update to json2args 0.6.2

Author: mmaelicke

Dockerfile

@@ -2,8 +2,12 @@
 FROM python:3.12
 
 # install the toolbox runner tools
-RUN pip install json2args
+RUN pip install "json2args[data]>=0.6.2"
 
+# if you do not need data-preloading as your tool does that on its own
+# you can use this instread of the line above to use a json2args version
+# with less dependencies
+# RUN pip install json2args>=0.6.2
 
 # Do anything you need to install tool dependencies here
 RUN echo "Replace this line with a tool"

in/input.json

@@ -0,0 +1,15 @@
+{
+    "foobar": {
+        "parameters": {
+            "foo_int": 42,
+            "foo_float": 13.37,
+            "foo_string": "Never eat yellow snow",
+            "foo_enum": "bar",
+            "foo_array": [34, 55, 23, 43, 23]
+        },
+        "data": {
+            "foo_matrix": "/in/foo_matrix.dat",
+            "foo_csv": "/in/foo_csv.csv"
+        }
+    }
+}

in/parameters.json

@@ -3,9 +3,11 @@
 from pprint import pprint
 
 from json2args import get_parameter
+from json2args.data import get_data
 
 # parse parameters
 kwargs = get_parameter()
+data = get_data(as_dict=True)
 
 # check if a toolname was set in env
 toolname = os.environ.get('TOOL_RUN', 'foobar').lower()
@@ -18,6 +20,11 @@
     # write parameters to STDOUT.log
     pprint(kwargs)
 
+    for name, ds in data.items():
+        print(f"\n### {name}")
+        print(ds)
+    
+
 # In any other case, it was not clear which tool to run
 else:
     raise AttributeError(f"[{dt.now().isocalendar()}] Either no TOOL_RUN environment variable available, or '{toolname}' is not valid.\n")

src/run.py

@@ -19,7 +19,10 @@ tools:
       foo_array:
         type: integer
         array: true
+    data:
       foo_matrix:
-        type: file
+        extension: dat
+        description: A matrix file that can be read by numpy
       foo_csv:
-        type: file
+        extension: csv
+        description: A standard formatted CSV file, for autoloading using pandas