From 17d099d37c3990eb13bb50f94e59ce3d9a6a376e Mon Sep 17 00:00:00 2001
From: Jonathan Karr <jonrkarr@gmail.com>
Date: Sun, 5 Dec 2021 20:28:28 -0500
Subject: [PATCH] fix: fixed escaping of arguments to entrypoint of Docker
 image

---
 Dockerfile                        | 6 ++++--
 biosimulators_opencor/__main__.py | 2 +-
 biosimulators_opencor/_version.py | 2 +-
 scripts/biosimulators-opencor     | 4 ++++
 setup.py                          | 2 +-
 5 files changed, 11 insertions(+), 5 deletions(-)
 create mode 100755 scripts/biosimulators-opencor

diff --git a/Dockerfile b/Dockerfile
index 3772b06..b46dad1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,5 @@
 # VERSION
-ARG VERSION=0.0.8
+ARG VERSION=0.0.9
 ARG SIMULATOR_VERSION="2021-10-05"
 
 # Base OS
@@ -57,6 +57,8 @@ ENV VERBOSE=0 \
 # - ugo+w permissions to `${OPENCORDIR}/python/bin` are needed because the OpenCOR Python pluging dynamically generates these files
 RUN mkdir ${HOMEDIR}/Biosimulators_OpenCOR \
     && chmod -R ugo+w ${OPENCORDIR}/python/bin
+ENV PATH=${OPENCORDIR}/python/bin:$PATH
 WORKDIR ${HOMEDIR}/Biosimulators_OpenCOR
-ENTRYPOINT ["pythonshell", "-m", "biosimulators_opencor"]
+COPY scripts/biosimulators-opencor ${OPENCORDIR}/python/bin
+ENTRYPOINT ["biosimulators-opencor"]
 CMD []
diff --git a/biosimulators_opencor/__main__.py b/biosimulators_opencor/__main__.py
index 9da77f5..43e5b49 100644
--- a/biosimulators_opencor/__main__.py
+++ b/biosimulators_opencor/__main__.py
@@ -11,7 +11,7 @@
 from .core import exec_sedml_docs_in_combine_archive
 from biosimulators_utils.simulator.cli import build_cli
 
-App = build_cli('opencor', __version__,
+App = build_cli('biosimulators-opencor', __version__,
                 'OpenCOR', get_simulator_version(), 'https://opencor.ws',
                 exec_sedml_docs_in_combine_archive)
 
diff --git a/biosimulators_opencor/_version.py b/biosimulators_opencor/_version.py
index 9123cf0..9d1ffab 100644
--- a/biosimulators_opencor/_version.py
+++ b/biosimulators_opencor/_version.py
@@ -1 +1 @@
-__version__ = '0.0.8'
+__version__ = '0.0.9'
diff --git a/scripts/biosimulators-opencor b/scripts/biosimulators-opencor
new file mode 100755
index 0000000..354c0ac
--- /dev/null
+++ b/scripts/biosimulators-opencor
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+opencor_path=$(which OpenCOR)
+"$(cd "$(dirname "$opencor_path")"; pwd)/bin/OpenCOR" -c PythonShell -m biosimulators_opencor "$@"
diff --git a/setup.py b/setup.py
index 1a8e935..90b72c3 100644
--- a/setup.py
+++ b/setup.py
@@ -56,7 +56,7 @@
     ],
     entry_points={
         'console_scripts': [
-            'biosimulators-opencor = biosimulators_opencor.__main__:main',
+            # 'biosimulators-opencor = biosimulators_opencor.__main__:main',
         ],
     },
 )