Merge pull request #16 from brsynth/feat-dwl-zenodo

Download Knime from Zenodo
brsynth · Jan 26, 2023 · 6fb96d1 · 6fb96d1
2 parents 8e21784 + e49a455
commit 6fb96d1
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diff --git a/README.md b/README.md
@@ -102,6 +102,15 @@ conda install -c conda-forge pytest
 python -m pytest tests
 ```
 
+To run functional tests, the environment variable `RP2_FUNCTIONAL=TRUE` is required.
+
+### Knime dependencies
+
+Knime software and packages are available at:
+* [KNIME](https://www.knime.com/)
+* [KNIME v4.6.4 - Zenodo](https://zenodo.org/record/7515771)
+* [KNIME v4.7.0 - Zenodo](https://zenodo.org/record/7564938)
+
 ## Known issues
 
 1. Could not load native RDKit library, libfreetype.so.6: cannot open shared object file

diff --git a/retropath2_wrapper/Args.py b/retropath2_wrapper/Args.py
@@ -12,21 +12,8 @@
 DEFAULT_MSC_TIMEOUT = 10  # minutes
 DEFAULT_KNIME_VERSION = "4.6.4"
 DEFAULT_RP2_VERSION = 'r20220104'
-KNIME_PACKAGE = {
-    '4.5.0': {
-         'org.knime.features.chem.types.feature.group': '4.5.0.v202107011901',
-         'org.knime.features.datageneration.feature.group': '4.5.0.v202107011901',
-         'org.knime.features.python.feature.group': '4.5.2.v202203041212',
-         'org.rdkit.knime.feature.feature.group': '4.5.0.v202207051536',
-         'org.rdkit.knime.feature.feature.group': '4.6.0.v202212061437',
-    },
-    "4.6.4": {
-         "org.knime.features.chem.types.feature.group": "4.6.0.v202202251610",
-         "org.knime.features.datageneration.feature.group": "4.6.0.v202202251621",
-         "org.knime.features.python.feature.group": "4.6.0.v202206100850",
-         "org.rdkit.knime.feature.feature.group": "4.6.1.v202212070507",
-    },
-}
+KNIME_ZENODO = {"4.6.4": "7515771", "4.7.0": "7564938"} # Map to Zenodo ID
+DEFAULT_ZENODO_VERSION = "NA"
 RETCODES = {
     'OK': 0,
     'NoError': 0,
@@ -110,7 +97,6 @@ def _add_arguments(parser):
     parser.add_argument(
         '--kver',
         type=str,
-        choices=list(KNIME_PACKAGE.keys()),
         default=DEFAULT_KNIME_VERSION,
         help='version of KNIME (mandatory if --kexec is passed).',
     )
@@ -120,6 +106,13 @@ def _add_arguments(parser):
         default=False,
         help='Install Knime packages (default: False).'
     )
+    parser.add_argument(
+        '--kzenodo',
+        choices=[DEFAULT_ZENODO_VERSION] + list(KNIME_ZENODO.keys()),
+        default=DEFAULT_ZENODO_VERSION,
+        help='install Knime and its dependencies from Zenodo.'
+    )
+
     parser.add_argument(
         '--rp2_version',
         type=str,