ModuleNotFoundError: No module named 'psycopg2' during k8 installation

[devysh1907]

Hi,
While deploying super set using helm chart, i am getting "ModuleNotFoundError: No module named 'psycopg2'" in superset-init-db

[dosubot[bot]]

To resolve the "ModuleNotFoundError: No module named 'psycopg2'" error during the deployment of Superset using a Helm chart, you should ensure that the correct version of psycopg2 is pinned. According to the changelog, there is a specific commit related to pinning the correct psycopg2 version in the Helm chart:

- **helm:** pin correct psycopg2 version ([#17999](https://github.com/apache/superset/issues/17999)) ([cdcdf11](https://github.com/apache/superset/commit/cdcdf11d0736f223aaf2a594323be869e0860169))

Make sure your Helm chart is updated to include this change, which should resolve the module not found error by ensuring the correct version of psycopg2 is installed ^[1].

To continue talking to Dosu, mention @dosu.

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[dosubot[bot]]

The error "ModuleNotFoundError: No module named 'psycopg2'" indicates that the psycopg2 package is not installed in your environment. To resolve this, you need to ensure that psycopg2 is included in your Helm chart deployment.

You can add psycopg2 to the bootstrap script in your Helm chart configuration. Here's an example of how you can specify the installation of psycopg2:

bootstrapScript: |
  #!/bin/bash
  pip install psycopg2==2.9.6 \
    sqlalchemy-bigquery==1.6.1 \
    elasticsearch-dbapi==0.2.5 &&\
  if [ ! -f ~/bootstrap ]; then echo "Running Superset with uid {{ .Values.runAsUser }}" > ~/bootstrap; fi

Make sure your Helm chart is updated to include this script. This should resolve the "ModuleNotFoundError: No module named 'psycopg2'" error by ensuring the correct version of psycopg2 is installed ^[1].

To continue talking to Dosu, mention @dosu.

---

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[devysh1907]

  copying lib/errorcodes.py -> build/lib.linux-x86_64-cpython-310/psycopg2
  copying lib/errors.py -> build/lib.linux-x86_64-cpython-310/psycopg2
  copying lib/extensions.py -> build/lib.linux-x86_64-cpython-310/psycopg2
  copying lib/extras.py -> build/lib.linux-x86_64-cpython-310/psycopg2
  copying lib/pool.py -> build/lib.linux-x86_64-cpython-310/psycopg2
  copying lib/sql.py -> build/lib.linux-x86_64-cpython-310/psycopg2
  copying lib/tz.py -> build/lib.linux-x86_64-cpython-310/psycopg2
  running build_ext
  building 'psycopg2._psycopg' extension
  creating build/temp.linux-x86_64-cpython-310/psycopg
  gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC "-DPSYCOPG_VERSION=2.9.6 (dt dec pq3 ext lo64)" -DPSYCOPG_DEBUG=1 -DPG_VERSION_NUM=150009 -DHAVE_LO64=1 -DPSYCOPG_DEBUG=1 -I/usr/local/include/python3.10 -I. -I/usr/include/postgresql -I/usr/include/postgresql/15/server -I/usr/include/libxml2 -c psycopg/adapter_asis.c -o build/temp.linux-x86_64-cpython-310/psycopg/adapter_asis.o -Wdeclaration-after-statement
  
  It appears you are missing some prerequisite to build the package from source.
  
  You may install a binary package by installing 'psycopg2-binary' from PyPI.
  If you want to install psycopg2 from source, please install the packages
  required for the build and try again.
  
  For further information please check the 'doc/src/install.rst' file (also at
  <https://www.psycopg.org/docs/install.html>).
  
  error: command 'gcc' failed: No such file or directory
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for psycopg2
Running setup.py clean for psycopg2
Failed to build psycopg2
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (psycopg2)
Upgrading DB schema...
Loaded your LOCAL configuration at [/app/pythonpath/superset_config.py]
2024-12-13 09:12:36,174:ERROR:superset.app:Failed to create app
Traceback (most recent call last):
File "/app/superset/app.py", line 40, in create_app
app_initializer.init_app()
File "/app/superset/initialization/init.py", line 476, in init_app
self.setup_db()
File "/app/superset/initialization/init.py", line 667, in setup_db
pessimistic_connection_handling(db.engine)
File "/usr/local/lib/python3.10/site-packages/flask_sqlalchemy/init.py", line 998, in engine
return self.get_engine()
File "/usr/local/lib/python3.10/site-packages/flask_sqlalchemy/init.py", line 1017, in get_engine
return connector.get_engine()
File "/usr/local/lib/python3.10/site-packages/flask_sqlalchemy/init.py", line 594, in get_engine
self._engine = rv = self._sa.create_engine(sa_url, options)
File "/usr/local/lib/python3.10/site-packages/flask_sqlalchemy/init.py", line 1027, in create_engine
return sqlalchemy.create_engine(sa_url, **engine_opts)
File "", line 2, in create_engine
File "/usr/local/lib/python3.10/site-packages/sqlalchemy/util/deprecations.py", line 375, in warned
return fn(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/create.py", line 544, in create_engine
dbapi = dialect_cls.dbapi(**dbapi_args)
File "/usr/local/lib/python3.10/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 811, in dbapi
import psycopg2
ModuleNotFoundError: No module named 'psycopg2'
Traceback (most recent call last):
File "/usr/local/bin/superset", line 8, in
sys.exit(superset())
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1685, in invoke
super().invoke(ctx)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/flask/cli.py", line 355, in decorator
app = __ctx.ensure_object(ScriptInfo).load_app()
File "/usr/local/lib/python3.10/site-packages/flask/cli.py", line 309, in load_app
app = locate_app(import_name, name)
File "/usr/local/lib/python3.10/site-packages/flask/cli.py", line 238, in locate_app
return find_app_by_string(module, app_name)
File "/usr/local/lib/python3.10/site-packages/flask/cli.py", line 166, in find_app_by_string
app = attr(*args, **kwargs)
File "/app/superset/app.py", line 40, in create_app
app_initializer.init_app()
File "/app/superset/initialization/init.py", line 476, in init_app
self.setup_db()
File "/app/superset/initialization/init.py", line 667, in setup_db
pessimistic_connection_handling(db.engine)
File "/usr/local/lib/python3.10/site-packages/flask_sqlalchemy/init.py", line 998, in engine
return self.get_engine()
File "/usr/local/lib/python3.10/site-packages/flask_sqlalchemy/init.py", line 1017, in get_engine
return connector.get_engine()
File "/usr/local/lib/python3.10/site-packages/flask_sqlalchemy/init.py", line 594, in get_engine
self._engine = rv = self._sa.create_engine(sa_url, options)
File "/usr/local/lib/python3.10/site-packages/flask_sqlalchemy/init.py", line 1027, in create_engine
return sqlalchemy.create_engine(sa_url, **engine_opts)
File "", line 2, in create_engine
File "/usr/local/lib/python3.10/site-packages/sqlalchemy/util/deprecations.py", line 375, in warned
return fn(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/create.py", line 544, in create_engine
dbapi = dialect_cls.dbapi(**dbapi_args)
File "/usr/local/lib/python3.10/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 811, in dbapi
import psycopg2
ModuleNotFoundError: No module named 'psycopg2'

@dosu

[dosubot[bot]]

The error message indicates that the psycopg2 package is not installed because the build process failed due to missing system dependencies, specifically the gcc compiler. To resolve this, you can either:

1. Install psycopg2-binary: This package is a pre-compiled version of psycopg2 that doesn't require building from source, thus avoiding the need for gcc and other build dependencies. You can modify your Helm chart's bootstrap script to install psycopg2-binary instead:

   bootstrapScript: |
     #!/bin/bash
     pip install psycopg2-binary==2.9.6 \
       sqlalchemy-bigquery==1.6.1 \
       elasticsearch-dbapi==0.2.5 &&\
     if [ ! -f ~/bootstrap ]; then echo "Running Superset with uid {{ .Values.runAsUser }}" > ~/bootstrap; fi

2. Install System Dependencies: If you prefer to use psycopg2, ensure that all necessary system packages are installed in your environment. This typically includes gcc, libpq-dev, and python3-dev. You can add these installations to your Dockerfile or Kubernetes setup script.

Switching to psycopg2-binary is often the simpler solution in containerized environments like Kubernetes, as it avoids the need for additional system dependencies.

To continue talking to Dosu, mention @dosu.

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[devysh1907]

@dobu
No module named 'MySQLdb',
also not able to see any mySQL option while adding databse connection

[lsikora1]

You'll need to modify your values.yaml file to install the required dependencies.

Add this to your values.yaml:

bootstrapScript: |
  #!/bin/bash
  
  # Install system-level dependencies
  apt-get update && apt-get install -y \
    python3-dev \
    default-libmysqlclient-dev \
    build-essential \
    pkg-config

  # Install required Python packages
  pip install \
    authlib \
    psycopg2-binary \
    mysqlclient \

  # Create bootstrap file if it doesn't exist
  if [ ! -f ~/bootstrap ]; then
    echo "Running Superset with uid {{ .Values.runAsUser }}" > ~/bootstrap
  fi