Ogc api processes wrapper for the zoo project (#113)

* address problem: parameter 'channels_rgb_red': the attribute 'value' must be set for non optional parameters

* change output from collection to single txt file

* update test

* correct test, reduce number of processes to around 100

tools/zoo_project_ogc_api_processes/.shed.yml

@@ -4,7 +4,7 @@ owner: ecology
 remote_repository_url: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper
 homepage_url: https://github.com/AquaINFRA/galaxy
 long_description: |
-  This tool is a wrapper for OGC API Processes coming from the Zoo Project 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.
+  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.
 type: unrestricted
 auto_tool_repositories:
   name_template: "{{ tool_id }}"

tools/zoo_project_ogc_api_processes/macros.xml

@@ -27,7 +27,7 @@
         </citations>
     </xml>
     <xml name="help">
-        <help>This tool is a wrapper for OGC API Processes 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>
+        <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>
@@ -37,8 +37,12 @@
                 <param name="out" value="float"/>
                 <param name="ram" value="256"/>
                 <param name="exp" value="im1b3,im1b2,im1b1"/>
-                <param name="out_outformat" value="image/png"/>
-                <output_collection name="output_data" type="list" count="2"/>
+                <param name="out_outformat" value="image/tiff"/>
+                <output name="output_data">
+                    <assert_contents>
+                        <has_n_lines n="1"/>
+                    </assert_contents>
+                </output>
             </test>
             <test>
                 <param name="select_process" value="OTB.MeanShiftSmoothing"/>
@@ -51,9 +55,13 @@
                 <param name="maxiter" value="100"/>
                 <param name="rangeramp" value="0"/>
                 <param name="modesearch" value="False"/>
-                <param name="fout_outformat" value="image/png"/>
-                <param name="foutpos_outformat" value="image/png"/>
-                <output_collection name="output_data" type="list" count="2"/>
+                <param name="fout_outformat" value="image/tiff"/>
+                <param name="foutpos_outformat" value="image/tiff"/>
+                <output name="output_data">
+                    <assert_contents>
+                        <has_n_lines n="2"/>
+                    </assert_contents>
+                </output>
             </test>
         </tests>    
     </xml>

tools/zoo_project_ogc_api_processes/ogc_api_processes_wrapper.R

@@ -5,7 +5,6 @@ library("getopt")
 cat("start generic wrapper service \n")
 
 getParameters <- function(){
-    args <- commandArgs(trailingOnly = TRUE)
     con <- file("inputs.json", "r")
     line <- readLines(con, n = 1)
     json <- fromJSON(line)
@@ -112,9 +111,9 @@ retrieveResults <- function(server, jobID, outputData) {
                   resultBody <- parseResponseBody(result$body)
                   urls <- unname(unlist(lapply(resultBody, function(x) x$href)))
                   urls_with_newline <- paste(urls, collapse = "\n")
-                  sink(paste0(outputData, "_result_urls.txt"))
-                    cat(urls_with_newline, "\n")
-                  sink()
+                  con <- file(outputData, "w")
+                  writeLines(urls_with_newline, con = con)
+                  close(con)
                 }
             } else if (jobStatus == "failed") {
               status <- jobStatus
@@ -141,7 +140,8 @@ server <- "https://ospd.geolabs.fr:8300/ogc-api/"
 
 inputParameters <- getParameters()
 
-outputLocation <- inputParameters$outputData
+args <- commandArgs(trailingOnly = TRUE)
+outputLocation <- args[2]
 
 outputs <- getOutputs(inputParameters, outputLocation, server)