Mercurial > repos > ecology > aquainfra_ogc_api_processes

changeset 7:c805cb663bac draft default tip

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planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 176da50f4af1ff7f4e0e325984c8edd27fe93926
author ecology
date Mon, 21 Jul 2025 06:19:08 +0000
parents 8f9d34c780de
children
files aquainfra_ogc_api_processes.R aquainfra_ogc_api_processes.xml test-data/points_att_polygon_test_input_1.txt
diffstat 3 files changed, 29 insertions(+), 97 deletions(-) [+]
line wrap: on
line diff
--- a/aquainfra_ogc_api_processes.R	Tue May 13 17:57:28 2025 +0000
+++ b/aquainfra_ogc_api_processes.R	Mon Jul 21 06:19:08 2025 +0000
@@ -2,7 +2,7 @@
 library("jsonlite")
 library("getopt")
 
-cat("start generic wrapper service \n")
+cat("START GENERIC WRAPPER SERVICE \n")
 
 remove_null_values <- function(x) {
   if (is.list(x)) {
@@ -33,36 +33,6 @@
   return(jsonObject)
 }
 
-getOutputs <- function(inputs, output, server) {
-  url <-
-    paste(paste(server, "processes/", sep = ""),
-          inputs$select_process,
-          sep = "")
-  print(url)
-  request <- request(url)
-  response <- req_perform(request)
-  responseBody <- parseResponseBody(response$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) {
   url <-
     paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "")
@@ -77,9 +47,10 @@
     req_body_json(body) %>%
     req_perform()
   
-  cat("\n Process executed")
-  cat("\n status: ", response$status_code)
+  cat("\n 3.1: Process executed")
+  cat("\n 3.1: Status code: ", response$status_code)
   jobId <- parseResponseBody(response$body)$jobID
+  cat("\n 3.1: Job ID: ", jobId, "\n")
   
   return(jobId)
 }
@@ -93,9 +64,7 @@
   return(jobStatus)
 }
 
-getStatusCode <- function(server, process, jobID) {
-  url <- paste0(server, "jobs/", jobID)
-  print(url)
+getStatusCode <- function(url) {
   response <- request(url) %>%
     req_perform()
   status_code <- response$status_code
@@ -125,15 +94,17 @@
 }
 
 retrieveResults <- function(server, process, jobID, outputData) {
-  status_code <- getStatusCode(server, process, jobID)
-  print(status_code)
+  url <- paste0(server, "jobs/", jobID)
+  cat(" 4.1: Job URL: ", url)
+  status_code <- getStatusCode(url)
+  cat("\n 4.2: Status code: ", status_code, "\n")
   
   if (status_code == 200) {
     status <- "running"
     
     while (status == "running") {
       jobStatus <- checkJobStatus(server, process, jobID)
-      print(jobStatus)
+      cat(" 4.3: Job status: ", jobStatus, "\n")
       
       if (jobStatus == "successful") {
         status <- jobStatus
@@ -141,27 +112,25 @@
         
         if (result$status_code == 200) {
           resultBody <- parseResponseBody(result$body)
+          cat("\n 4.4 Outputs: \n")
           print(resultBody)
           hrefs <- findHref(resultBody)
           
           if (length(hrefs) > 0) {
             urls_with_newline <- paste(hrefs, collapse = "\n")
-            print(urls_with_newline)
             con <- file(outputData, "w")
             writeLines(urls_with_newline, con = con)
             close(con)
           } else {
-            print("No hrefs found.")
+            stop(paste0("Job failed. No hrefs found. See details at: ", server, "jobs/", jobID))
           }
         }
       } else if (jobStatus == "failed") {
-        status <- jobStatus
+        stop(paste0("Job failed. See details at: ", server, "jobs/", jobID))
       }
       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) {
@@ -185,19 +154,15 @@
 
 server <- "https://aquainfra.ogc.igb-berlin.de/pygeoapi/"
 
-print("--> Retrieve parameters")
+cat("\n1: START RETRIEVING PARAMETERS\n\n")
 inputParameters <- getParameters()
-print("--> Parameters retrieved")
+print(inputParameters)
+cat("1: END RETRIEVING PARAMETERS\n")
 
 args <- commandArgs(trailingOnly = TRUE)
 outputLocation <- args[2]
 
-print("--> Retrieve outputs")
-outputs <- getOutputs(inputParameters, outputLocation, server)
-print("--> Outputs retrieved")
-
-print("--> Parse inputs")
-
+cat("\n2: START PARSING INPUTS\n\n")
 convertedKeys <- c()
 
 for (key in names(inputParameters)) {
@@ -209,62 +174,29 @@
 
     con <- file(inputParameters[[key]], "r")
     lines <- readLines(con)
-    print(length(lines))
     close(con)
 
-    json_string <- paste(lines, collapse = "\n")
+    json_string <- paste(lines, collapse = ",")
     inputParameters[[key]] <- json_string
 
     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(value)
-      } 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 {
     if (!is.null(inputParameters[[key]])) {
       convertedKeys <- append(convertedKeys, key)
     }
   }
 }
+names(inputParameters) <- convertedKeys
 print(inputParameters)
-names(inputParameters) <- convertedKeys
-print("--> Inputs parsed")
-
-print("--> Prepare process execution")
-jsonData <- list("inputs" = inputParameters,
-                 "outputs" = outputs)
+cat("2: END PARSING INPUTSs\n")
 
-print("--> Execute process")
+cat("\n3: START EXECUTING PROCESS\n")
+jsonData <- list("inputs" = inputParameters)
 jobId <- executeProcess(server, inputParameters$select_process, jsonData)
-print("--> Process executed")
+cat("\n3: END EXECUTING PROCESS\n")
 
-print("--> Retrieve results")
+cat("\n4: START RETRIEVING RESULTS\n\n")
 retrieveResults(server, inputParameters$select_process, jobId, outputLocation)
-print("--> Results retrieved")
\ No newline at end of file
+cat("4: END RETRIEVING RESULTS\n")
+
+cat("\n5: DONE.")
\ No newline at end of file
--- a/aquainfra_ogc_api_processes.xml	Tue May 13 17:57:28 2025 +0000
+++ b/aquainfra_ogc_api_processes.xml	Mon Jul 21 06:19:08 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="aquainfra_ogc_api_processes" name="AquaINFRA OGC API Processes" version="0.6.0" profile="22.05">
+<tool id="aquainfra_ogc_api_processes" name="AquaINFRA OGC API Processes" version="0.6.1" profile="22.05">
     <description/>
     <macros>
         <import>macros.xml</import>
--- a/test-data/points_att_polygon_test_input_1.txt	Tue May 13 17:57:28 2025 +0000
+++ b/test-data/points_att_polygon_test_input_1.txt	Mon Jul 21 06:19:08 2025 +0000
@@ -1,1 +1,1 @@
-https://maps.helcom.fi/arcgis/rest/directories/arcgisoutput/MADS/tools_GPServer/_ags_HELCOM_subbasin_with_coastal_WFD_waterbodies_or_wa.zip
\ No newline at end of file
+https://zenodo.org/records/15234377/files/inputdata_shapefile.zip?download=1
\ No newline at end of file