Mercurial > repos > ecology > hirondelle_crim
changeset 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 |
|---|---|
| date | Fri, 06 Sep 2024 10:30:30 +0000 |
| parents | afede0916f0a |
| children | |
| files | crim_project_ogc_api_processes.xml macros.xml ogc_api_processes_wrapper.R test-data/product_url.txt |
| diffstat | 4 files changed, 257 insertions(+), 275 deletions(-) [+] |
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--- a/crim_project_ogc_api_processes.xml Fri Jun 07 11:37:33 2024 +0000 +++ b/crim_project_ogc_api_processes.xml Fri Sep 06 10:30:30 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="hirondelle_crim" name="Hirondelle CRIM OGC API Processes" version="0.1.0" profile="22.05"> +<tool id="hirondelle_crim" name="Hirondelle CRIM OGC API Processes" version="0.2.0" profile="22.05"> <description>executes remote processes.</description> <macros> <import>macros.xml</import> @@ -14,87 +14,52 @@ <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"/> + <param name="calc" label="Calculation" optional="false" help="Calculation to perform with band references." type="text"/> + <param name="band_a" label="Band A" optional="true" type="data" format="txt"/> + <param name="band_b" label="Band B" optional="true" type="data" format="txt"/> + <param name="band_c" label="Band C" optional="true" type="data" format="txt"/> + <param name="band_d" label="Band D" optional="true" type="data" format="txt"/> + <param name="band_e" label="Band E" optional="true" type="data" format="txt"/> + <param name="band_f" label="Band F" optional="true" type="data" format="txt"/> + <param name="band_g" label="Band G" optional="true" type="data" format="txt"/> + <param name="band_h" label="Band H" optional="true" type="data" format="txt"/> + <param name="band_i" label="Band I" optional="true" type="data" format="txt"/> + <param name="band_j" label="Band J" optional="true" type="data" format="txt"/> + <param name="band_k" label="Band K" optional="true" type="data" format="txt"/> + <param name="band_l" label="Band L" optional="true" type="data" format="txt"/> + <param name="band_m" label="Band M" optional="true" type="data" format="txt"/> + <param name="band_n" label="Band N" optional="true" type="data" format="txt"/> + <param name="band_o" label="Band O" optional="true" type="data" format="txt"/> + <param name="band_p" label="Band P" optional="true" type="data" format="txt"/> + <param name="band_q" label="Band Q" optional="true" type="data" format="txt"/> + <param name="band_r" label="Band R" optional="true" type="data" format="txt"/> + <param name="band_s" label="Band S" optional="true" type="data" format="txt"/> + <param name="band_t" label="Band T" optional="true" type="data" format="txt"/> + <param name="band_u" label="Band U" optional="true" type="data" format="txt"/> + <param name="band_v" label="Band V" optional="true" type="data" format="txt"/> + <param name="band_w" label="Band W" optional="true" type="data" format="txt"/> + <param name="band_x" label="Band X" optional="true" type="data" format="txt"/> + <param name="band_y" label="Band Y" optional="true" type="data" format="txt"/> + <param name="band_z" label="Band Z" optional="true" type="data" format="txt"/> </when> <when value="download-band-sentinel2-product-safe"> - <param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/> + <param name="product_url" label="Product URL" help="S3 URL to a Sentinel-2 product in SAFE format." optional="false" type="data" format="txt"/> + <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"> + <param name="resolution" label="resolution" optional="true" type="select"> + <option value="10m">10m</option> + <option value="20m">20m</option> + <option value="60m">60m</option> + </param> + <param name="band" label="band" optional="false" type="select"> <option value="B01">B01</option> <option value="B02">B02</option> <option value="B03">B03</option> @@ -112,103 +77,38 @@ <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"/> + <param name="debug" label="Debug" optional="true" type="boolean"/> </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"/> + <param name="input_image" label="Input image" optional="false" help="Image to map with the colors bins." type="data" format="txt"/> + <param name="color_scale" label="Color mappings to bin scales to apply to the image." optional="false" 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" label="Output name" optional="true" type="text"/> + <param name="plot_name" label="Plot name" optional="true" type="text"/> + <param name="plot_title" label="Plot title" optional="true" 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"/> + <param name="output_dimensions_Array_integer" label="output_dimensions" optional="true" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="output_resolution_Array_integer" label="Output resolution" optional="true" help="Please provide comma-seperated values of type integer here." 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"> + <param name="date" label="Central date" optional="true" help="Date around which ±delta-days will be applied for search. If omitted, 'toi' input must be provided instead." type="text"/> + <param name="delta" label="Delta" optional="true" type="integer"/> + <param name="toi_Array_text" label="Time of interest" optional="true" help="Start and end date-time strings. Must be provided if 'date' input is omitted. Please provide comma-seperated values of type text here." type="text"/> + <param name="aoi" label="Area of interest" optional="false" help="Polygon defining the area of interest." type="data" format="txt"/> + <param name="collection" label="Collection" optional="false" type="text"/> + <param name="product_level" label="Product level" optional="true" help="Please provide comma-seperated values of type text here." type="select"> + <option value="L1C">L1C</option> + <option value="L2A">L2A</option> + </param> + <param name="catalog" label="catalog" optional="false" 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"/> + <param name="cloud_cover" label="Cloud cover" optional="true" type="float"/> </when> </conditional> </inputs> @@ -218,4 +118,4 @@ <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> +</tool> \ No newline at end of file
--- a/macros.xml Fri Jun 07 11:37:33 2024 +0000 +++ b/macros.xml Fri Sep 06 10:30:30 2024 +0000 @@ -35,13 +35,13 @@ <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="product_url" value="product_url.txt"/> + <param name="resolution" value="10m"/> <param name="band" value="B04"/> <assert_stderr> <has_text text="HTTP 401 Unauthorized"/> </assert_stderr> </test> - </tests> + </tests> </xml> -</macros> +</macros> \ No newline at end of file
--- a/ogc_api_processes_wrapper.R Fri Jun 07 11:37:33 2024 +0000 +++ b/ogc_api_processes_wrapper.R Fri Sep 06 10:30:30 2024 +0000 @@ -4,14 +4,27 @@ cat("start generic wrapper service \n") -getParameters <- function(){ - con <- file("inputs.json", "r") - lines <- readLines(con) - close(con) +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) +} - json_string <- paste(lines, collapse = "\n") - json_data <- fromJSON(json_string) - return(json_data$conditional_process) +getParameters <- function() { + con <- file("inputs.json", "r") + lines <- readLines(con) + close(con) + + json_string <- paste(lines, collapse = "\n") + json_data <- fromJSON(json_string) + + # Remove NULL values from json_data + cleaned_json_data <- remove_null_values(json_data) + return(cleaned_json_data$conditional_process) } parseResponseBody <- function(body) { @@ -24,68 +37,87 @@ } 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 + 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$format <- format + } } - - names(outputs) <- names(responseBody$outputs) - return(outputs) + 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)$jobID - - return(jobID) + url <- + paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "") + requestBodyData$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)$jobID + + return(jobID) } checkJobStatus <- function(server, process, jobID, cookie) { url <- paste0(server, "processes/", process, "/jobs/", jobID) response <- request(url) %>% - req_headers( - "Cookie" = cookie - ) %>% + req_headers("Cookie" = cookie) %>% req_perform() jobStatus <- parseResponseBody(response$body)$status jobProgress <- parseResponseBody(response$body)$progress @@ -95,47 +127,54 @@ getStatusCode <- function(server, process, jobID, cookie) { url <- paste0(server, "processes/", process, "/jobs/", jobID) response <- request(url) %>% - req_headers( - "Cookie" = cookie - ) %>% + req_headers("Cookie" = cookie) %>% req_perform() status_code <- response$status_code return(status_code) } getResult <- function (server, process, jobID, cookie) { - response <- request(paste0(server, "processes/", process, "/jobs/", jobID, "/results")) %>% - req_headers( - "Cookie" = cookie - ) %>% + response <- + request(paste0(server, "processes/", process, "/jobs/", jobID, "/results")) %>% + req_headers("Cookie" = cookie) %>% req_perform() return(response) } -retrieveResults <- function(server, process, jobID, outputData, cookie) { +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$href))) - urls_with_newline <- paste(urls, collapse = "\n") - con <- file(outputData, "w") - writeLines(urls_with_newline, con = con) - close(con) - } - } else if (jobStatus == "failed") { - status <- jobStatus + if (status_code == 200) { + status <- "running" + while (status == "running") { + jobStatus <- checkJobStatus(server, process, jobID, cookie) + print(jobStatus) + if (jobStatus == "succeeded") { + status <- jobStatus + result <- getResult(server, process, jobID, cookie) + if (result$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$href))) } - Sys.sleep(3) + urls_with_newline <- paste(urls, collapse = "\n") + con <- file(outputData, "w") + writeLines(urls_with_newline, con = con) + close(con) + } + } else if (jobStatus == "failed") { + status <- jobStatus } - cat("\n done \n") + Sys.sleep(3) + } + cat("\n done \n") } else if (status_code1 == 400) { print("A query parameter has an invalid value.") } else if (status_code1 == 404) { @@ -145,7 +184,7 @@ } else { print(paste("HTTP", status_code1, "Error:", resp1$status_message)) } -} + } is_url <- function(x) { grepl("^https?://", x) @@ -155,6 +194,7 @@ print("--> Retrieve parameters") inputParameters <- getParameters() +#print(inputParameters) print("--> Parameters retrieved") args <- commandArgs(trailingOnly = TRUE) @@ -167,7 +207,9 @@ print("--> Parse inputs") convertedKeys <- c() for (key in names(inputParameters)) { - if (is.character(inputParameters[[key]]) && (endsWith(inputParameters[[key]], ".dat") || endsWith(inputParameters[[key]], ".txt"))) { + 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) { @@ -177,11 +219,36 @@ #} con <- file(inputParameters[[key]], "r") lines <- readLines(con) + print("--------------------------------------------------------------------1") + print(length(lines)) close(con) - json_string <- paste(lines, collapse = "\n") - json_data <- fromJSON(json_string) - - inputParameters[[key]] <- json_data + 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)) { @@ -189,51 +256,65 @@ type <- keyParts[length(keyParts)] values <- inputParameters[[key]] value_list <- strsplit(values, split = ",") - convertedValues <- c() - + for (value in value_list) { - if(type == "integer") { + 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 + convertedValues <- append(convertedValues, value) + + convertedKey <- "" + for (part in keyParts) { + if (part == "Array") { + break + } + convertedKey <- + paste(convertedKey, paste(part, "_", sep = ""), sep = "") } - convertedKey <- paste(convertedKey, paste(part, "_", sep=""), sep="") + convertedKey <- substr(convertedKey, 1, nchar(convertedKey) - 1) } - convertedKey <- substr(convertedKey, 1, nchar(convertedKey)-1) -} - + inputParameters[[key]] <- convertedValues + #print("-------------------------") + #print(convertedValues) + #print("-------------------------") convertedKeys <- append(convertedKeys, convertedKey) } else { - convertedKeys <- append(convertedKeys, key) + #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 -) +jsonData <- list("inputs" = inputParameters, + "outputs" = outputs) cookie <- inputParameters$cookie print("--> Execute process") -jobID <- executeProcess(server, inputParameters$select_process, jsonData, cookie) +jobID <- + executeProcess(server, inputParameters$select_process, jsonData, cookie) print("--> Process executed") print("--> Retrieve results") -retrieveResults(server, inputParameters$select_process, jobID, outputLocation, cookie) +retrieveResults(server, + inputParameters$select_process, + jobID, + outputLocation, + cookie) print("--> Results retrieved") \ No newline at end of file