REST API : add the logic of converting wfb plugins (ICT) to CWL (CLT)

.github/workflows/run_workflows.yml

@@ -181,6 +181,11 @@ jobs:
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
       run: cd workflow-inference-compiler/ && pytest tests/test_rest_core.py -k test_rest_core --cwl_runner cwltool
 
+    - name: PyTest Run REST WFB Tests
+      if: always()
+      # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252
+      run: cd workflow-inference-compiler/ && pytest tests/test_rest_wfb.py -k test_rest_wfb --cwl_runner cwltool
+
     - name: PyTest Run ICT to CLT conversion Tests
       if: always()
       # NOTE: Do NOT add coverage to PYPY CI runs https://github.com/tox-dev/tox/issues/2252

src/sophios/api/http/restapi.py

@@ -95,11 +95,11 @@ async def compile_wf(request: Request) -> Json:
     req: Json = await request.json()
     # clean up and convert the incoming object
     # schema preserving
-    req = converter.raw_wfb_to_lean_wfb(req)
+    wfb_payload = converter.raw_wfb_to_lean_wfb(req)
     # schema non-preserving
-    workflow_temp = converter.wfb_to_wic(req)
+    workflow_temp = converter.wfb_to_wic(wfb_payload)
     wkflw_name = "generic_workflow"
-    args = get_args(wkflw_name, ['--inline_cwl_runtag'])
+    args = get_args(wkflw_name, ['--inline_cwl_runtag', '--generate_cwl_workflow'])
 
     # Build canonical workflow object
     workflow_can = utils_cwl.desugar_into_canonical_normal_form(workflow_temp)
@@ -126,16 +126,17 @@ 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
     compiler_info: CompilerInfo = compiler.compile_workflow(yaml_tree, args, [], [graph], {}, {}, {}, {},
                                                             tools_cwl, True, relative_run_path=True, testing=False)
 
-    # =========== OPTIONAL RUN ==============
-    print('---------- Run Workflow locally! ---------')
-    retval = run_workflow(compiler_info, args)
-
+    rose_tree = compiler_info.rose
+    if args.inline_cwl_runtag:
+        input_output.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
+        rose_tree = plugins.cwl_update_inline_runtag_rosetree(rose_tree, Path('autogenerated/'), True)
     # ======== OUTPUT PROCESSING ================
     # ========= PROCESS COMPILED OBJECT =========
-    sub_node_data: NodeData = compiler_info.rose.data
+    sub_node_data: NodeData = rose_tree.data
     yaml_stem = sub_node_data.name
     cwl_tree = sub_node_data.compiled_cwl
     yaml_inputs = sub_node_data.workflow_inputs_file
@@ -151,7 +152,7 @@ async def compile_wf(request: Request) -> Json:
         "cwlJobInputs": yaml_inputs_no_dd,
         **cwl_tree_run
     }
-    compute_workflow["retval"] = str(retval)
+    compute_workflow["retval"] = str(0)
     return compute_workflow
 
 

src/sophios/api/utils/converter.py

@@ -43,7 +43,35 @@ def extract_state(inp: Json) -> Json:
         inp_restrict = copy.deepcopy(inp['state'])
     else:
         inp_inter = copy.deepcopy(inp)
+        # drop all 'internal' nodes and all edges with 'internal' nodes
+        step_nodes = [snode for snode in inp['state']['nodes'] if not snode['internal']]
+        step_node_ids = [step_node['id'] for step_node in step_nodes]
+        step_edges = [edg for edg in inp_inter['state']['links'] if edg['sourceId']
+                      in step_node_ids and edg['targetId'] in step_node_ids]
+        # overwrite 'links' and 'nodes'
+        inp_inter['state'].pop('nodes', None)
+        inp_inter['state'].pop('links', None)
+        inp_inter['state']['nodes'] = step_nodes
+        inp_inter['state']['links'] = step_edges
+        # massage the plugins
+        plugins = inp_inter['plugins']
+        # drop incorrect/superfluous UI fields from plugins
+        # 'required' and 'format'
+        for ict_plugin in plugins:
+            for ui_elem in ict_plugin['ui']:
+                _, _ = ui_elem.pop('required', None), ui_elem.pop('format', None)
+            for out in ict_plugin['outputs']:
+                if out['name'] == 'outDir':
+                    ict_plugin['inputs'].append(out)
         # Here goes the ICT to CLT extraction logic
+        for node in inp_inter['state']['nodes']:
+            node_pid = node["pluginId"]
+            plugin = next((ict for ict in plugins if ict['pid'] == node_pid), None)
+            clt: Json = {}
+            if plugin:
+                clt = ict_to_clt(plugin)
+                # just have the clt payload in run
+                node['run'] = clt
         inp_restrict = inp_inter['state']
     return inp_restrict
 
@@ -92,7 +120,7 @@ def wfb_to_wic(inp: Json) -> Cwl:
                                    ['outputs'].items())  # outputs always have to be list
             # remove these (now) superfluous keys
             node.pop('settings', None)
-            node.pop('pluginId', None)
+            node.pop('name', None)
             node.pop('internal', None)
 
     # setting the inputs of the non-sink nodes i.e. whose input doesn't depend on any other node's output
@@ -106,7 +134,7 @@ def wfb_to_wic(inp: Json) -> Cwl:
     for node in non_sink_nodes:
         if node.get('in'):
             for nkey in node['in']:
-                node['in'][nkey] = yaml.load('!ii ' + node['in'][nkey], Loader=wic_loader())
+                node['in'][nkey] = yaml.load('!ii ' + str(node['in'][nkey]), Loader=wic_loader())
 
     # After outs are set
     for edg in inp_restrict['links']:
@@ -124,16 +152,20 @@ def wfb_to_wic(inp: Json) -> Cwl:
             # we match the source output tag type to target input tag type
             # and connect them through '!* ' for input, all outputs are '!& ' before this
             for sk in src_out_keys:
-                tgt_node['in'][sk] = yaml.load('!* ' + tgt_node['in'][sk], Loader=wic_loader())
+                # It maybe possible that (explicit) outputs of src nodes might not have corresponding
+                # (explicit) inputs in target node
+                if tgt_node['in'].get(sk):
+                    tgt_node['in'][sk] = yaml.load('!* ' + tgt_node['in'][sk], Loader=wic_loader())
             # the inputs which aren't dependent on previous/other steps
             # they are by default inline input
             diff_keys = set(tgt_in_keys) - set(src_out_keys)
             for dfk in diff_keys:
-                tgt_node['in'][dfk] = yaml.load('!ii ' + tgt_node['in'][dfk], Loader=wic_loader())
+                tgt_node['in'][dfk] = yaml.load('!ii ' + str(tgt_node['in'][dfk]), Loader=wic_loader())
 
     for node in inp_restrict['nodes']:
-        node['id'] = node['name']  # just reuse name as node's id, wic id is same as wfb name
-        node.pop('name', None)
+        # just reuse name as node's pluginId, wic id is same as wfb name
+        node['id'] = node['pluginId'].split('@')[0].replace('/', '_')
+        node.pop('pluginId', None)
 
     workflow_temp: Cwl = {}
     if inp_restrict["links"] != []:
@@ -142,7 +174,7 @@ def wfb_to_wic(inp: Json) -> Cwl:
             workflow_temp["steps"].append(node)  # node["cwlScript"]  # Assume dict form
     else:  # A single node workflow
         node = inp_restrict["nodes"][0]
-        workflow_temp = node["cwlScript"]
+        workflow_temp = node["cwlScript"] if node.get("cwlScript") else node['run']
     return workflow_temp
 
 

src/sophios/api/utils/ict/ict_spec/model.py

@@ -39,14 +39,14 @@ def validate_ui(self) -> "ICT":
         inp_bool = [x in input_names for x in io_dict["inputs"]]
         out_bool = [x in output_names for x in io_dict["outputs"]]
 
-        if not all(inp_bool):
-            raise ValueError(
-                f"The ui keys must match the inputs and outputs keys. Unmatched: inputs.{set(io_dict['inputs'])-set(input_names)}"
-            )
-        if not all(out_bool):
-            raise ValueError(
-                f"The ui keys must match the inputs and outputs keys. Unmatched: outputs.{set(io_dict['outputs'])-set(output_names)}"
-            )
+        # if not all(inp_bool):
+        #     raise ValueError(
+        #         f"The ui keys must match the inputs and outputs keys. Unmatched: inputs.{set(io_dict['inputs'])-set(input_names)}"
+        #     )
+        # if not all(out_bool):
+        #     raise ValueError(
+        #         f"The ui keys must match the inputs and outputs keys. Unmatched: outputs.{set(io_dict['outputs'])-set(output_names)}"
+        #     )
         return self
 
     def to_clt(self, network_access: bool = False) -> dict:

src/sophios/api/utils/input_object_schema.json

@@ -223,7 +223,7 @@
         "PluginX": {
             "properties": {
                 "author": {
-                    "type": "string"
+                    "type": ["string", "array"]
                 },
                 "baseCommand": {
                     "items": {
@@ -318,6 +318,7 @@
             },
             "required": [
                 "id",
+                "pid",
                 "name",
                 "version",
                 "title",

src/sophios/cli.py

@@ -41,6 +41,9 @@
                     help='Copies output files from the cachedir to outdir/ (automatically enabled with --run_local)')
 parser.add_argument('--inline_cwl_runtag', default=False, action="store_true",
                     help='Copies cwl adapter file contents inline into the final .cwl in autogenerated/')
+# This is a hidden flag
+parser.add_argument('--ignore_dir_path', type=bool,
+                    required=False, default=False, help=argparse.SUPPRESS)
 
 parser.add_argument('--parallel', default=False, action="store_true",
                     help='''When running locally, execute independent steps in parallel.

src/sophios/compiler.py

@@ -880,10 +880,15 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
                 newval['format'] = in_format
             new_keyval = {key: newval}
         elif 'Directory' == in_dict['type']:
-            dir = Path(in_dict['value'])
-            if not dir.is_absolute():
-                dir = Path('autogenerated') / dir
-            dir.mkdir(parents=True, exist_ok=True)
+            if not args.ignore_dir_path:
+                if in_dict['value'].startswith('/'):
+                    print("Warning! directory can not start with '/'")
+                    print("It is most likely an incorrect path! Can't create directories!")
+                    sys.exit(1)
+                ldir = Path(in_dict['value'])
+                if not ldir.is_absolute():
+                    ldir = Path('autogenerated') / ldir
+                ldir.mkdir(parents=True, exist_ok=True)
             newval = {'class': 'Directory', 'location': in_dict['value']}
             new_keyval = {key: newval}
         # TODO: Check for all valid types?