Install and use Knime smoothly

README.md

@@ -2,12 +2,12 @@
 
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/retropath2_wrapper/badges/version.svg)](https://anaconda.org/conda-forge/retropath2_wrapper) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/retropath2_wrapper/badges/latest_release_date.svg)](https://anaconda.org/conda-forge/retropath2_wrapper)
 
-Implementation of the KNIME retropath2.0 workflow. Takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The tool  expects the following files: `rules.csv`, `sink.csv` and `source.csv` and produces results in an output folder.
+Implementation of the KNIME retropath2.0 workflow. Takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The tool expects the following files: `rules.csv`, `sink.csv` and `source.csv` and produces results in an output folder.
 
 ## Prerequisites
 
-* Python 3
-* KNIME (code was tested on `4.6.4`, `4.7.0` versions)
+- Python 3
+- KNIME (code was tested on `4.6.4`, `4.7.0` versions)
 
 ## Install
 
@@ -20,6 +20,7 @@ The tool tries to install the KNIME Anlytical Platform as well as the RetroPath2
 ### conda package
 
 Install in the `<my_env>` conda environment:
+
 ```shell
 conda install -c conda-forge -n <my_env> retropath2_wrapper
 ```
@@ -29,13 +30,15 @@ conda install -c conda-forge -n <my_env> retropath2_wrapper
 **Disclaimer**: we recommand to provide absolute path to files, problems can arise with relative paths.
 
 ### From CLI (Linux, macOS)
+
 ```sh
 python -m retropath2_wrapper <sink-file> <rules-file> <out-dir> --source_file <source-file>
 ```
 
 ### From Python code
 
 The minimal required arguments are `sink_file`, `source_file`, `rules_file` and `outdir`.
+
 ```python
 from retropath2_wrapper import retropath2
 
@@ -48,6 +51,7 @@ r_code = retropath2(
 ```
 
 Exploration settings have default values and can be tuned:
+
 ```python
 from retropath2_wrapper import retropath2
 
@@ -65,15 +69,21 @@ r_code = retropath2(
 ```
 
 Already installed KNIME app can hence be used that way, eg:
+
 ```python
 from retropath2_wrapper import retropath2
+from retropath2_wrapper.knime import Knime
 
+knime = Knime(
+    kinstall="/path/to/knime/directory",
+    workflow="/path/to/workflow",
+)
 r_code = retropath2(
     sink_file='/path/to/sink/file',
     source_file='/path/to/source/file',
     rules_file='/path/to/rules/file',
     outdir='/path/to/outdir'
-    kexec='/Applications/KNIME 4.3.0.app/Contents/MacOS/knime',
+    knime=knime,
     )
 ```
 
@@ -82,17 +92,22 @@ Executions can be timed out using the `timeout` arguments (in minutes).
 ### Return codes
 
 `retropath2()` function returns one of the following codes:
-* 0: No error
-* 1: File is not found
-* 2: Running the RetroPath2.0 Knime program produced an OSError
-* 3: InChI is malformated
-* 10: Source has been found in the sink (warning)
-* 11: No solution is found (warning)
+
+- 0: No error
+- 1: File is not found
+- 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)
 
 ## Tests
+
 Test can be run with the following commands:
 
 ### Natively
+
 ```sh
 conda install -c conda-forge pytest
 python -m pytest tests
@@ -102,30 +117,40 @@ To run functional tests, the environment variable `RP2_FUNCTIONAL=TRUE` is requi
 
 ### Knime dependencies
 
-Two options are available:
-1. You provide a path of the Knime executable through the argument `--kexec`. 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 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.
+Availbale 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 \
+    --kinstall "/path/to/knime/root/dir" \
+    --kver {4.6.4,4.7.0}
+```
 
 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)
+
+- [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
-Some Knime versions (like: 4.3.0) or environments can't load RDKit library.
-You need to append the `$CONDA_PREFIX/lib` path to the `LD_LIBRARY_PATH` variable where the `libfreetype` library is available:
+   Some Knime versions (like: 4.3.0) or environments can't load RDKit library.
+   You need to append the `$CONDA_PREFIX/lib` path to the `LD_LIBRARY_PATH` variable where the `libfreetype` library is available:
+
 ```sh
 conda activate <env_name>
 export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$CONDA_PREFIX/lib"
 ```
 
 ## CI/CD
-For further tests and development tools, a CI toolkit is provided in `cicd-toolkit` folder (see [cicd-toolkit/README.md](cicd-toolit/README.md)).
 
+For further tests and development tools, a CI toolkit is provided in `cicd-toolkit` folder (see [cicd-toolkit/README.md](cicd-toolit/README.md)).
 
 ### How to cite RetroPath2.0?
+
 Please cite:
 
 Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: https://doi.org/10.1016/j.ymben.2017.12.002

environment.macos-arm64.yml

@@ -0,0 +1,9 @@
+name: retropath2_wrapper
+channels:
+  - conda-forge
+dependencies:
+  - python >=3.10
+  - brs_utils >=1.23.1
+  - filetype
+  - colored
+  - freetype

retropath2_wrapper/Args.py

@@ -15,37 +15,10 @@
 )
 DEFAULTS = {
     'MSC_TIMEOUT': 10,  # minutes
-    'KNIME_VERSION': "4.6.4",
     'RP2_VERSION': 'r20250728',
     'KNIME_FOLDER': __PACKAGE_FOLDER,
-    'KNIME_REPOS': [
-            # 'http://update.knime.com/partner/',
-            'http://update.knime.com/community-contributions/trunk/',
-            'http://update.knime.com/community-contributions/trusted/4.6',
-            'http://update.knime.com/analytics-platform/4.6'
-        ],
-    'KNIME_PLUGINS': ','.join(
-        [
-            'org.knime.base',
-            'org.knime.python.nodes',
-            'org.knime.datageneration',
-            'org.knime.chem.base',
-            'org.rdkit.knime.feature.feature.group/4.8.1.v202312052327',
-            'org.rdkit.knime.nodes/4.8.1.v202312052327',
-            # 'org.knime.python.nodes/4.6.0.v202203011403',
-            # 'org.knime.datageneration/4.6.0.v202202251621',
-            # 'org.knime.chem.base/4.6.0.v202202251610',
-            # 'org.rdkit.knime.feature.feature.group/4.8.1.v202312052327',
-            # 'org.rdkit.knime.nodes/4.8.1.v202312052327',
-        ]
-    ),
-    'NO_NETWORK': False,
     "STD_HYDROGEN": "auto",  # How hydrogens are represented in chemical rules
 }
-# DEFAULTS['KNIME_PLUGINS'] = ','.join(
-#     [pkg.split('/')[0] for pkg in DEFAULTS['KNIME_PLUGINS'].split(',')]
-# )
-KNIME_ZENODO = {"4.6.4": "7515771", "4.7.0": "7564938"} # Map to Zenodo ID
 RETCODES = {
     'OK': 0,
     'NoError': 0,
@@ -57,6 +30,7 @@
     'OSError': 2,
     'InChI': 3,
     'SinkFileMalformed': 4,
+    'KnimeInstallationError': 5,
 }
 
 
@@ -109,34 +83,11 @@ def _add_arguments(parser):
 
     # Knime
     parser_knime = parser.add_argument_group("Knime arguments")
-    parser_knime.add_argument(
-        '--kexec',
-        type=str,
-        default=None,
-        help='path to KNIME executable file (KNIME will be \
-              downloaded if not already installed or path is \
-              wrong).'
-    )
     parser_knime.add_argument(
         '--kinstall',
         type=str,
         default=DEFAULTS['KNIME_FOLDER'],
-        help='path to KNIME executable file (KNIME will be \
-              downloaded if not already installed or path is \
-              wrong).'
-    )
-    parser_knime.add_argument(
-        '--kver',
-        type=str,
-        default=DEFAULTS['KNIME_VERSION'],
-        choices=list(KNIME_ZENODO.keys()),
-        help='version of KNIME (mandatory if --kexec is passed).',
-    )
-    parser_knime.add_argument(
-        '--kplugins',
-        type=str,
-        default="",
-        help='KNIME plugins to use (separated by a comma).',
+        help='Directory where to find a KNIME executable file',
     )
 
     # RetroPath2.0 workflow options
@@ -149,14 +100,6 @@ def _add_arguments(parser):
         help=f'version of RetroPath2.0 workflow (default: {DEFAULTS["RP2_VERSION"]}).'
     )
 
-    # No network option
-    parser_rp.add_argument(
-        '--no-network',
-        action='store_true',
-        default=DEFAULTS['NO_NETWORK'],
-        help='Do not use network.'
-    )
-
     parser_rp.add_argument('--max_steps'    , type=int, default=3)
     parser_rp.add_argument('--topx'         , type=int, default=100)
     parser_rp.add_argument('--dmin'         , type=int, default=0)

retropath2_wrapper/RetroPath2.py

@@ -45,11 +45,7 @@ def retropath2(
     rules_file: str,
     outdir: str,
     std_hydrogen: str,
-    kinstall: str = DEFAULTS['KNIME_FOLDER'],
-    kexec: str = None,
-    kver: str = DEFAULTS['KNIME_VERSION'],
-    knime: Knime = None,
-    kplugins: list = DEFAULTS['KNIME_PLUGINS'],
+    knime: Knime,
     rp2_version: str = DEFAULTS['RP2_VERSION'],
     max_steps: int = 3,
     topx: int = 100,
@@ -65,9 +61,6 @@ def retropath2(
     logger.debug(f'rules_file: {rules_file}')
     logger.debug(f'outdir: {outdir}')
     logger.debug(f'std_hydrogen: {std_hydrogen}')
-    logger.debug(f'kexec: {kexec}')
-    logger.debug(f'kinstall: {kinstall}')
-    logger.debug(f'kver: {kver}')
     logger.debug(f'rp2_version: {rp2_version}')
     logger.debug(f'max_steps: {max_steps}')
     logger.debug(f'topx: {topx}')
@@ -78,12 +71,15 @@ def retropath2(
 
     # Create Knime object
     if knime is None:
-        knime = Knime(kexec=kexec, kinstall=kinstall, kver=kver)
+        knime = Knime()
     if rp2_version is not None:
         knime.workflow = os_path.join(
             here, 'workflows', f'RetroPath2.0_{rp2_version}.knwf'
         )
-
+    if knime.kexec == "":
+        # Install KNIME
+        if not knime.install(kver=Knime.DEFAULT_VERSION, logger=logger):
+            return RETCODES["KnimeInstallationError"]
     logger.debug('knime: ' + str(knime))
 
     # Store RetroPath2 params into a dictionary
@@ -101,11 +97,6 @@ def retropath2(
     if r_code != RETCODES['OK']:
         return r_code, None
 
-    # Install KNIME
-    r_code = knime.install(logger=logger)
-    if r_code > 0:
-        return r_code, None
-
     logger.info('{attr1}Initializing{attr2}'.format(attr1=attr('bold'), attr2=attr('reset')))
 
     # Preferences

retropath2_wrapper/__main__.py

@@ -79,18 +79,11 @@ def _cli():
 
     # Create Knime object
     here = os_path.dirname(os_path.realpath(__file__))
-    if args.kplugins == "":
-        kplugins = []
-    else:
-        kplugins = args.kplugins.split(',')
     knime = Knime(
-        kexec=args.kexec,
         kinstall=args.kinstall,
-        kver=args.kver,
-        kplugins=kplugins,
         workflow=os_path.join(here, 'workflows', 'RetroPath2.0_%s.knwf' % (args.rp2_version,)),
-        network=not args.no_network,
     )
+
     # Print out configuration
     if not args.silent and args.log.lower() not in ['critical', 'error']:
         print_conf(knime, prog = parser.prog)
@@ -194,12 +187,6 @@ def parse_and_check_args(
 
     args = parser.parse_args()
 
-    if args.kexec is not None:
-        if not os.path.isfile(args.kexec):
-            parser.error("--kexec is not a file: %s" %(args.kexec,))
-        if not os.access(args.kexec, os.X_OK):
-            parser.error("--kexec is not executable: %s" %(args.kexec,))
-
     # Create outdir if does not exist
     if not os_path.exists(args.outdir):
         os_mkdir(args.outdir)