody, function(x) + x$value))) + } else if (process == "download-band-sentinel2-product-safe" || + process == "calculate-band" || + process == "plot-image" || process == "reproject-image") { + 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(inputParameters) +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) + print("--------------------------------------------------------------------1") + print(length(lines)) + close(con) + if (!length(lines) > 1 && endsWith(lines, ".jp2") && startsWith(lines, "https")) { + print("--------------------------------------------------------------------2") + tmp <- list() + tmp$href <- lines + tmp$type <- "image/jp2" + inputParameters[[key]] <- tmp + } + else if (!length(lines) > 1 && endsWith(lines, ".SAFE") && startsWith(lines, "s3:")) { + print("--------------------------------------------------------------------3") + json_string <- paste(lines, collapse = "\n") + inputParameters[[key]] <- json_string + } else if (inputParameters$select_process == "plot-image" || + inputParameters$select_process == "reproject-image") { + print("--------------------------------------------------------------------4") + tmp <- list() + tmp$href <- lines + tmp$type <- "image/tiff; application=geotiff" + if (inputParameters$select_process == "reproject-image") { + tmp$type <- "image/tiff; subtype=geotiff" + } + inputParameters[[key]] <- tmp + } else { + print("-----------------------------------5") + 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 + #print("-------------------------") + #print(convertedValues) + #print("-------------------------") + convertedKeys <- append(convertedKeys, convertedKey) + } else { + #print("-------------------------") + #print(key) + #print(inputParameters[[key]]) + if (!is.null(inputParameters[[key]])) { + convertedKeys <- append(convertedKeys, key) + } + #print("-------------------------") + + } +} +#print(inputParameters) +names(inputParameters) <- convertedKeys +#print(inputParameters) +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 92ca20fdb790 test-data/crim_test_input.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crim_test_input.json Fri Sep 06 10:30:22 2024 +0000 @@ -0,0 +1,4 @@ +{ + "s3_access_key": "1234", + "s3_secret_key": "abcd" +} diff -r 000000000000 -r 92ca20fdb790 test-data/product_url.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/product_url.txt Fri Sep 06 10:30:22 2024 +0000 @@ -0,0 +1,1 @@ +s3:///eodata/Sentinel-2/MSI/L2A/2019/07/01/S2A_MSIL2A_20190701T110621_N0212_R137_T29SPC_20190701T120906.SAFE \ No newline at end of file