changeset 0:afede0916f0a draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
author ecology
date Fri, 07 Jun 2024 11:37:33 +0000
parents
children
files crim_project_ogc_api_processes.xml macros.xml ogc_api_processes_wrapper.R test-data/crim_test_input.json
diffstat 4 files changed, 511 insertions(+), 0 deletions(-) [+]
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--- /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 @@
+<tool id="hirondelle_crim" name="Hirondelle CRIM OGC API Processes" version="0.1.0" profile="22.05">
+	<description>executes remote processes.</description>
+	<macros>
+		<import>macros.xml</import>
+	</macros>
+	<expand macro="requirements"/>
+	<command detect_errors="exit_code"><![CDATA[
+	Rscript '$__tool_directory__/ogc_api_processes_wrapper.R'
+		--outputData '$output_data'
+]]></command>
+	<configfiles>
+		<inputs name="inputs" filename="inputs.json" data_style="paths"/>
+	</configfiles>
+	<inputs>
+		<conditional name="conditional_process">
+			<param name="select_process" type="select" label="Select process">
+				<option value="algae-usecase-workflow-copernicus">algae-usecase-workflow-copernicus: Algae bloom for water quality assessment on Sentinel-2 imagery offered by Copernicus platform.</option>
+				<option value="algae-usecase-workflow-copernicus-process">algae-usecase-workflow-copernicus-process: Processing on Sentinel-2 bands to evaluate algae bloom.</option>
+				<option value="algae-usecase-workflow-earth-search">algae-usecase-workflow-earth-search: Algae bloom for water quality assessment on Sentinel-2 L2A imagery offered by Earth-Search platform.</option>
+				<option value="algae-usecase-workflow-earth-search-process">algae-usecase-workflow-earth-search-process: Processing on Sentinel-2 L2A bands to evaluate algae bloom.</option>
+				<option value="calculate-band">calculate-band: Performs a calculation with bands.</option>
+				<option value="download-band-sentinel2-product-safe">download-band-sentinel2-product-safe: Downloads Copernicus products.</option>
+				<option value="download-band-sentinel2-stac-item">download-band-sentinel2-stac-item: Downloads Sentinel-2 GeoTiff from STAC Item.</option>
+				<option value="EchoProcess">EchoProcess</option>
+				<option value="file_index_selector">file_index_selector: File Index Selector</option>
+				<option value="file2string_array">file2string_array: File to String-Array</option>
+				<option value="jsonarray2netcdf">jsonarray2netcdf: JSON array to NetCDF</option>
+				<option value="metalink2netcdf">metalink2netcdf: Metalink to NetCDF</option>
+				<option value="ogc-tb16-land-cover-mapping">ogc-tb16-land-cover-mapping: OGC Testbed-16 Pixel-Wise Classifier for Land Cover Mapping</option>
+				<option value="plot-image">plot-image: Plots an image with colors.</option>
+				<option value="reproject-image">reproject-image: Performs image reprojection.</option>
+				<option value="select-products-sentinel2">select-products-sentinel2: Searches the specified catalog for Sentinel-2 products matching filtering criteria.</option>
+			</param>
+			<when value="algae-usecase-workflow-copernicus">
+				<param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/>
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="date" label="date" optional="false" value="" type="text"/>
+				<param name="delta_Array_integer" label="delta" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/>
+				<param name="aoi" label="aoi" optional="false" value="" type="data" format="txt"/>
+				<param name="collection" label="collection" optional="false" value="" type="text"/>
+				<param name="cloud_cover_Array_float" label="cloud_cover" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/>
+			</when>
+			<when value="algae-usecase-workflow-copernicus-process">
+				<param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/>
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="product_url" label="product_url" optional="false" value="" type="text"/>
+			</when>
+			<when value="algae-usecase-workflow-earth-search">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="date_Array_text" label="date" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+				<param name="delta_Array_integer" label="delta" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/>
+				<param name="toi_Array_text" label="toi" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+				<param name="aoi" label="aoi" optional="false" value="" help="Polygon defining the area of interest." type="data" format="txt"/>
+				<param name="collection" label="collection" optional="false" value="" type="text"/>
+				<param name="cloud_cover_Array_float" label="cloud_cover" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/>
+			</when>
+			<when value="algae-usecase-workflow-earth-search-process">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="product_url" label="product_url" optional="false" value="" help="The STAC Item should contain Assets with Sentinel-2 product bands." type="text"/>
+			</when>
+			<when value="calculate-band">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="name" label="name" optional="false" value="" help="Name to apply for the output GeoTiff file." type="text"/>
+				<param name="calc" label="calc" optional="false" value="" help="Calculation to perform with band references." type="text"/>
+				<param name="band_a" label="band_a" optional="false" value="" type="text"/>
+				<param name="band_b" label="band_b" optional="false" value="" type="text"/>
+				<param name="band_c" label="band_c" optional="false" value="" type="text"/>
+				<param name="band_d" label="band_d" optional="false" value="" type="text"/>
+				<param name="band_e" label="band_e" optional="false" value="" type="text"/>
+				<param name="band_f" label="band_f" optional="false" value="" type="text"/>
+				<param name="band_g" label="band_g" optional="false" value="" type="text"/>
+				<param name="band_h" label="band_h" optional="false" value="" type="text"/>
+				<param name="band_i" label="band_i" optional="false" value="" type="text"/>
+				<param name="band_j" label="band_j" optional="false" value="" type="text"/>
+				<param name="band_k" label="band_k" optional="false" value="" type="text"/>
+				<param name="band_l" label="band_l" optional="false" value="" type="text"/>
+				<param name="band_m" label="band_m" optional="false" value="" type="text"/>
+				<param name="band_n" label="band_n" optional="false" value="" type="text"/>
+				<param name="band_o" label="band_o" optional="false" value="" type="text"/>
+				<param name="band_p" label="band_p" optional="false" value="" type="text"/>
+				<param name="band_q" label="band_q" optional="false" value="" type="text"/>
+				<param name="band_r" label="band_r" optional="false" value="" type="text"/>
+				<param name="band_s" label="band_s" optional="false" value="" type="text"/>
+				<param name="band_t" label="band_t" optional="false" value="" type="text"/>
+				<param name="band_u" label="band_u" optional="false" value="" type="text"/>
+				<param name="band_v" label="band_v" optional="false" value="" type="text"/>
+				<param name="band_w" label="band_w" optional="false" value="" type="text"/>
+				<param name="band_x" label="band_x" optional="false" value="" type="text"/>
+				<param name="band_y" label="band_y" optional="false" value="" type="text"/>
+				<param name="band_z" label="band_z" optional="false" value="" type="text"/>
+			</when>
+			<when value="download-band-sentinel2-product-safe">
+				<param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/>
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="product_url" label="product_url" optional="false" value="" type="text"/>
+				<param name="resolution_Array_text" label="resolution" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+				<param name="band" label="band" optional="false" value="" type="select">
+					<option value="B01">B01</option>
+					<option value="B02">B02</option>
+					<option value="B03">B03</option>
+					<option value="B04">B04</option>
+					<option value="B05">B05</option>
+					<option value="B06">B06</option>
+					<option value="B07">B07</option>
+					<option value="B08">B08</option>
+					<option value="B8A">B8A</option>
+					<option value="B09">B09</option>
+					<option value="B11">B11</option>
+					<option value="B12">B12</option>
+					<option value="AOT">AOT</option>
+					<option value="SCL">SCL</option>
+					<option value="TCI">TCI</option>
+					<option value="WVP">WVP</option>
+				</param>
+				<param name="debug_Array_boolean" label="debug" value="" help="Please provide comma-seperated values of type boolean here." type="text"/>
+			</when>
+			<when value="download-band-sentinel2-stac-item">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="product_url" label="product_url" optional="false" value="" type="text"/>
+				<param name="band" label="band" optional="false" value="" type="select">
+					<option value="B01">B01</option>
+					<option value="B02">B02</option>
+					<option value="B03">B03</option>
+					<option value="B04">B04</option>
+					<option value="B05">B05</option>
+					<option value="B06">B06</option>
+					<option value="B07">B07</option>
+					<option value="B08">B08</option>
+					<option value="B8A">B8A</option>
+					<option value="B09">B09</option>
+					<option value="B11">B11</option>
+					<option value="B12">B12</option>
+					<option value="AOT">AOT</option>
+					<option value="SCL">SCL</option>
+					<option value="TCI">TCI</option>
+					<option value="WVP">WVP</option>
+				</param>
+			</when>
+			<when value="EchoProcess">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="stringInput" label="stringInput" optional="false" value="" type="select">
+					<option value="Value1">Value1</option>
+					<option value="Value2">Value2</option>
+					<option value="Value3">Value3</option>
+				</param>
+				<param name="measureInput" label="measureInput" optional="false" help="This is an example of a NUMERIC literal with an associated unit of measure." type="text"/>
+				<param name="dateInput" label="dateInput" optional="false" value="" help="This is an example of a DATE literal input." type="text"/>
+				<param name="doubleInput" label="doubleInput" optional="false" value="" help="This is an example of a DOUBLE literal input that is bounded between a value greater than 0 and 10. The default value is 5." type="float"/>
+				<param name="arrayInput_Array_integer" label="arrayInput" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/>
+				<param name="complexObjectInput" label="complexObjectInput" optional="false" help="This is an example of a complex object input." type="text"/>
+				<param name="geometryInput" label="geometryInput" optional="false" value="" help="This is an example of a geometry input. In this case the geometry can be expressed as a GML of GeoJSON geometry." type="text"/>
+				<param name="boundingBoxInput" label="boundingBoxInput" optional="false" help="This is an example of an image input. In this case, the input is an array of up to 150 images that might, for example, be a set of tiles.  The oneOf[] conditional is used to indicate the acceptable image content types; GeoTIFF and JPEG 2000 in this case.  Each input image in the input array can be included inline in the execute request as a base64-encoded string or referenced using the link.yaml schema.  The use of a base64-encoded string is implied by the specification and does not need to be specified in the definition of the input." type="data" format="txt"/>
+				<param name="imagesInput" label="imagesInput" optional="false" help="This is an example of an image input.  In this case, the input is an array of up to 150 images that might, for example, be a set of tiles.  The oneOf[] conditional is used to indicate the acceptable image content types; GeoTIFF and JPEG 2000 in this case.  Each input image in the input array can be included inline in the execute request as a base64-encoded string or referenced using the link.yaml schema.  The use of a base64-encoded string is implied by the specification and does not need to be specified in the definition of the input." type="data" format="txt"/>
+				<param name="featureCollectionInput" label="featureCollectionInput" optional="false" help="This is an example of an input that is a feature collection that can be encoded in one of three ways. As a GeoJSON feature collection, as a GML feature collection retrieved from a WFS or as a KML document." type="text"/>
+			</when>
+			<when value="file_index_selector">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="files" label="files" optional="false" type="data" format="txt"/>
+				<param name="index" label="index" optional="false" value="" type="integer"/>
+			</when>
+			<when value="file2string_array">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="input" label="input" optional="false" value="" type="data" format="txt"/>
+			</when>
+			<when value="jsonarray2netcdf">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="input" label="input" optional="false" value="" help="JSON file formed of an array of file URIs, each representing NetCDF contents." type="text"/>
+			</when>
+			<when value="metalink2netcdf">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="input" label="input" optional="false" type="text"/>
+				<param name="index" label="index" optional="false" value="" help="Index of the MetaLink file to extract. This index is 1-based." type="integer"/>
+			</when>
+			<when value="ogc-tb16-land-cover-mapping">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="raster_file" label="raster_file" optional="false" help="Input raster onto which to run object classification. Either a Sentinel-2 SAFE ZIP or a RBG-NIR GeoTiff." type="data" format="txt"/>
+				<param name="raster_bands_Array_integer" label="raster_bands" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/>
+				<param name="raster_mean_Array_float" label="raster_mean" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/>
+				<param name="raster_std_Array_float" label="raster_std" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/>
+				<param name="patch_size_Array_integer" label="patch_size" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/>
+				<param name="batch_size_Array_integer" label="batch_size" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/>
+				<param name="device_Array_text" label="device" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+			</when>
+			<when value="plot-image">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="input_image" label="input_image" optional="false" value="" help="Image to map with the colors bins." type="data" format="txt"/>
+				<param name="color_scale" label="color_scale" optional="false" value="" help="JSON-like array with each item being an array of 2 elements, the first for the bin scale value and the second for the RGB color. Each RGB value can be either a [0-1] floating point or a [0-255] integer. Example: '[ [0, [0,0,0]], [20, [0,0,255]], [50, [255,100,0]] ]'" type="text"/>
+				<param name="output_name_Array_text" label="output_name" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+				<param name="plot_name_Array_text" label="plot_name" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+				<param name="plot_title_Array_text" label="plot_title" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+			</when>
+			<when value="reproject-image">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="input_image" label="input_image" optional="false" type="data" format="txt"/>
+				<param name="output_dimensions_Array_integer" label="output_dimensions" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/>
+				<param name="output_resolution_Array_integer" label="output_resolution" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/>
+				<param name="output_name" label="output_name" optional="false" value="" help="Name to apply for the output GeoTiff file." type="text"/>
+			</when>
+			<when value="select-products-sentinel2">
+				<param name="cookie" label="cookie" optional="false" value="" type="text"/>
+				<param name="date_Array_text" label="date" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+				<param name="delta_Array_integer" label="delta" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/>
+				<param name="toi_Array_text" label="toi" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+				<param name="aoi" label="aoi" optional="false" value="" help="Polygon defining the area of interest." type="data" format="txt"/>
+				<param name="collection" label="collection" optional="false" value="" type="text"/>
+				<param name="product_level_Array_text" label="product_level" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/>
+				<param name="catalog" label="catalog" optional="false" value="" type="select">
+					<option value="copernicus">copernicus</option>
+					<option value="earth-search">earth-search</option>
+				</param>
+				<param name="cloud_cover_Array_float" label="cloud_cover" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/>
+			</when>
+		</conditional>
+	</inputs>
+	<outputs>
+		<data name="output_data" format="txt" label="$select_process"/>
+	</outputs>
+	<expand macro="tests"/>
+	<help>Use the dropdown menu at the top to select the process and then complete the corresponding from, which is different for every process.</help>
+	<expand macro="citations"/>
+</tool>
--- /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 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="4.3.1">r-base</requirement>
+            <requirement type="package" version="1.20.4">r-getopt</requirement>
+            <requirement type="package" version="0.2.3">r-httr2</requirement>
+            <requirement type="package" version="1.8.7">r-jsonlite</requirement>
+        </requirements>
+    </xml>
+    <xml name="out_options">
+        <option value="uint8">uint8</option>
+        <option value="uint16">uint16</option>
+        <option value="int16">int16</option>
+        <option value="int32">int32</option>
+        <option value="float">float</option>
+        <option value="double">double</option>
+    </xml>
+    <xml name="format_options">
+        <option value="image/tiff">image/tiff</option>
+        <option value="image/jpeg">image/jpeg</option>
+        <option value="image/png">image/png</option>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@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},}</citation>
+            <citation type="doi">10.48550/arXiv.1403.2805</citation>
+        </citations>
+    </xml>
+    <xml name="help">
+        <help>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.</help>
+    </xml>
+    <xml name="tests">
+        <tests>
+            <test expect_failure="true">
+                <param name="select_process" value="download-band-sentinel2-product-safe"/>
+                <param name="user_credentials" value="crim_test_input.json"/>
+                <param name="cookie" value=""/>
+                <param name="product_url" value="s3:///eodata/Sentinel-2/MSI/L2A/2019/07/01/S2A_MSIL2A_20190701T110621_N0212_R137_T29SPC_20190701T120906.SAFE"/>
+                <param name="resolution_Array_text" value="10m"/>
+                <param name="band" value="B04"/>
+                <assert_stderr>
+                    <has_text text="HTTP 401 Unauthorized"/>
+                </assert_stderr>
+            </test>
+        </tests> 
+    </xml>
+</macros>
--- /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
--- /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"
+}