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Configure kernel provisioner and default environment file #81

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Configure kernel provisioner and default environment file #81

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2 changes: 2 additions & 0 deletions systemuser.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -153,6 +153,8 @@ fi

chown -R $USER:$USER $JPY_DIR $JPY_LOCAL_DIR $IPYTHONDIR
export SWAN_ENV_FILE=$SCRATCH_HOME/.bash_profile
# Used by swanprojects for the default folder environment
export SWAN_DEFAULT_ENV_FILE=$SCRATCH_HOME/.swan_default_env

sudo -E -u $USER sh /srv/singleuser/userconfig.sh

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18 changes: 17 additions & 1 deletion userconfig.sh
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Expand Up @@ -124,7 +124,14 @@ import json

def addEnv(dtext):
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This code exists here to be able to retrieve the user environment. If you no longer need to get it and write it in the kernel.json file, I would move it to the logic where we set the kernels (when we copy them from cvmfs). It would be more logical to do everything together there.

d=eval(dtext)
d["env"]=dict(os.environ)

# Configure a provisioner in kernel.json, that will load the enviornment
# dynamically from a folder-specific file or the default enviornment file
d["metadata"] = {
"kernel_provisioner": {
"provisioner_name": "swan-provisioner"
}
}
return d

kdirs = os.listdir("$KERNEL_DIR")
Expand All @@ -141,6 +148,15 @@ with open("$SWAN_ENV_FILE", "w") as termEnvFile:
if key == "PYTHONPATH":
val = re.sub('/usr/local/lib/swan/(extensions/)?:', '', val)
termEnvFile.write("export %s=\"%s\"\n" % (key, val))
# Write an enviornment file to be read by the provisioner
# for folders without a defined environment
with open("$SWAN_DEFAULT_ENV_FILE", "w") as defaultEnvFile:
for key, val in dict(os.environ).items():
if key == "SUDO_COMMAND":
continue
if key == "PYTHONPATH":
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This env file is going to be used by the kernels as well, right? Please note that you're not setting the same environment as before. We removed this extra path from the file that is loaded from the terminal, but it is supposed to exist in the kernel (otherwise, the spark stuff will break).

val = re.sub('/usr/local/lib/swan/(extensions/)?:', '', val)
defaultEnvFile.write("%s=%s\n" % (key, val))
EOF

# Make sure that `python` points to the correct python bin from CVMFS
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