operational options: add initfiles

AUTHORS.rst

@@ -3,6 +3,7 @@ Authors
 
 The list of contributors in alphabetical order:
 
+- `Adelina Lintuluoto <https://orcid.org/0000-0002-0726-1452>`_
 - `Daniel Prelipcean <https://orcid.org/0000-0002-4855-194X>`_
 - `Diego Rodriguez <https://orcid.org/0000-0003-0649-2002>`_
 - `Dinos Kousidis <https://orcid.org/0000-0002-4914-4289>`_

CHANGES.rst

@@ -10,6 +10,7 @@ Version master (UNRELEASED)
 - Performs workflow specification load logic. Before in ``reana-client``.
 - Adds VOMS proxy support as a new authentication method.
 - Add Black formatter support.
+- Adds initfiles as an operational option for Yadage.
 
 Version 0.6.1 (2020-05-25)
 --------------------------

reana_workflow_engine_yadage/cli.py

@@ -13,6 +13,7 @@
 import json
 import logging
 import os
+import yaml
 
 import click
 import yadageschemas
@@ -53,6 +54,12 @@ def load_yadage_operational_options(ctx, param, operational_options):
     operational_options["initdir"] = os.path.join(
         workflow_workspace, operational_options.get("initdir", "")
     )
+
+    operational_options["initfiles"] = [
+        os.path.join(workflow_workspace, initfile)
+        for initfile in operational_options.get("initfiles", [])
+    ]
+
     return operational_options
 
 
@@ -123,12 +130,18 @@ def run_yadage_workflow(
             )
             workflow_kwargs = dict(workflow_json=workflow_json)
         dataopts = {"initdir": operational_options["initdir"]}
+
+        initdata = {}
+        for initfile in operational_options["initfiles"]:
+            initdata.update(**yaml.safe_load(open(initfile)))
+        initdata.update(workflow_parameters)
+
         check_connection_to_job_controller()
 
         with steering_ctx(
             dataarg=workflow_workspace,
             dataopts=dataopts,
-            initdata=workflow_parameters if workflow_parameters else {},
+            initdata=initdata,
             visualize=True,
             updateinterval=5,
             loginterval=5,

setup.py

@@ -59,6 +59,7 @@
     "yadage==0.20.1",
     "yadage-schemas==0.10.6",
     "webcolors==1.9.1",  # FIXME remove once yadage-schemas solves yadage deps.
+    "checksumdir>=1.1.4,<1.2",
 ]
 
 packages = find_packages()