Merge pull request #100 from mvdbeek/arrays_of_workflow_input_parameters

Arrays of workflow input parameters

.github/workflows/tox.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v2

docs/design.md

@@ -2,14 +2,14 @@
 
 ## Goals
 
-1) gxformat2 should be human readable and writable
-1) gxformat2 should be able to be consumed by Galaxy without access to a Galaxy toolbox
-1) gxformat2 should be convertible to Galaxy's original workflow format without a Galaxy runtime
-1) gxformat2 should align with workflows standards (and specifically the Common Workflow Langauge) when it is pratical
-1) We will work on solidifying a version of gxformat2 called 19.09 that is compatible with the workflow models in
-   Galaxy versions 19.09-24.1 and which can be fixed for older versions with just a gxformat2 dependency upgrade.
-   At some point in the future there will be a new a version for implementation ideas
-   the require changes to the Galaxy model.
+- gxformat2 should be human readable and writable
+- gxformat2 should be able to be consumed by Galaxy without access to a Galaxy toolbox
+- gxformat2 should be convertible to Galaxy's original workflow format without a Galaxy runtime
+- gxformat2 should align with workflows standards (and specifically the Common Workflow Langauge) when it is pratical
+- We will work on solidifying a version of gxformat2 called 19.09 that is compatible with the workflow models in
+  Galaxy versions 19.09-24.1 and which can be fixed for older versions with just a gxformat2 dependency upgrade.
+  At some point in the future there will be a new a version for implementation ideas
+  the require changes to the Galaxy model.
 
 ## Specific
 

gxformat2/converter.py

@@ -296,9 +296,8 @@ def transform_input(context, step, default_name):
         "name": name,
         "description": "",
     })
-    tool_state = {
-        "name": name
-    }
+    tool_state = step.get("tool_state", {})
+    tool_state["name"] = name
     for attrib in ["collection_type", "parameter_type", "optional", "default", "format", "restrictions", "restrictOnConnections", "suggestions"]:
         if attrib in step:
             tool_state[attrib] = step[attrib]

gxformat2/model.py

@@ -240,7 +240,7 @@ def prune_position(step):
     return {k: v for k, v in step.get('position', {}).items() if k in ('left', 'top')}
 
 
-def native_input_to_format2_type(step: dict, tool_state: dict) -> str:
+def native_input_to_format2_type(step: dict, tool_state: dict) -> Union[str, List[str]]:
     """Return a Format2 input type ('type') from a native input step dictionary."""
     module_type = step.get("type")
     if module_type == 'data_collection_input':
@@ -254,6 +254,8 @@ def native_input_to_format2_type(step: dict, tool_state: dict) -> str:
             format2_type = "int"
         elif native_type == "text":
             format2_type = "string"
+        if tool_state.get("multiple", False):
+            return [format2_type]
     return format2_type
 
 
@@ -330,6 +332,13 @@ def inputs_as_native_steps(workflow_dict: dict):
             raise Exception("Input label must not be empty.")
 
         input_type = input_def.pop("type", "data")
+        if isinstance(input_type, list):
+            if len(input_type) != 1:
+                raise Exception("Only simple arrays of workflow inputs are currently supported")
+            input_type = input_type[0]
+            if input_type in ["File", "data", "data_input"]:
+                raise Exception(f"Array of {input_type} is not supported")
+            input_def["tool_state"] = {"multiple": True}
         if input_type in ["File", "data", "data_input"]:
             step_type = "data_input"
         elif input_type in ["collection", "data_collection", "data_collection_input"]: