REST API Tests : remove redundant validation in old test and add new …

…tests

src/sophios/api/http/restapi.py

@@ -40,21 +40,6 @@ def remove_dot_dollar(tree: Cwl) -> Cwl:
     return tree_no_dd
 
 
-def get_yaml_tree(req: Json) -> Json:
-    """
-    Get the Sophios yaml tree from incoming JSON
-    Args:
-        req (JSON): A raw JSON content of incoming JSON object
-    Returns:
-        Cwl: A Cwl document with . and $ removed from $namespaces and $schemas
-    """
-    wkflw_name = "generic_workflow"
-    # args = converter.get_args(wkflw_name)
-    # yaml_tree_json: Json = converter.wfb_to_wic(req)
-    yaml_tree_json: Json = {}
-    return yaml_tree_json
-
-
 def run_workflow(compiler_info: CompilerInfo, args: argparse.Namespace) -> int:
     """
     Get the Sophios yaml tree from incoming JSON
@@ -116,8 +101,8 @@ async def compile_wf(request: Request) -> Json:
     wkflw_name = "generic_workflow"
     args = get_args(wkflw_name, ['--inline_cwl_runtag'])
 
+    # Build canonical workflow object
     workflow_can = utils_cwl.desugar_into_canonical_normal_form(workflow_temp)
-    print(yaml.safe_dump(workflow_can, default_flow_style=False))
 
     # ========= BUILD WIC COMPILE INPUT =========
     # Build a list of CLTs

src/sophios/api/utils/converter.py

@@ -4,7 +4,6 @@
 from jsonschema import Draft202012Validator
 from sophios.utils_yaml import wic_loader
 
-# from sophios import cli
 from sophios.wic_types import Json, Cwl
 
 SCHEMA: Json = {

tests/multi_node.json

@@ -0,0 +1,76 @@
+{
+	"nodes": [
+		{
+			"id": 7,
+			"x": 462,
+			"y": 206,
+			"z": 2,
+			"name": "touch",
+			"pluginId": "touch",
+			"height": 50,
+			"width": 250,
+			"settings": {
+				"inputs": {
+					"filename": "empty.txt"
+				},
+				"outputs": {
+					"file": "file_touch"
+				}
+			},
+			"internal": false
+		},
+		{
+			"id": 18,
+			"x": 155,
+			"y": 195,
+			"z": 1,
+			"name": "append",
+			"pluginId": "append",
+			"height": 50,
+			"width": 250,
+			"settings": {
+				"inputs": {
+					"str": "Hello",
+					"file": "file_touch"
+				},
+				"outputs": {
+					"file": "file_append1"
+				}
+			},
+			"internal": false
+		},
+		{
+			"id": 9,
+			"x": 790.3254637299812,
+			"y": 449.8103498684344,
+			"z": 5,
+			"name": "append",
+			"pluginId": "append",
+			"height": 50,
+			"width": 250,
+			"settings": {
+				"inputs": {
+					"str": "World!",
+					"file": "file_append1"
+				},
+				"outputs": {
+					"file": "file_append2"
+				}
+			},
+			"internal": false
+		}
+	],
+	"links": [
+		{
+			"sourceId": 7,
+			"targetId": 18,
+			"id": 1
+		},
+		{
+			"sourceId": 18,
+			"targetId": 9,
+			"id": 5
+		}
+	],
+	"selection": []
+}

tests/multi_node_inline_cwl.json

@@ -0,0 +1,181 @@
+{
+	"nodes": [
+		{
+			"id": 7,
+			"x": 462,
+			"y": 206,
+			"z": 2,
+			"name": "touch",
+			"pluginId": "touch",
+			"height": 50,
+			"width": 250,
+			"settings": {
+				"inputs": {
+					"filename": "empty.txt"
+				},
+				"outputs": {
+					"file": "file_touch"
+				}
+			},
+			"run": {
+				"cwlVersion": "v1.0",
+				"class": "CommandLineTool",
+				"requirements": {
+					"DockerRequirement": {
+						"dockerPull": "docker.io/bash:4.4"
+					},
+					"InlineJavascriptRequirement": {}
+				},
+				"baseCommand": "touch",
+				"inputs": {
+					"filename": {
+						"type": "string",
+						"inputBinding": {
+							"position": 1
+						}
+					}
+				},
+				"outputs": {
+					"file": {
+						"type": "File",
+						"outputBinding": {
+							"glob": "$(inputs.filename)"
+						}
+					}
+				}
+			},
+			"internal": false
+		},
+		{
+			"id": 18,
+			"x": 155,
+			"y": 195,
+			"z": 1,
+			"name": "append",
+			"pluginId": "append",
+			"height": 50,
+			"width": 250,
+			"settings": {
+				"inputs": {
+					"str": "Hello",
+					"file": "file_touch"
+				},
+				"outputs": {
+					"file": "file_append1"
+				}
+			},
+			"run": {
+				"class": "CommandLineTool",
+				"cwlVersion": "v1.0",
+				"requirements": {
+					"ShellCommandRequirement": {},
+					"InlineJavascriptRequirement": {},
+					"InitialWorkDirRequirement": {
+						"listing": [
+							"$(inputs.file)"
+						]
+					}
+				},
+				"inputs": {
+					"str": {
+						"type": "string",
+						"inputBinding": {
+							"shellQuote": false,
+							"position": 1,
+							"prefix": "echo"
+						}
+					},
+					"file": {
+						"type": "File",
+						"inputBinding": {
+							"shellQuote": false,
+							"position": 2,
+							"prefix": ">>"
+						}
+					}
+				},
+				"outputs": {
+					"file": {
+						"type": "File",
+						"outputBinding": {
+							"glob": "$(inputs.file.basename)"
+						}
+					}
+				}
+			},
+			"internal": false
+		},
+		{
+			"id": 9,
+			"x": 790.3254637299812,
+			"y": 449.8103498684344,
+			"z": 5,
+			"name": "append",
+			"pluginId": "append",
+			"height": 50,
+			"width": 250,
+			"settings": {
+				"inputs": {
+					"str": "World!",
+					"file": "file_append1"
+				},
+				"outputs": {
+					"file": "file_append2"
+				}
+			},
+			"run": {
+				"class": "CommandLineTool",
+				"cwlVersion": "v1.0",
+				"requirements": {
+					"ShellCommandRequirement": {},
+					"InlineJavascriptRequirement": {},
+					"InitialWorkDirRequirement": {
+						"listing": [
+							"$(inputs.file)"
+						]
+					}
+				},
+				"inputs": {
+					"str": {
+						"type": "string",
+						"inputBinding": {
+							"shellQuote": false,
+							"position": 1,
+							"prefix": "echo"
+						}
+					},
+					"file": {
+						"type": "File",
+						"inputBinding": {
+							"shellQuote": false,
+							"position": 2,
+							"prefix": ">>"
+						}
+					}
+				},
+				"outputs": {
+					"file": {
+						"type": "File",
+						"outputBinding": {
+							"glob": "$(inputs.file.basename)"
+						}
+					}
+				}
+			},
+			"internal": false
+		}
+	],
+	"links": [
+		{
+			"sourceId": 7,
+			"targetId": 18,
+			"id": 1
+		},
+		{
+			"sourceId": 18,
+			"targetId": 9,
+			"id": 5
+		}
+	],
+	"selection": []
+}