Add foundation for resource override in WDL

(made simpler if openwdl/wdl/issues/262 and openwdl/wdl/pull/301
are resolved)

janis/translations/__init__.py

@@ -37,3 +37,15 @@ def translate_tool(tool, translation: SupportedTranslation, with_docker, with_re
     else:
         raise NotImplementedError(f"The requested translation ('{translation}') has not been implemented yet, "
                                   f"why not contribute one at '{GITHUB_URL}'.")
+
+
+def build_resources_input(workflow, translation: SupportedTranslation, hints):
+    if translation == SupportedTranslations.CWL:
+        raise NotImplementedError("CWL implementation is coming soon!")
+
+    elif translation == SupportedTranslations.WDL:
+        return wdl.build_wdl_resource_inputs(workflow, hints)
+
+    else:
+        raise NotImplementedError(f"The requested translation ('{translation}') has not been implemented yet, "
+                                  f"why not contribute one at '{GITHUB_URL}'.")

janis/translations/wdl.py

@@ -1,13 +1,14 @@
 import os
-from typing import List, Dict, Optional
+from typing import List, Dict, Optional, Any
 import itertools
 
 import wdlgen as wdl
+import janis.workflow.workflow as JW
 from janis.workflow.step import StepNode
 
 from janis.graph.stepinput import Edge, StepInput
 
-from janis.types import InputSelector, WildcardSelector
+from janis.types import InputSelector, WildcardSelector, CpuSelector, MemorySelector
 
 from janis.types.common_data_types import Stdout, Array, Boolean, Filename, File
 
@@ -350,6 +351,17 @@ def translate_tool(tool, with_docker):
     if with_docker:
         r.add_docker(tool.docker())
 
+    # generate resource inputs, for memory, cpu and disk at the moment
+    ins.extend([
+        wdl.Input(wdl.WdlType.parse_type("Int?"), "runtime_cpu"),
+        wdl.Input(wdl.WdlType.parse_type("String?"), "runtime_memory"),
+        wdl.Input(wdl.WdlType.parse_type("String?"), "runtime_disks"),
+    ])
+
+    r.add_cpus("runtime_cpu")
+    r.add_memory("${runtime_memory}")
+    r.kwargs["disks"] = "runtime_disks"
+
     return wdl.Task(tool.id(), ins, outs, commands, r, version="development")
 
 
@@ -566,9 +578,10 @@ def translate_step_node(node, step_identifier: str, step_alias: str):
                 f = edge.finish.inputs()[edge.ftag]
                 secs = f.input_type.subtype().secondary_files() if isinstance(f.input_type, Array) \
                     else f.input_type.secondary_files()
-                for sec in secs:
-                    inputs_map[get_secondary_tag_from_original_tag(k, sec)] = \
-                        "[" + ", ".join(get_secondary_tag_from_original_tag(kk, sec) for kk in edge.dotted_source()) + "]"
+                if secs:
+                    for sec in secs:
+                        inputs_map[get_secondary_tag_from_original_tag(k, sec)] = \
+                            "[" + ", ".join(get_secondary_tag_from_original_tag(kk, sec) for kk in edge.dotted_source()) + "]"
                 continue
                 # source = source[0]
                 # raise Exception("Conversion to WDL does not currently support multiple sources")
@@ -644,4 +657,25 @@ def translate_step_node(node, step_identifier: str, step_alias: str):
 
     return call
 
-# def map_inputs_for_non_secondary_scatterable_field():
+
+def build_wdl_resource_inputs(wf, hints, prefix=None) -> Dict[str, Any]:
+    # returns a list of key, value pairs
+    steps = {}
+    if not prefix:
+        prefix = "" # wf.id() + "."
+
+    for s in wf._steps:
+        tool: Tool = s.step.tool()
+
+        if isinstance(tool, CommandTool):
+            tool_pre = prefix + "_" + tool.id() + "_"
+            steps.update([
+                (tool_pre + "runtime_memory", tool.memory(hints)),
+                (tool_pre + "runtime_cpu", tool.cpus(hints)),
+                (tool_pre + "runtime_disks", None)
+            ])
+        elif isinstance(tool, JW.Workflow):
+            tool_pre = prefix + "." + s.id()
+            steps.update(build_wdl_resource_inputs(tool, hints, tool_pre))
+
+    return steps

janis/workflow/workflow.py

@@ -744,3 +744,7 @@ def dump_translation(self, translation: SupportedTranslation, to_console=True, t
                                                should_zip=should_zip,
                                                write_inputs_file=write_inputs_file,
                                                should_validate=should_validate)
+
+    def generate_resources_file(self, translation: SupportedTranslation, hints: Dict[str, Any]):
+        return translations.build_resources_input(self, translation, hints)
+