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feat(macOS): make natively runnable on macOS
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@breakthewall
breakthewall committed Jan 5, 2022
1 parent b757eeb commit 0103cf5
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8 changes: 4 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -15,9 +15,9 @@ Implementation of the KNIME retropath2.0 workflow. Takes for input the minimal (

The conda package manager is required. Fresh instructions on how to install conda are [available online](https://docs.conda.io/projects/conda/en/latest/user-guide/install/).

On Linux system, the tool tries to install the KNIME Anlytical Platform as well as the RetroPath2.0 node dependancies.
On Linux and macOS systems, the tool tries to install the KNIME Anlytical Platform as well as the RetroPath2.0 node dependancies.

On MacOS, the user needs to first install by himself KNIME, and be sure that the RetroPath2.0 node dependancies are installed. To install node dependancies, we recommand to follow the RetroPath2.0 instructions from https://www.myexperiment.org/workflows/4987.html.
On Windows, the user needs to first install by himself KNIME, and be sure that the RetroPath2.0 node dependancies are installed. To install node dependancies, we recommand to follow the RetroPath2.0 instructions from https://www.myexperiment.org/workflows/4987.html.

### conda package

Expand All @@ -30,12 +30,12 @@ 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)
### From CLI (Linux, macOS)
```sh
python -m retropath2_wrapper <sink-file> <rules-file> <out-dir> --source_file <source-file>
```

### From CLI (MacOS)
### From CLI (Windows)
```sh
python -m retropath2_wrapper <sink-file> <rules-file> <out-dir> --source_file <source-file> --kexec <path-to-knime-exec>
```
Expand Down
152 changes: 80 additions & 72 deletions retropath2_wrapper/RetroPath2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,26 +16,33 @@
# getegid
)
from getpass import getuser
from shutil import copyfile
from shutil import (
copyfile,
copytree,
rmtree
)
from sys import platform as sys_platform
from subprocess import (
run,
STDOUT,
TimeoutExpired
) # nosec
from brs_utils import (
download_and_extract_tar_gz,
download,
extract_gz,
chown_r
chown_r,
subprocess_call
)
from filetype import guess
from tempfile import (
NamedTemporaryFile,
TemporaryDirectory
)
from filetype import guess
from tempfile import TemporaryDirectory
from typing import (
from typing import (
Dict,
List,
Tuple
)
from logging import (
from logging import (
Logger,
getLogger
)
Expand Down Expand Up @@ -79,19 +86,23 @@ def set_vars(
kexec_install = False
if kexec is None:
kinstall = os_path.dirname(os_path.abspath(__file__))
kpath = os_path.join(
kinstall,
'knime_'
) + kver
kexec = os_path.join(
kpath,
'knime'
)
if sys_platform == 'linux':
kpath = os_path.join(kinstall, f'knime_{kver}')
kexec = os_path.join(kpath, 'knime')
elif sys_platform == 'darwin':
kpath = os_path.join(kinstall, f'KNIME_{kver}.app')
kexec = os_path.join(kpath, 'Contents', 'MacOS', 'knime')
if not os_path.exists(kexec):
kexec_install = True
else:
kpath = kexec[:kexec.rfind('/')]
kinstall = kpath[:kpath.rfind('/')]
if sys_platform == 'linux':
kpath = kexec[:kexec.rfind('/')]
kinstall = kpath[:kpath.rfind('/')]
elif sys_platform == 'darwin':
kpath = kexec[:kexec.rfind('/')]
kinstall = kpath[:kpath.rfind('/')]
print(kpath, kinstall)
exit()

# Build a dict to store KNIME vars
return {
Expand Down Expand Up @@ -156,10 +167,15 @@ def retropath2(
kvars['kver'],
logger
)
if sys_platform == 'linux':
kpkg_install = kvars['kpath']
elif sys_platform == 'darwin':
kpkg_install = os_path.join(kvars['kpath'], 'Contents', 'Eclipse')
r_code = install_knime_pkgs(
kvars['kpath'],
kvars['kver'],
logger
kpkg_install=kpkg_install,
kver=kvars['kver'],
kexec=kvars['kexec'],
logger=logger
)
if r_code > 0:
return str(r_code), None
Expand All @@ -168,10 +184,15 @@ def retropath2(
else:
# Add packages to KNIME
if kvars['kpkg_install']:
if sys_platform == 'linux':
kpkg_install = kvars['kpath']
elif sys_platform == 'darwin':
kpkg_install = os_path.join(kvars['kpath'], 'Contents', 'Eclipse')
r_code = install_knime_pkgs(
kvars['kpath'],
kvars['kver'],
logger
kpkg_install=kpkg_install,
kver=kvars['kver'],
kexec=kvars['kexec'],
logger=logger
)
if r_code > 0:
return str(r_code), None
Expand Down Expand Up @@ -399,21 +420,34 @@ def install_knime(
logger.info('{attr1}Downloading KNIME {kver}...{attr2}'.format(attr1=attr('bold'), kver=kver, attr2=attr('reset')))

if sys_platform == 'linux':
kurl = 'http://download.knime.org/analytics-platform/linux/knime_'+kver+'.linux.gtk.x86_64.tar.gz'
kurl = f'http://download.knime.org/analytics-platform/linux/knime_{kver}.linux.gtk.x86_64.tar.gz'
download_and_extract_tar_gz(kurl, kinstall)
chown_r(kinstall, getuser())
# chown_r(kinstall, geteuid(), getegid())

elif sys_platform == 'darwin':
# kurl = 'https://download.knime.org/analytics-platform/macosx/knime-'+kver+'-app.macosx.cocoa.x86_64.dmg'
kurl = 'https://download.knime.org/analytics-platform/macosx/knime-latest-app.macosx.cocoa.x86_64.dmg'
dmg = f'knime_{kver}.app.macosx.cocoa.x86_64.dmg'
kurl = f'https://download.knime.org/analytics-platform/macosx/{dmg}'
with NamedTemporaryFile() as tempf:
download(kurl, tempf.name)
app_path = f'{kinstall}/KNIME_{kver}.app'
if os_path.exists(app_path):
rmtree(app_path)
with TemporaryDirectory() as tempd:
cmd = f'hdiutil mount -noverify {tempf.name} -mountpoint {tempd}/KNIME'
returncode = subprocess_call(cmd, logger=logger)
copytree(
f'{tempd}/KNIME/KNIME {kver}.app',
app_path
)
cmd = f'hdiutil unmount {tempd}/KNIME'
returncode = subprocess_call(cmd, logger=logger)

else:
kurl = 'https://download.knime.org/analytics-platform/win/knime-'+kver+'-installer-win32.win32.x86_64.exe'
else: # Windows
kurl = f'https://download.knime.org/analytics-platform/win/knime-{kver}-installer-win32.win32.x86_64.exe'

logger.info(' |--url: '+kurl)
logger.info(' |--install_dir: '+kinstall)

download_and_extract_tar_gz(kurl, kinstall)
chown_r(kinstall, getuser())
# chown_r(kinstall, geteuid(), getegid())


def gunzip_to_csv(filename: str, indir: str) -> str:
Expand Down Expand Up @@ -482,8 +516,8 @@ def format_files_for_knime(
'rules' : os_path.abspath(rulesfile),
'results' : 'results'+'.csv',
'src-in-sk' : 'source-in-sink'+'.csv',
'outdir' : outdir
}
'outdir' : os_path.abspath(outdir)
}
# Because KNIME accepts only '.csv' file extension,
# files have to be renamed
for key in ['sink', 'source', 'rules']:
Expand All @@ -499,8 +533,9 @@ def format_files_for_knime(


def install_knime_pkgs(
kpath: str,
kpkg_install: str,
kver: str,
kexec: str,
logger: Logger = getLogger(__name__)
) -> int:
"""
Expand All @@ -522,7 +557,7 @@ def install_knime_pkgs(
"""
StreamHandler.terminator = ""
logger.info( ' |- Checking KNIME packages...')
logger.debug(' + kpath: '+kpath)
logger.debug(' + kpkg_install: '+kpkg_install)
logger.debug(' + kver: '+kver)

args = \
Expand All @@ -535,32 +570,14 @@ def install_knime_pkgs(
+ 'org.knime.features.datageneration.feature.group,' \
+ 'org.knime.features.python.feature.group,' \
+ 'org.rdkit.knime.feature.feature.group' \
+ ' -bundlepool ' + kpath + ' -d ' + kpath

if ' ' in kpath:
cmd = '"'+os_path.join(kpath, 'knime')+'"' \
+ args
else:
cmd = os_path.join(kpath, 'knime') \
+ args

try:
printout = open(devnull, 'wb') if logger.level > 10 else None
CPE = run(
cmd.split(),
stdout=printout,
stderr=printout,
shell=False
) # nosec
logger.debug(CPE)
StreamHandler.terminator = "\n"
logger.info(' OK')
return CPE.returncode
+ ' -bundlepool ' + kpkg_install + ' -d ' + kpkg_install

except OSError as e:
logger.error(e)
return -1
cmd = f'{kexec} {args}'

returncode = subprocess_call(cmd, logger=logger)
StreamHandler.terminator = "\n"
logger.info(' OK')
return returncode

def call_knime(
kvars: Dict,
Expand Down Expand Up @@ -621,22 +638,13 @@ def call_knime(
os_environ['CONDA_PREFIX'],
"lib"
)
# print(' '.join([kvars['kexec']] + args.split()))
# exit()
CPE = run(
[kvars['kexec']] + args.split(),
stdout=printout,
stderr=printout,
timeout=timeout*60,
shell=False
) # nosec
returncode = subprocess_call(cmd=kvars['kexec'] + args, logger=logger)
os_environ['LD_LIBRARY_PATH'] = ':'.join(
os_environ['LD_LIBRARY_PATH'].split(':')[:-1]
)
logger.debug(CPE)
StreamHandler.terminator = "\n"
logger.info(' {bold}OK{reset}'.format(bold=attr('bold'), reset=attr('reset')))
return CPE.returncode
return returncode

except TimeoutExpired as e:
logger.warning(' |- Time limit ({timeout} min) is reached'.format(timeout=timeout))
Expand Down

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