feat: add kinstall option

brsynth · Sep 23, 2022 · 5728dfc · 5728dfc
1 parent 7f7ddc5
commit 5728dfc
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Showing 3 changed files with 35 additions and 8 deletions.
diff --git a/retropath2_wrapper/Args.py b/retropath2_wrapper/Args.py
@@ -4,7 +4,7 @@
 @author: Joan Hérisson
 
 """
-
+from os import path as os_path
 from argparse import ArgumentParser
 from retropath2_wrapper._version import __version__
 
@@ -24,6 +24,10 @@
     'OSError': 2,
     'InChI': 3
 }
+__PACKAGE_FOLDER = os_path.dirname(
+    os_path.realpath(__file__)
+)
+DEFAULT_KNIME_FOLDER = __PACKAGE_FOLDER
 
 
 def build_args_parser():
@@ -81,6 +85,14 @@ def _add_arguments(parser):
               downloaded if not already installed or path is \
               wrong).'
     )
+    parser.add_argument(
+        '--kinstall',
+        type=str,
+        default=DEFAULT_KNIME_FOLDER,
+        help='path to KNIME executable file (KNIME will be \
+              downloaded if not already installed or path is \
+              wrong).'
+    )
     parser.add_argument(
         '--kver',
         type=str,

diff --git a/retropath2_wrapper/RetroPath2.py b/retropath2_wrapper/RetroPath2.py
@@ -53,6 +53,7 @@
 from logging import StreamHandler
 from csv import reader
 from .Args import (
+    DEFAULT_KNIME_FOLDER,
     DEFAULT_TIMEOUT,
     DEFAULT_KNIME_VERSION,
     DEFAULT_RP2_VERSION,
@@ -65,8 +66,10 @@
 def set_vars(
     kexec: str,
     kpkg_install: bool,
+    kinstall: str = DEFAULT_KNIME_FOLDER,
     kver: str = DEFAULT_KNIME_VERSION,
-    rp2_version: str = DEFAULT_RP2_VERSION
+    rp2_version: str = DEFAULT_RP2_VERSION,
+    logger: Logger = getLogger(__name__)
 ) -> Dict:
     """
     Set variables and store them into a dictionary.
@@ -84,10 +87,16 @@ def set_vars(
 
     """
 
+    logger.debug(f'kexec: {kexec}')
+    logger.debug(f'kver: {kver}')
+    logger.debug(f'kpkg_install: {kpkg_install}')
+    logger.debug(f'kinstall: {kinstall}')
+    logger.debug(f'rp2_version: {rp2_version}')
+
     # Setting kexec, kpath, kinstall, kver
     kexec_install = False
     if kexec is None:
-        kinstall = os_path.join(here, '.knime', sys_platform)
+        kinstall = os_path.join(kinstall, '.knime', sys_platform)
         if sys_platform == 'darwin':
             kpath = os_path.join(kinstall, f'KNIME_{kver}.app')
             kexec = os_path.join(kpath, 'Contents', 'MacOS', 'knime')
@@ -125,6 +134,7 @@ def set_vars(
 def retropath2(
     sink_file: str, source_file: str, rules_file: str,
     outdir: str,
+    kinstall: str = DEFAULT_KNIME_FOLDER,
     kexec: str = None, kpkg_install: bool = True, kver: str = DEFAULT_KNIME_VERSION,
     rp2_version: str = DEFAULT_RP2_VERSION,
     kvars: Dict = None,
@@ -142,6 +152,7 @@ def retropath2(
     logger.debug(f'outdir: {outdir}')
     logger.debug(f'kexec: {kexec}')
     logger.debug(f'kpkg_install: {kpkg_install}')
+    logger.debug(f'kinstall: {kinstall}')
     logger.debug(f'kver: {kver}')
     logger.debug(f'rp2_version: {rp2_version}')
     logger.debug(f'kvars: {kvars}')
@@ -158,7 +169,9 @@ def retropath2(
             kexec=kexec,
             kver=kver,
             kpkg_install=kpkg_install,
-            rp2_version=rp2_version
+            rp2_version=rp2_version,
+            kinstall=kinstall,
+            logger=logger
         )
         logger.debug('kvars: ' + str(kvars))
     # Store RetroPath2 params into a dictionary

diff --git a/retropath2_wrapper/__main__.py b/retropath2_wrapper/__main__.py
@@ -72,21 +72,23 @@ def _cli():
     if args.log.lower() in ['silent', 'quiet'] or args.silent:
         args.log = 'CRITICAL'
 
+    # Create logger
+    logger = create_logger(parser.prog, args.log)
+
     # Store KNIME vars into a dictionary
     kvars = set_vars(
         kexec=args.kexec,
         kver=args.kver,
         kpkg_install=args.kpkg_install,
-        rp2_version=args.rp2_version
+        rp2_version=args.rp2_version,
+        kinstall=args.kinstall,
+        logger=logger
     )
 
     # Print out configuration
     if not args.silent and args.log.lower() not in ['critical', 'error']:
         print_conf(kvars, prog = parser.prog)
 
-    # Create logger
-    logger = create_logger(parser.prog, args.log)
-
     logger.debug('args: ' + str(args))
     logger.debug('kvars: ' + str(kvars))