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-# Using PDB to Troubleshoot Python Code
-
-## Tags
-* type: documentation
-* keywords: debugging, python
-
-Historically, debugging GeneNetwork code has been a bit of a pain where you would have `print' and `logging' statements to help view offending code chunks.  This is not efficient, and we can do better!  One painful side-effect wrt logging worth mentioning is that our logs grow quite fast and we need to rotate them, atm manually:
-
-Here are examples of some logging that we do:
-
-```
-@app.route("/n/logout")
-def logout():
-    logger.debug("Logging out...")
-    UserSession().delete_session()
-    flash("You are now logged out. We hope you come back soon!")
-    response = make_response(redirect(url_for('index_page')))
-    # Delete the cookie
-    response.set_cookie(UserSession.user_cookie_name, '', expires=0)
-    return response
-```
-
-```
-@app.route("/tmp/<img_path>") def
-tmp_page(img_path): logger.info("In tmp_page")
-logger.info("img_path:", img_path)
-logger.info(request.url) initial_start_vars =
-request.form logger.info("initial_start_vars:",
-initial_start_vars) imgfile =
-open(GENERATED_IMAGE_DIR + img_path, 'rb') imgdata
-= imgfile.read() imgB64 =
-base64.b64encode(imgdata) bytesarray =
-array.array('B', imgB64) return
-render_template("show_image.html",
-img_base64=bytesarray)
-```
-
-Earlier this year, one of our members introduced us to pudb---a graphical based logging utility for Python.  I have gravitated away from this because it adds yet another dependency in our toolchain; in addition to it being ncurses-based, lacking guarantees in how it behaves in different terminals.  It also lacks support in different OS'es, thereby forcing end-users to SSH into one of our remote servers to troubleshoot.
-
-Python PDB ships with Python, and as such, works well in different setups. There are multiple ways of getting into a pdb session, the easiest being to set a `breakpoint()'. Assume we are trouble-shooting this function:
-
-```
-from typing import List
-
-
-def avg(numbers: List) -> int:
-    return sum(numbers)/len(numbers)
-
-
-print(avg([20, 21]))
-```
-
-This will fail for a list that contains non-integer value, say a list containing ["1", "2"]. The first step to troubleshoot, assuming we have no test would be to set a `breakpoint()' as such:
-
-```
-from typing import List
-
-
-def avg(numbers: List) -> int:
-    breakpoint()
-    return sum(numbers)/len(numbers)
-
-
-print(avg([20, "21"]))
-```
-
-Useful commands while you are in pdb that are useful:
-
-* "l ." --- show where you are in the context
-* "n" --- go to the next line
-* "s" --- step into a function
-* "c" --- continues execution until a breakpoint is encountered
-* "p" --- print a variable
-* "pp" --- pretty print a variable
-
-When we step into our debug session, we can view all the variables in a local scope using: "locals()"; and the global scope using: "globals()". With this information, we can quickly work out where our problem is by just inspecting the variables we have at hand.
-
-Another cool trick/pattern when debugging is to tell pdb to jump to where the error occured in a try/except block using `import pdb; pdb.post_mortem()' like so:
-
-```
-from typing import List
-
-
-def avg(numbers: List) -> int:
-    try:
-        return sum(numbers)/len(numbers)
-    except Exception:
-        import pdb; pdb.post_mortem()
-
-
-print(avg([20, "21"]))
-```
-
-With regards to testing, pdb is also integrated with test-runners. To use pdb with pytest, simply run:
-
-,----
-| pytest --pdb
-`----
-
-## Running Flask Applications Under pdb
-
-To troubleshoot a Flask application (and any other application running via an
-applicationsserver of sorts), you might need to start the application server under
-the debugger, otherwise, you will get an error like:
-
-```
-BdbQuit
-```
-
-Ideally, you shouldn't need to, as the terminal where you started the
-application server (Flask) should drop you into the debugger automatically.
-
-If you run the application under other application servers like gunicorn, then
-you might need to increase the timeout period to prevent gunicorn from killing
-the process, leading to the error above. Generally speaking, you **SHOULD NOT**
-be running the debugger in production anyway, and therefore you should not need
-to deal with the gunicorn issues.
-
-That said, you can start the Flask application under pdb with something like:
-
-```
-python3 -m pdb flask run [OPTIONAL-ARGUMENTS-TO-FLASK]
-```
-
-
-## Useful Tutorials
-
-To learn more about pdb, you can check out:
-
-=> https://www.youtube.com/watch?v=0LPuG825eAk python debugger crash course: pdb/breakpoint
-=> https://www.youtube.com/watch?v=s8Nx2frW4ps postmortem debugging in python