feat: add KNIME python and rdkit versions

brsynth · Mar 16, 2023 · 19f4d3a · 19f4d3a
1 parent 41f2a20
commit 19f4d3a
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Showing 3 changed files with 30 additions and 11 deletions.
diff --git a/retropath2_wrapper/Args.py b/retropath2_wrapper/Args.py
@@ -17,8 +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_PYTHON_VERSION': '4.6.0.v202206100850',
+    'KNIME_RDKIT_VERSION': '4.6.1.v202212212136',
     'KNIME_FOLDER': __PACKAGE_FOLDER
 }
 KNIME_ZENODO = {"4.6.4": "7515771", "4.7.0": "7564938"} # Map to Zenodo ID

diff --git a/retropath2_wrapper/RetroPath2.py b/retropath2_wrapper/RetroPath2.py
@@ -41,7 +41,9 @@ def retropath2(
     sink_file: str, source_file: str, rules_file: str,
     outdir: str,
     kinstall: str = DEFAULTS['KNIME_FOLDER'],
-    kexec: str = None, kpkg_install: bool = True, kver: str = DEFAULTS['KNIME_VERSION'],
+    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'],
@@ -78,6 +80,8 @@ def retropath2(
             kinstall=kinstall,
             is_kpkg_install=kpkg_install,
             kver=kver,
+            kpython_ver=kpython_ver,
+            krdkit_ver=krdkit_ver,
             kzenodo_ver=kzenodo_ver
         )
     if rp2_version is not None:
@@ -105,11 +109,7 @@ def retropath2(
     #      if kexec is not specified
     #  and executable not detected in default path
     knime.install_exec(logger=logger)
-    r_code = knime.install_pkgs(
-        kpython_ver=kpython_ver,
-        krdkit_ver=krdkit_ver,
-        logger=logger
-    )
+    r_code = knime.install_pkgs(logger=logger)
     if r_code > 0:
         return r_code, None
     elif r_code == RETCODES['OSError']:

diff --git a/retropath2_wrapper/knime.py b/retropath2_wrapper/knime.py
@@ -77,10 +77,23 @@ def standardize_path(cls, path: str) -> str
     ZENODO_API = "https://zenodo.org/api/"
     KNIME_URL = "http://download.knime.org/analytics-platform/"
 
-    def __init__(self, workflow: str="", kinstall: str=DEFAULTS['KNIME_FOLDER'], kver: str = DEFAULTS['KNIME_VERSION'], is_kpkg_install: bool=False, kexec: Optional[str]=None, kzenodo_ver: str=DEFAULTS['ZENODO_VERSION'], *args, **kwargs) -> None:
+    def __init__(
+        self,
+        workflow: str="",
+        kinstall: str=DEFAULTS['KNIME_FOLDER'],
+        kver: str = DEFAULTS['KNIME_VERSION'],
+        kpython_ver: str=DEFAULTS['KNIME_PYTHON_VERSION'],
+        krdkit_ver: str=DEFAULTS['KNIME_RDKIT_VERSION'],
+        is_kpkg_install: bool=False,
+        kexec: Optional[str]=None,
+        kzenodo_ver: str=DEFAULTS['ZENODO_VERSION'],
+        # *args, **kwargs
+    ) -> None:
 
         self.workflow = workflow
         self.kver = kver
+        self.kpython_ver = kpython_ver
+        self.krdkit_ver = krdkit_ver
         self.is_kpkg_install = is_kpkg_install
         self.kexec = kexec
         self.kzenodo_ver = kzenodo_ver
@@ -140,6 +153,8 @@ def __repr__(self):
         s = ["Knime vars:"]
         s.append("workflow: " + self.workflow)
         s.append("kver: " + self.kver)
+        s.append("kpython_ver: " + self.kpython_ver)
+        s.append("krdkit_ver: " + self.krdkit_ver)
         s.append("is_kpkg_install: " + str(self.kpkg_install))
         s.append("kpkg_install: " + self.kpkg_install)
         s.append("kexec: " + self.kexec)
@@ -220,8 +235,8 @@ def install_exec(self, logger: Logger = getLogger(__name__)) -> None:
 
     def install_pkgs(
         self,
-        kpython_ver: str,
-        krdkit_ver: str,
+        kpython_ver: str = None,
+        krdkit_ver: str = None,
         logger: Logger = getLogger(__name__)
     ) -> int:
         """Install KNIME packages needed to execute RetroPath2.0 workflow.
@@ -235,6 +250,10 @@ def install_pkgs(
         ------
         int
         """
+        if kpython_ver is None:
+            kpython_ver = self.kpython_ver
+        if krdkit_ver is None:
+            krdkit_ver = self.krdkit_ver
         returncode = 0
         if self.kexec_install or self.is_kpkg_install:
             StreamHandler.terminator = ""