fix: add version for kpython + krdkit

brsynth · Mar 16, 2023 · 41f2a20 · 41f2a20
1 parent 4c0feda
commit 41f2a20
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Showing 5 changed files with 43 additions and 8 deletions.
diff --git a/retropath2_wrapper/Args.py b/retropath2_wrapper/Args.py
@@ -17,6 +17,8 @@
     'KNIME_VERSION': '4.6.4',
     'RP2_VERSION': 'r20220104',
     'ZENODO_VERSION': "NA",
+    'KNIME_PYTHON_VERSION': '4.5.2.v202203041212',
+    'KNIME_RDKIT_VERSION': '4.5.0.v202207051536',
     'KNIME_FOLDER': __PACKAGE_FOLDER
 }
 KNIME_ZENODO = {"4.6.4": "7515771", "4.7.0": "7564938"} # Map to Zenodo ID
@@ -112,15 +114,29 @@ def _add_arguments(parser):
         '--kzenodo',
         choices=[DEFAULTS['ZENODO_VERSION']] + list(KNIME_ZENODO.keys()),
         default=DEFAULTS['ZENODO_VERSION'],
-        help='install Knime and its dependencies from Zenodo.'
+        help='Install Knime and its dependencies from Zenodo.'
     )
 
     parser.add_argument(
         '--rp2_version',
         type=str,
         default=DEFAULTS['RP2_VERSION'],
         choices=['v9', 'r20210127', 'r20220104', "r20220224"],
-        help=f'version of RetroPath2.0 workflow (default: {DEFAULTS["RP2_VERSION"]}).'
+        help=f'Version of RetroPath2.0 workflow (default: {DEFAULTS["RP2_VERSION"]}).'
+    )
+
+    parser.add_argument(
+        '--kpython_version',
+        type=str,
+        default=DEFAULTS['KNIME_PYTHON_VERSION'],
+        help=f'Version of KNIME\'s PYTHON (default: {DEFAULTS["KNIME_PYTHON_VERSION"]}).'
+    )
+
+    parser.add_argument(
+        '--krdkit_version',
+        type=str,
+        default=DEFAULTS['KNIME_RDKIT_VERSION'],
+        help=f'Version of RDKit KNIME\'s plugin (default: {DEFAULTS["KNIME_RDKIT_VERSION"]}).'
     )
 
     # RetroPath2.0 workflow options

diff --git a/retropath2_wrapper/RetroPath2.py b/retropath2_wrapper/RetroPath2.py
@@ -42,6 +42,8 @@ def retropath2(
     outdir: str,
     kinstall: str = DEFAULTS['KNIME_FOLDER'],
     kexec: str = None, kpkg_install: bool = True, kver: str = DEFAULTS['KNIME_VERSION'],
+    kpython_ver: str = DEFAULTS['KNIME_PYTHON_VERSION'],
+    krdkit_ver: str = DEFAULTS['KNIME_RDKIT_VERSION'],
     kzenodo_ver: str = DEFAULTS['ZENODO_VERSION'],
     knime: Knime = None,
     rp2_version: str = DEFAULTS['RP2_VERSION'],
@@ -71,7 +73,13 @@ def retropath2(
 
     # Create Knime object
     if knime is None:
-        knime = Knime(kexec=kexec, kinstall=kinstall, is_kpkg_install=kpkg_install, kver=kver, kzenodo_ver=kzenodo_ver)
+        knime = Knime(
+            kexec=kexec,
+            kinstall=kinstall,
+            is_kpkg_install=kpkg_install,
+            kver=kver,
+            kzenodo_ver=kzenodo_ver
+        )
     if rp2_version is not None:
         knime.workflow = os_path.join(
             here, 'workflows', f'RetroPath2.0_{rp2_version}.knwf'
@@ -97,7 +105,11 @@ def retropath2(
     #      if kexec is not specified
     #  and executable not detected in default path
     knime.install_exec(logger=logger)
-    r_code = knime.install_pkgs(logger=logger)
+    r_code = knime.install_pkgs(
+        kpython_ver=kpython_ver,
+        krdkit_ver=krdkit_ver,
+        logger=logger
+    )
     if r_code > 0:
         return r_code, None
     elif r_code == RETCODES['OSError']:

diff --git a/retropath2_wrapper/__main__.py b/retropath2_wrapper/__main__.py
@@ -81,6 +81,8 @@ def _cli():
         kinstall=args.kinstall,
         is_kpkg_install=args.kpkg_install,
         kver=args.kver,
+        kpython_ver=args.kpython_version,
+        krdkit_ver=args.krdkit_version,
         kzenodo_ver=args.kzenodo,
         workflow=os_path.join(here, 'workflows', 'RetroPath2.0_%s.knwf' % (args.rp2_version,)),
     )

diff --git a/retropath2_wrapper/knime.py b/retropath2_wrapper/knime.py
@@ -218,7 +218,12 @@ def install_exec(self, logger: Logger = getLogger(__name__)) -> None:
             logger.info('   |--url: ' + self.kurl)
             logger.info('   |--install_dir: ' + self.kinstall)
 
-    def install_pkgs(self, logger: Logger = getLogger(__name__)) -> int:
+    def install_pkgs(
+        self,
+        kpython_ver: str,
+        krdkit_ver: str,
+        logger: Logger = getLogger(__name__)
+    ) -> int:
         """Install KNIME packages needed to execute RetroPath2.0 workflow.
 
         Parameters
@@ -262,8 +267,8 @@ def install_pkgs(self, logger: Logger = getLogger(__name__)) -> int:
                     + 'http://update.knime.com/analytics-platform/'+self.kver[:3]]
             args += ["-i", 'org.knime.features.chem.types.feature.group,' \
                 + 'org.knime.features.datageneration.feature.group,' \
-                + 'org.knime.features.python.feature.group,' \
-                + 'org.rdkit.knime.feature.feature.group']
+                + f'org.knime.features.python.feature.group/{kpython_ver},' \
+                + f'org.rdkit.knime.feature.feature.group/{krdkit_ver}']
             args += ['-bundlepool', self.kpkg_install]
             args += ['-d', self.kpkg_install]
 

diff --git a/tests/test_knime.py b/tests/test_knime.py
@@ -6,7 +6,7 @@
 
 import pytest
 from retropath2_wrapper.Args import (
-    DEFAULTS,KNIME_ZENODO, RETCODES
+    DEFAULTS, KNIME_ZENODO, RETCODES
 )
 from retropath2_wrapper.knime import Knime