add required files for rest api (core)

pyproject.toml

@@ -33,11 +33,15 @@ dependencies = [
     # See https://github.com/common-workflow-language/cwl-utils/releases/
     "typeguard",
     "pydantic>=2.6",
+    "pydantic-settings",
     "docker",
     # FYI also need uidmap to run podman rootless
     "podman",
     # We are using the official release for these packages for now
     "toil[cwl]",
+    "fastapi",
+    "python-jose",
+    "uvicorn"
 ]
 
 [project.readme]

src/sophios/api/http/restapi.py

@@ -0,0 +1,175 @@
+from pathlib import Path
+import argparse
+import yaml
+
+import uvicorn
+from fastapi import FastAPI, Request, status
+from fastapi.middleware.cors import CORSMiddleware
+
+from sophios import __version__, compiler
+from sophios import run_local, input_output
+from sophios.utils_graphs import get_graph_reps
+from sophios.utils_yaml import wic_loader
+from sophios import utils_cwl
+from sophios.cli import get_args
+from sophios.wic_types import CompilerInfo, Json, Tool, Tools, StepId, YamlTree, Cwl
+# from wic.api.utils import converter
+# from .auth.auth import authenticate
+# from utils import converter
+
+
+# helper functions
+
+
+def remove_dot_dollar(tree: Cwl) -> Cwl:
+    """Removes . and $ from dictionary keys, e.g. $namespaces and $schemas. Otherwise, you will get
+    {'error': {'statusCode': 500, 'message': 'Internal Server Error'}}
+    This is due to MongoDB:
+    See https://www.mongodb.com/docs/manual/reference/limits/#Restrictions-on-Field-Names
+    Args:
+        tree (Cwl): A Cwl document
+    Returns:
+        Cwl: A Cwl document with . and $ removed from $namespaces and $schemas
+    """
+    tree_str = str(yaml.dump(tree, sort_keys=False, line_break='\n', indent=2))
+    tree_str_no_dd = tree_str.replace('$namespaces', 'namespaces').replace(
+        '$schemas', 'schemas').replace('.wic', '_wic')
+    tree_no_dd: Cwl = yaml.load(tree_str_no_dd, Loader=wic_loader())  # This effectively copies tree
+    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
+    Args:
+        req (JSON): A raw JSON content of incoming JSON object
+    Returns:
+        Cwl: A Cwl document with . and $ removed from $namespaces and $schemas
+    """
+    # ========= WRITE OUT =======================
+    input_output.write_to_disk(compiler_info.rose, Path('autogenerated/'), relative_run_path=True)
+    # ======== TEST RUN =========================
+    retval = run_local.run_local(args, compiler_info.rose, args.cachedir, 'cwltool', False)
+    return retval
+
+
+app = FastAPI()
+
+origins = ["*"]
+
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=origins,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+
+@app.get("/", status_code=status.HTTP_200_OK)
+# @authenticate
+async def root(request: Request) -> Json:
+    """The api has 1 route: compile
+
+    Returns:
+        Dict[str, str]: {"message": "The api has 1 route: compile"}
+    """
+    return {"message": "The api has 1 route: compile"}
+
+
+@app.post("/compile")
+# @authenticate
+async def compile_wf(request: Request) -> Json:
+    """The compile route compiles the json object from http request object built elsewhere
+
+    Args:
+        request (Request): request object built elsewhere
+
+    Returns:
+        compute_workflow (JSON): workflow json object ready to submit to compute
+    """
+    print('---------- Compile Workflow! ---------')
+    # ========= PROCESS REQUEST OBJECT ==========
+    req: Json = await request.json()
+    wkflw_name = "generic_workflow"
+    args = get_args(wkflw_name)
+    # yaml_tree_json: Json = converter.wfb_to_wic(req)
+    # yaml_tree_json = get_yaml_tree(req)
+
+    workflow_temp = req["templates"]["ict"]["cwlScript"]  # Assume dict form
+    workflow_can = utils_cwl.desugar_into_canonical_normal_form(workflow_temp)
+
+    # ========= BUILD WIC COMPILE INPUT =========
+    # ict_plugins = req["templates"]
+    tools_cwl: Tools = {StepId(content["id"], "global"):
+                        Tool(".", content["run"]) for content in workflow_can["steps"]}
+    # run tag will have the actual CommandLineTool
+    wic_obj = {'wic': workflow_can.get('wic', {})}
+    plugin_ns = wic_obj['wic'].get('namespace', 'global')
+
+    graph = get_graph_reps(wkflw_name)
+    yaml_tree: YamlTree = YamlTree(StepId(wkflw_name, plugin_ns), workflow_can)
+
+    # ========= COMPILE WORKFLOW ================
+    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)
+
+    compute_workflow: Json = {}
+    compute_workflow.get('retval', str(retval))
+    return compute_workflow
+
+
+if __name__ == '__main__':
+    uvicorn.run(app, host="0.0.0.0", port=3000)
+
+
+# # ========= PROCESS COMPILED OBJECT =========
+    # sub_node_data: NodeData = compiler_info.rose.data
+    # yaml_stem = sub_node_data.name
+    # cwl_tree = sub_node_data.compiled_cwl
+    # yaml_inputs = sub_node_data.workflow_inputs_file
+
+    # # ======== OUTPUT PROCESSING ================
+    # 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_key in cwl_tree['steps']:
+    #     step_name_i = step_key
+    #     step_name_i = step_name_i.replace('.yml', '_yml')  # Due to calling remove_dot_dollar above
+    #     step_name = '__'.join(step_key.split('__')[3:])  # Remove prefix
+
+    #     # Get step CWL from templates
+    #     run_val = next((tval['cwlScript']
+    #                    for _, tval in ict_plugins.items() if step_name == tval['name']), None)
+    #     cwl_tree_run['steps'][step_name_i]['run'] = run_val
+
+    # TODO: set name and driver in workflow builder ui
+    # compute_workflow: Json = {}
+    # compute_workflow = {
+    #     "name": yaml_stem,
+    #     "driver": "argo",
+    #     # "driver": "cwltool",
+    #     "cwlJobInputs": yaml_inputs_no_dd,
+    #     **cwl_tree_run
+    # }