one step wfb payload test case with no basecommand/entrypoint in ICT

src/sophios/api/http/restapi.py

@@ -94,14 +94,15 @@ async def compile_wf(request: Request) -> Json:
     print('---------- Compile Workflow! ---------')
     # ========= PROCESS REQUEST OBJECT ==========
     req: Json = await request.json()
+    suppliedargs = ['--cwl_inline_runtag', '--generate_cwl_workflow']
     # clean up and convert the incoming object
     # schema preserving
     req = converter.update_payload_missing_inputs_outputs(req)
     wfb_payload = converter.raw_wfb_to_lean_wfb(req)
     # schema non-preserving
     workflow_temp = converter.wfb_to_wic(wfb_payload)
     wkflw_name = "generic_workflow"
-    args = get_args(wkflw_name, ['--cwl_inline_runtag', '--generate_cwl_workflow'])
+    args = get_args(wkflw_name, suppliedargs)
 
     # Build canonical workflow object
     workflow_can = utils_cwl.desugar_into_canonical_normal_form(workflow_temp)
@@ -128,7 +129,10 @@ async def compile_wf(request: Request) -> Json:
     yaml_tree: YamlTree = YamlTree(StepId(wkflw_name, plugin_ns), workflow_can)
 
     # ========= COMPILE WORKFLOW ================
-    args.ignore_dir_path = True
+    if req.get('run_local_env') == 'true':
+        args.ignore_dir_path = False
+    else:
+        args.ignore_dir_path = True
     compiler_info: CompilerInfo = compiler.compile_workflow(yaml_tree, args, [], [graph], {}, {}, {}, {},
                                                             tools_cwl, True, relative_run_path=True, testing=False)
 
@@ -141,11 +145,21 @@ async def compile_wf(request: Request) -> Json:
     yaml_stem = sub_node_data.name
     cwl_tree = sub_node_data.compiled_cwl
     yaml_inputs = sub_node_data.workflow_inputs_file
+    # The following two conversions should be conditionalon the compute environment
+    # they are called from, removing dot and dollar won't make it run on compute-ci
     cwl_tree_no_dd = remove_dot_dollar(cwl_tree)
     yaml_inputs_no_dd = remove_dot_dollar(yaml_inputs)
 
     # Convert the compiled yaml file to json for labshare Compute.
     cwl_tree_run = copy.deepcopy(cwl_tree_no_dd)
+    for step in cwl_tree_run['steps']:
+        node_name = step['id']
+        step.pop('id', None)
+        step = {node_name: step}
+        cwl_tree_run['steps_dict'] = copy.deepcopy(step)
+
+    cwl_tree_run.pop('steps', None)
+    cwl_tree_run['steps'] = cwl_tree_run.pop('steps_dict', None)
 
     compute_workflow: Json = {}
     compute_workflow = {

src/sophios/api/pythonapi.py

@@ -2,7 +2,6 @@
 """CLT utilities."""
 import logging
 from pathlib import Path
-import subprocess as sub
 from typing import Any, ClassVar, Optional, TypeVar, Union
 
 import cwl_utils.parser as cu_parser

src/sophios/api/utils/ict/ict_spec/tools/cwl_ict.py

@@ -20,6 +20,12 @@ def requirements(ict_: "ICT", network_access: bool) -> dict:
     return reqs
 
 
+def split_entrypoint_string(enrtypoint: str) -> list[str]:
+    """Fix str to list of str for entrypoint/baseCommand"""
+    list_of_str_entry = enrtypoint.split(' ')
+    return list_of_str_entry
+
+
 def clt_dict(ict_: "ICT", network_access: bool) -> dict:
     """Return a dict of a CommandLineTool from an ICT object."""
 
@@ -37,7 +43,7 @@ def clt_dict(ict_: "ICT", network_access: bool) -> dict:
             for io in ict_.outputs
         },
         "requirements": requirements(ict_, network_access),
-        "baseCommand": ict_.entrypoint,
+        "baseCommand": '' if ict_.entrypoint == '' else split_entrypoint_string(str(ict_.entrypoint)),
         "label": ict_.title,
         "doc": str(ict_.documentation),
     }

tests/rest_wfb_objects/bbbc_download_wfb.json

@@ -0,0 +1,85 @@
+{
+    "state": {
+        "nodes": [
+            {
+                "id": 1,
+                "x": 259,
+                "y": 209,
+                "z": 1,
+                "name": "BBBC Download",
+                "expanded": true,
+                "pluginId": "polusai/bbbc-download-plugin@0.1.0-dev1",
+                "height": 50,
+                "width": 250,
+                "settings": {
+                    "inputs": {
+                        "name": "BBBC001",
+                        "outDir": "bbbcdownload.outDir"
+                    }
+                },
+                "internal": false
+            }
+        ],
+        "links": [],
+        "selection": []
+    },
+    "plugins": [
+        {
+            "name": "polusai/bbbc-download-plugin:0.1.0-dev1",
+            "version": "0.1.0-dev1",
+            "title": "BBBC Download",
+            "description": "Downloads the datasets on the Broad Bioimage Benchmark Collection website",
+            "createdBy": "Serebryakov, Artem (NIH/NCATS) [C]",
+            "updatedBy": "Serebryakov, Artem (NIH/NCATS) [C]",
+            "author": [
+                "Hamdah Abbasi"
+            ],
+            "contact": "hamdahshafqat.abbasi@nih.gov",
+            "container": "polusai/bbbc-download-plugin:0.1.0-dev1",
+            "entrypoint": "",
+            "inputs": [
+                {
+                    "description": "The name of the dataset(s) to be downloaded (separate the datasets with a comma. eg BBBC001,BBBC002,BBBC003)",
+                    "format": [
+                        "collection"
+                    ],
+                    "name": "name",
+                    "required": true,
+                    "type": "string"
+                }
+            ],
+            "outputs": [
+                {
+                    "description": "Output collection",
+                    "name": "outDir",
+                    "format": [
+                        "directory"
+                    ],
+                    "required": true,
+                    "type": "path"
+                }
+            ],
+            "repository": "https://github.com/LabShare/polus-plugins",
+            "specVersion": "1.0.0",
+            "ui": [
+                {
+                    "description": "The name of the dataset(s) to be downloaded (separate the datasets with a comma. eg BBBC001,BBBC002,BBBC003)",
+                    "format": [
+                        "collection"
+                    ],
+                    "name": "name",
+                    "required": true,
+                    "type": "string"
+                }
+            ],
+            "path": "visualization",
+            "tags": [
+                "bbbc-download"
+            ],
+            "createdAt": "2024-10-29T18:59:55.843Z",
+            "updatedAt": "2024-10-29T20:01:42.463Z",
+            "id": "672130abad801ccee7f5eaad",
+            "pid": "polusai/bbbc-download-plugin@0.1.0-dev1"
+        }
+    ]
+}

tests/rest_wfb_objects/single_node_bbbc_download.json

@@ -0,0 +1,74 @@
+{
+	"state": {
+		"nodes": [
+			{
+				"id": 1,
+				"name": "bbbcdownload",
+				"pluginId": "",
+				"run": {
+					"baseCommand": ["python3", "-m", "polus.plugins.utils.bbbc_download"],
+					"class": "CommandLineTool",
+					"cwlVersion": "v1.2",
+					"inputs": {
+						"name": {
+							"label": "The name of the dataset(s) to be downloaded (separate the datasets with a comma. eg BBBC001,BBBC002,BBBC003)",
+							"doc": "The name of the dataset(s) to be downloaded (separate the datasets with a comma. eg BBBC001,BBBC002,BBBC003)",
+							"inputBinding": {
+								"prefix": "--name"
+							},
+							"type": "string"
+						},
+						"outDir": {
+							"label": "Output collection",
+							"doc": "Output collection",
+							"inputBinding": {
+								"prefix": "--outDir"
+							},
+							"type": "Directory"
+						}
+					},
+					"outputs": {
+						"outDir": {
+							"label": "Output collection",
+							"doc": "Output collection",
+							"type": "Directory",
+							"outputBinding": {
+								"glob": "$(inputs.outDir.basename)"
+							}
+						}
+					},
+					"stdout": "output",
+					"requirements": {
+						"DockerRequirement": {
+							"dockerPull": "polusai/bbbc-download-plugin:0.1.0-dev1"
+						},
+						"InitialWorkDirRequirement": {
+							"listing": [
+								{
+									"entry": "$(inputs.outDir)",
+									"writable": true
+								}
+							]
+						},
+						"InlineJavascriptRequirement": {},
+						"NetworkAccess": {
+							"networkAccess": true
+						}
+					}
+				},
+				"settings": {
+					"inputs": {
+						"name": "BBBC001",
+						"outDir": "bbbcdownload.outDir"
+					},
+					"outputs": {
+						"outDir": "bbbcdownload.outDir"
+					}
+				},
+				"internal": false
+			}
+		],
+		"links": []
+	},
+	"plugins": []
+}

tests/test_rest_core.py

@@ -143,6 +143,60 @@ async def receive() -> Json:
     assert retval == 0
 
 
+def test_rest_core_single_node_bbbc() -> None:
+    """A simple single node sophios/restapi test"""
+    inp_file = "single_node_bbbc_download.json"
+    inp: Json = {}
+    inp_path = Path(__file__).parent / 'rest_wfb_objects' / inp_file
+    with open(inp_path, 'r', encoding='utf-8') as f:
+        inp = json.load(f)
+    inp['run_local_env'] = 'true'
+    print('----------- from rest api ----------- \n\n')
+    scope = {}
+    scope['type'] = 'http'
+
+    async def receive() -> Json:
+        inp_byte = json.dumps(inp).encode('utf-8')
+        return {"type": "http.request", "body": inp_byte}
+
+    # create a request object and pack it with our json payload
+    req: Request = Request(scope)
+    req._receive = receive
+    res: Json = asyncio.run(restapi.compile_wf(req))  # call to rest api
+    workflow_name = inp_file.split('.', maxsplit=1)[0]
+    # write compiled_cwl and inputs_yml
+    write_out_to_disk(res, workflow_name)
+    retval = run_cwl_local(workflow_name, 'cwltool', 'docker', False)
+    assert retval == 0
+
+
+def test_rest_core_bbbc_download_wfb() -> None:
+    """A simple multi node (inline cwl) sophios/restapi test"""
+    inp_file = "bbbc_download_wfb.json"
+    inp: Json = {}
+    inp_path = Path(__file__).parent / 'rest_wfb_objects' / inp_file
+    with open(inp_path, 'r', encoding='utf-8') as f:
+        inp = json.load(f)
+    inp['run_local_env'] = 'true'
+    print('----------- from rest api ----------- \n\n')
+    scope = {}
+    scope['type'] = 'http'
+
+    async def receive() -> Json:
+        inp_byte = json.dumps(inp).encode('utf-8')
+        return {"type": "http.request", "body": inp_byte}
+
+    # create a request object and pack it with our json payload
+    req: Request = Request(scope)
+    req._receive = receive
+    res: Json = asyncio.run(restapi.compile_wf(req))  # call to rest api
+    workflow_name = inp_file.split('.', maxsplit=1)[0]
+    # write compiled_cwl and inputs_yml
+    write_out_to_disk(res, workflow_name)
+    retval = run_cwl_local(workflow_name, 'cwltool', 'docker', False)
+    assert retval == 0
+
+
 @pytest.mark.fast
 def test_rest_core_multi_node_file() -> None:
     """A simple multi node sophios/restapi test"""