Allow online and local installation from Zenodo

README.md

@@ -98,7 +98,6 @@ Executions can be timed out using the `timeout` arguments (in minutes).
 - 2: Running the RetroPath2.0 Knime program produced an OSError
 - 3: InChI is malformated
 - 4: Sink file is malformed
-- 5: Knime installation returns an error
 - 10: Source has been found in the sink (warning)
 - 11: No solution is found (warning)
 
@@ -117,13 +116,13 @@ To run functional tests, the environment variable `RP2_FUNCTIONAL=TRUE` is requi
 
 ### Knime dependencies
 
-Availbale options:
+Available options:
 
 1. You provide a path of the Knime root directory through the argument `--kinstall`. You need to have the following libraries installed: `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`
 2. `retropath2_wrapper` will install Knime for you, at the root of the python package, by downloading the softwares available on Zenodo. You can choose a version among `4.6.4` or `4.7.0`. Optionally, you can locate a path for the installation. If an executable is found in the path, Knime will not be reinstalled.
 
 ```bash
-python -m retropath2_wrapper.knime \
+python -m retropath2_wrapper.knime online \
     --kinstall "/path/to/knime/root/dir" \
     --kver {4.6.4,4.7.0}
 ```
@@ -134,6 +133,14 @@ Knime software and packages are available at:
 - [KNIME v4.6.4 - Zenodo](https://zenodo.org/record/7515771)
 - [KNIME v4.7.0 - Zenodo](https://zenodo.org/record/7564938)
 
+All files from these repositories can be downloaded through the `Download all` button:
+
+```bash
+python -m retropath2_wrapper.knime local \
+    --kinstall "/path/to/knime/root/dir" \
+    --zenodo-zip "/path/to/7515771.zip"
+```
+
 ## Known issues
 
 1. Could not load native RDKit library, libfreetype.so.6: cannot open shared object file

retropath2_wrapper/Args.py

@@ -30,7 +30,6 @@
     'OSError': 2,
     'InChI': 3,
     'SinkFileMalformed': 4,
-    'KnimeInstallationError': 5,
 }
 
 

retropath2_wrapper/RetroPath2.py

@@ -19,6 +19,7 @@
 from filetype import guess
 from tempfile import TemporaryDirectory
 from typing import Dict, Tuple
+from types import SimpleNamespace
 from logging import (
     Logger,
     getLogger
@@ -32,6 +33,7 @@
     DEFAULTS,
     RETCODES,
 )
+from retropath2_wrapper import knime as knime_module
 from retropath2_wrapper.knime import Knime
 from retropath2_wrapper.preference import Preference
 
@@ -78,8 +80,16 @@ def retropath2(
         )
     if knime.kexec == "":
         # Install KNIME
-        if not knime.install(kver=Knime.DEFAULT_VERSION, logger=logger):
-            return RETCODES["KnimeInstallationError"]
+        args_knime = SimpleNamespace(
+            kinstall=knime.kinstall,
+            kver=Knime.DEFAULT_VERSION,
+        )
+        knime_module.install_online(args_knime, logger=logger)
+        # Init Knime again to set Knime.kexec
+        knime = Knime(
+            kinstall=knime.kinstall,
+            workflow=knime.workflow,
+        )
     logger.debug('knime: ' + str(knime))
 
     # Store RetroPath2 params into a dictionary