feat: pass workflow as CLI parameter

brsynth · Dec 21, 2021 · 355fa9c · 355fa9c
1 parent 9c8bbb2
commit 355fa9c
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Showing 4 changed files with 19 additions and 23 deletions.
diff --git a/retropath2_wrapper/Args.py b/retropath2_wrapper/Args.py
@@ -7,8 +7,11 @@
 
 from argparse import ArgumentParser
 from retropath2_wrapper._version import __version__
+from os import path as os_path 
+here = os_path.dirname(os_path.realpath(__file__))
 
 DEFAULT_TIMEOUT = 60
+DEFAULT_RETROPATH2_KWF = os_path.join(here, 'workflows', 'RetroPath2.0_r20210127.knwf')
 
 def build_args_parser():
     parser = ArgumentParser(prog='retropath2_wrapper', description='Python wrapper to parse RP2 to generate rpSBML collection of unique and complete (cofactors) pathways')
@@ -65,6 +68,12 @@ def _add_arguments(parser):
         default=None,
         help='InChI of compound to produce (not compliant with --source_file).'
     )
+    parser.add_argument(
+        '--workflow',
+        type=str,
+        default=DEFAULT_RETROPATH2_KWF,
+        help=f'RetroPath2.0 workflow to wrap (default: {DEFAULT_RETROPATH2_KWF}).'
+    )
     parser.add_argument(
         '--kexec',
         type=str,

diff --git a/retropath2_wrapper/RetroPath2.py b/retropath2_wrapper/RetroPath2.py
@@ -44,7 +44,8 @@
 from logging import StreamHandler
 from csv import reader
 from .Args import (
-    DEFAULT_TIMEOUT
+    DEFAULT_TIMEOUT,
+    DEFAULT_RETROPATH2_KWF
 )
 
 
@@ -56,7 +57,6 @@ def set_vars(
     kexec: str,
     kver: str,
     kpkg_install: bool,
-    workflow: str
 ) -> Dict:
     """
     Set variables and store them into a dictionary.
@@ -69,21 +69,11 @@ def set_vars(
         Version of KNIME to install.
     kpkg_install : bool
         Boolean to know if KNIME packages have to be installed.
-    workflow: str
-        Path to workflow to process.
     logger : Logger
         The logger object.
 
     """
 
-    # Take workflow in the package if not passed as an argument
-    if workflow is None:
-        workflow = os_path.join(
-            os_path.dirname(os_path.abspath(__file__)),
-            'workflows',
-            __RETROPATH2_KWF__
-            )
-
     # Setting kexec, kpath, kinstall, kver
     kexec_install = False
     if kexec is None:
@@ -111,16 +101,15 @@ def set_vars(
         'kver'          : kver,
         'kpath'         : kpath,
         'kinstall'      : kinstall,
-        'kpkg_install'  : kpkg_install,
-        'workflow'      : workflow
+        'kpkg_install'  : kpkg_install
     }
 
 
 def retropath2(
     sink_file: str, source_file: str, rules_file: str,
     outdir: str,
     kexec: str = None, kpkg_install: bool = True, kver: str = None,
-    workflow: str = None,
+    workflow: str = DEFAULT_RETROPATH2_KWF,
     kvars: Dict = None,
     max_steps: int = 3,
     topx: int = 100,
@@ -135,8 +124,7 @@ def retropath2(
         kvars = set_vars(
             kexec,
             kver,
-            kpkg_install,
-            workflow
+            kpkg_install
         )
         logger.debug('kvars: ' + str(kvars))
     # Store RetroPath2 params into a dictionary

diff --git a/retropath2_wrapper/__main__.py b/retropath2_wrapper/__main__.py
@@ -87,9 +87,9 @@ def _cli():
     kvars = set_vars(
         args.kexec,
         args.kver,
-        args.kpkg_install,
-        args.kwf
+        args.kpkg_install
     )
+    kvars['workflow'] = args.workflow
 
     # Print out configuration
     if not args.silent and args.log.lower() not in ['critical', 'error']:
@@ -106,6 +106,7 @@ def _cli():
         outdir=args.outdir,
         kvars=kvars,
         max_steps=args.max_steps, topx=args.topx, dmin=args.dmin, dmax=args.dmax, mwmax_source=args.mwmax_source, mwmax_cof=args.mwmax_cof,
+        workflow=args.workflow,
         timeout=args.timeout,
         logger=logger
     )

diff --git a/tests/test_RP2.py b/tests/test_RP2.py
@@ -86,8 +86,7 @@ def test_set_vars_None(self):
         kvars = set_vars(
             kexec        = None,
             kver         = None,
-            kpkg_install = True,
-            workflow     = None
+            kpkg_install = True
             )
 
         # Prepare expectd data
@@ -108,8 +107,7 @@ def test_set_vars_None(self):
             'kver'          : kver,
             'kpath'         : kpath,
             'kinstall'      : kinstall,
-            'kpkg_install'  : True,
-            'workflow'      : workflow
+            'kpkg_install'  : True
         }
         self.assertDictEqual(kvars, kvars_expected)