Merge pull request #208 from GEO-BON/error_message

Error message and output one-by-one implementation example

scripts/helloWorld/helloR.R

@@ -2,13 +2,13 @@
 # Script location can be used to access other scripts
 print(Sys.getenv("SCRIPT_LOCATION"))
 
-## Install required packages
-packages <- c("rjson")
-new.packages <- packages[!(packages %in% installed.packages()[,"Package"])]
-if(length(new.packages)) install.packages(new.packages)
+## Install required packages that are not available on Anaconda
+#packages <- c("someRarePackage")
+#new.packages <- packages[!(packages %in% installed.packages()[,"Package"])]
+#if(length(new.packages)) install.packages(new.packages)
 
-library("rjson")
-input <- fromJSON(file=file.path(outputFolder, "input.json"))
+# Reading inputs
+input <- biab_inputs()
 print("Inputs: ")
 print(input)
 
@@ -17,16 +17,22 @@ example_jpg = file.path(outputFolder, "example.jpg")
 if(!file.exists(example_jpg)) {
     download.file("https://geobon.org/wp-content/uploads/2018/01/default-image.png", example_jpg, "auto")
 }
+biab_output("some_picture", example_jpg)
 
 example_tiff = file.path(outputFolder, "utmsmall.tif")
 if(!file.exists(example_tiff)) {
     download.file("https://github.com/yeesian/ArchGDALDatasets/raw/master/data/utmsmall.tif", example_tiff, "auto")
 }
+biab_output("heat_map", example_tiff)
+
+# Uncomment this to stop the script here with an error message
+#biab_error_stop("Some error")
 
 example_json = file.path(outputFolder, "sample.json")
 if(!file.exists(example_json)) {
     download.file("https://gist.githubusercontent.com/wavded/1200773/raw/e122cf709898c09758aecfef349964a8d73a83f3/sample.json", example_json, "auto")
 }
+biab_output("geo_json", example_json)
 
 some_csv_data = file.path(outputFolder, "some_data.csv")
 write("Model,mpg,cyl,disp,hp,drat,wt,qsec,vs,am,gear,carb
@@ -35,6 +41,7 @@ Mazda RX4 Wag,21,6,160,110,3.9,2.875,17.02,0,1,4,4
 Datsun 710,22.8,4,108,93,3.85,2.32,18.61,1,1,4,1
 Hornet 4 Drive,21.4,6,258,110,3.08,3.215,19.44,1,0,3,1
 ", some_csv_data)
+biab_output("some_csv_data", some_csv_data)
 
 # Example from https://en.wikipedia.org/wiki/Tab-separated_values
 some_tsv_data = file.path(outputFolder, "some_data.tsv")
@@ -45,31 +52,22 @@ write("Sepal length	Sepal width	Petal length	Petal width	Species
 4.6	3.1	1.5	0.2	I. setosa
 5.0	3.6	1.4	0.2	I. setosa
 ", some_tsv_data)
+biab_output("some_tsv_data", some_tsv_data)
 
 # Example from https://en.wikipedia.org/wiki/Tab-separated_values
 some_html_output = file.path(outputFolder, "some_page.html")
 write(
     "<h1>This is a page</h1><p>With a fancy interactive graph or the like.</p>",
     some_html_output
 )
+biab_output("some_html_output", some_html_output)
 
-## Outputing result to JSON
-# notice that the warning string is not part of the yml spec, so it cannot be used by other scripts, but will still be displayed.
-output <- list(#"error" = "Some error", # Use error key to stop the rest of the pipeline
-                "info" = "Some information message",
-                "warning" = "Some warning",
-                "text" = "This is just an example. In case you have a very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very long text it will need to be unfolded to see it all.",
-                "number" = input$intensity * 3,
-                "heat_map" = example_tiff,
-                "geo_json" = example_json,
-                "some_csv_data" = some_csv_data,
-                "some_tsv_data" = some_tsv_data,
-                "some_html_output" = some_html_output,
-                "some_picture" = example_jpg,
-                "userdata_available" = list.files(file.path(Sys.getenv("USERDATA_LOCATION"))),
-                "undocumented_output" = "Some debug output")
+biab_info("Some information message")
+biab_warning("Some warning")
 
-jsonData <- toJSON(output, indent=2)
-write(jsonData, file.path(outputFolder,"output.json"))
+biab_output("text", "This is just an example. In case you have a very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very, very long text it will need to be unfolded to see it all.")
+biab_output("number", input$intensity * 3)
+biab_output("userdata_available", list.files(file.path(Sys.getenv("USERDATA_LOCATION"))))
+biab_output("undocumented_output", "Some debug output")
 
-# (If we get a problem with encoding, we could use utf-8 library to clean the output, since the server reads it as utf-8)
+# (If there is a problem with encoding, one could use utf-8 library to clean the output, since the server reads it as utf-8)

scripts/helloWorld/helloR.yml

@@ -49,9 +49,16 @@ inputs:
       - second option
       - third option
       - fourth option
+      - fifth options
+      - sixth options
+      - seventh option
+      - eight option
+      - ninth option
+      - tenth option
+      - eleventh option
     example:
-      - third option
-      - fourth option
+      - first option
+      - eleventh option
   freeflow_text:
     label: Freeflow text
     description: This is regular text, and can have multiple lines.
@@ -108,7 +115,7 @@ outputs:
     type: text/html
     example: /path/to/some/example.html
 references:
-  - text: John Doe, The ins and outs of copy-pasting, BioScience, Volume 71, Issue 5, May 2021, Pages 448–451
-    doi: 10.1093/biosci/biab041
+  - text: John Doe, The ins and outs of copy-pasting, CopyScience, Volume 71, Issue 5, May 2021, Pages 448–451
+    doi: 10.1093/copysci/biab041
   - text: Nick Copy, Rupert Paste, Replicating text in a documentation context, Textopasto, 405, (123456), (2022).
-    doi: 10.1016/j.biab.2021.115424
+    doi: 10.1016/j.tpasto.2021.115424