noentrypoints change

src/sophios/api/http/restapi.py

@@ -13,7 +13,7 @@
 from sophios.utils_graphs import get_graph_reps
 from sophios.utils_yaml import wic_loader
 from sophios import utils_cwl
-from sophios.post_compile import cwl_inline_runtag
+from sophios.post_compile import cwl_inline_runtag, remove_entrypoints
 from sophios.cli import get_args
 from sophios.wic_types import CompilerInfo, Json, Tool, Tools, StepId, YamlTree, Cwl, NodeData
 from sophios.api.utils import converter
@@ -94,7 +94,7 @@ 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']
+    suppliedargs = ['--cwl_inline_runtag', '--generate_cwl_workflow', '--docker_remove_entrypoints']
     # clean up and convert the incoming object
     # schema preserving
     req = converter.update_payload_missing_inputs_outputs(req)
@@ -139,6 +139,7 @@ async def compile_wf(request: Request) -> Json:
     rose_tree = compiler_info.rose
     input_output.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
     rose_tree = cwl_inline_runtag(args, rose_tree)
+    rose_tree = remove_entrypoints(args, rose_tree)
     # ======== OUTPUT PROCESSING ================
     # ========= PROCESS COMPILED OBJECT =========
     sub_node_data: NodeData = rose_tree.data

tests/rest_wfb_objects/bbbc_download_wfb.json

@@ -36,7 +36,7 @@
             ],
             "contact": "hamdahshafqat.abbasi@nih.gov",
             "container": "polusai/bbbc-download-plugin:0.1.0-dev1",
-            "entrypoint": "",
+            "entrypoint": "python3 -m polus.plugins.utils.bbbc_download",
             "inputs": [
                 {
                     "description": "The name of the dataset(s) to be downloaded (separate the datasets with a comma. eg BBBC001,BBBC002,BBBC003)",