simeon 0.0.26
A CLI tool to help process research data from edX
License: MIT License
Requires Python: >=3.6
Keywords: research, edx, MOOC, education, online-learning

simeon
~~~~~~

``simeon`` is a CLI tool to help with the processing of edx Research
data. It can ``list``, ``download``, and ``split`` edX data packages. It
can also ``push`` the output of the ``split`` subcommand to both GCS and
BigQuery. It is heavily inspired by the
`edx2bigquery <https://github.com/mitodl/edx2bigquery>`__ package. If
you’ve used that tool, you should be able to navigate the quirks that
may come with this one.

Installing from pypi
~~~~~~~~~~~~~~~~~~~~

.. code:: sh

   python3 -m pip install simeon
   # Or with geoip
   python3 -m pip install simeon[geoip]
   # Then invoke the CLI tool with
   simeon --help

Installing with git clone and pip
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: sh

   git clone git@github.com:MIT-IR/simeon.git
   cd simeon && python3 -m venv venv && source venv/bin/activate && python -m pip install .
   # Or with geoip
   cd simeon && python3 -m venv venv && source venv/bin/activate &&  python -m pip install .[geoip]
   # Then invoke the CLI tool with
   simeon --help

Using Docker
~~~~~~~~~~~~

.. code:: sh

   docker run --rm -it mitir/simeon:latest
   simeon --help

Developing
~~~~~~~~~~

.. code:: sh

   git clone git@github.com:MIT-IR/simeon.git
   cd simeon
   # Set up a virtual environment if you don't already have on
   python3 -m venv venv
   source venv/bin/activate
   # pip install the package in an editable way
   python3 -m pip install -e .[test,geoip]
   # Invoke the executable
   simeon --help
   # Run the tests
   tox
   # Write code and tests and submit PR's

Setups and configurations
~~~~~~~~~~~~~~~~~~~~~~~~~

``simeon`` is a glorified downloader and uploader set of scripts. Much
of the downloading and uploading that it does make the assumptions that
you have your AWS credentials configured properly and that you’ve got a
service account file for GCP services available on your machine. If the
latter is missing, you may have to authenticate to GCP services through
the SDK. However, both we and Google recommend you not do that.

Every downloaded file is decrypted either during the download process or
while it gets split by the ``simeon split`` command. So, this tool
assumes that you’ve installed and configured ``gpg`` to be able to
decrypt files from edX.

The following steps may be useful to someone just getting started with
the edX data package:

1. Credentials from edX

   -  Reach out to edX to get your data czar credentials
   -  Configure both AWS and gpg, so your credentials can access the S3
      buckets and your ``gpg`` key can decrypt the files there

2. Setup a GCP project

   -  Create a GCP project
   -  Set up a BigQuery workspace
   -  Create a GCS bucket
   -  Create a service account and download the associated file
   -  Give the service account Admin Role access to both the BigQuery
      project and the GCS bucket

If the above steps are carried out successfully, then you should be able
to use ``simeon`` without any issues.

However, if you’ve taken care of the above steps but are still unable to
get ``simeon`` to work, please open an issue.

Further, ``simeon`` can parse INI formatted configuration files. It, by
default, looks for files in the user’s home directory, or in the current
working directory of the running process. The base names that are
targeted when config files are looked up are: ``simeon.cfg`` or
``.simeon.cfg`` or ``simeon.ini`` or ``.simeon.ini``. You can also
provide ``simeon`` with a config file by using the global option
``--config-file`` or ``-C`` and giving it a path to the file with the
corresponding configurations.

The following is a sample file content:

.. code:: sh

   # Default section for things like the organization whose data package is processed
   # You can also set a default site as one of the following: edx, edge, patches
   [DEFAULT]
   site = edx
   org = yourorganizationx
   clistings_file = /path/to/file/with/course_ids

   # Section related to Google Cloud (project, bucket, service account)
   [GCP]
   project = your-gcp-project-id
   bucket = your-gcs-bucket
   service_account_file = /path/to/a/service_account_file.json
   wait_for_loads = True
   geo_table = your-gcp-project.geocode_latest.geoip
   youtube_table = your-gcp-project.videos.youtube
   youtube_token = your-YouTube-API-token

   # Section related to the AWS credentials needed to download data from S3
   [AWS]
   aws_cred_file = ~/.aws/credentials
   profile_name = default

The options in the config file(s) should match the optional arguments of
the CLI tool. For instance, the ``--service-account-file``,
``--project`` and ``--bucket`` options can be provided under the ``GCP``
section of the config file as ``service_account_file``, ``project`` and
``bucket``, respectively. Similarly, the ``--site`` and ``--org``
options can be provided under the ``DEFAULT`` section as ``site`` and
``org``, respectively.

List files
~~~~~~~~~~

``simeon`` can list files on S3 for your organization based on criteria
like file type (``sql`` or ``log`` or ``email``), time intervals (begin
and end dates), and site (``edx`` or ``edge`` or ``patches``).

-  Example: List the latest data packages for file types ``sql``,
   ``email``, and ``log``

   .. code:: sh

      # List the latest SQL bundle
      simeon list -s edx -o mitx -f sql -L
      # List the latest email data dump
      simeon list -s edx -o mitx -f email -L
      # List the latest tracking log file
      simeon list -s edx -o mitx -f log -L

Download and split files
~~~~~~~~~~~~~~~~~~~~~~~~

``simeon`` can download, decrypt and split up files into folders
belonging to specific courses.

-  Example 1: Download, split and push SQL bundles to both GCS and
   BigQuery

   .. code:: sh

      # Download the latest SQL bundle
      simeon download -s edx -o mitx -f sql -L -d data/

      # Download SQL bundles dumped any time since 2021-01-01 and
      # extract the contents for course ID MITx/12.3x/1T2021.
      # Place the downloaded files in data/ and the output of the split operation
      # in data/SQL
      simeon download -s edx -o mitx -c "MITx/12.3x/1T2021" -f sql \
          -b 2021-01-01 -d data -S -D data/SQL/

      # Push to GCS the split up SQL files inside data/SQL/MITx__12_3x__1T2021
      simeon push gcs -f sql -p ${GCP_PROJECT_ID} -b ${GCS_BUCKET} \
          -S ${SAFILE} data/SQL/MITx__12_3x__1T2021

      # Push the files to BigQuery and wait for the jobs to finish
      # Using -s or --use-storage tells BigQuery to extract the files
      # to be loaded from Google Cloud Storage.
      # So, use the option when you've already called simeon push gcs
      simeon push bq -w -s -f sql -p ${GCP_PROJECT_ID} -b ${GCS_BUCKET} \
          -S ${SAFILE} data/SQL/MITx__12_3x__1T2021

-  Example 2: Download, split and push tracking logs to both GCS and
   BigQuery

   .. code:: sh

      # Download the latest tracking log file
      simeon download -s edx -o mitx -f log -L -d data/

      # Download tracking logs dumped any time since 2021-01-01
      # and extract the contents for course ID MITx/12.3x/1T2021
      # Place the downloaded files in data/ and the output of the split operation
      # in data/TRACKING_LOGS
      simeon download -s edx -o mitx -c "MITx/12.3x/1T2021" -f log \
          -b 2021-01-01 -d data -S -D data/TRACKING_LOGS/

      # Push to GCS the split up tracking log files inside
      # data/TRACKING_LOGS/MITx__12_3x__1T2021
      simeon push gcs -f log -p ${GCP_PROJECT_ID} -b ${GCS_BUCKET} \
          -S ${SAFILE} data/TRACKING_LOGS/MITx__12_3x__1T2021

      # Push the files to BigQuery and wait for the jobs to finish
      # Using -s or --use-storage tells BigQuery to extract the files
      # to be loaded from Google Cloud Storage.
      # So, use the option when you've already called simeon push gcs
      simeon push bq -w -s -f log -p ${GCP_PROJECT_ID} -b ${GCS_BUCKET} \
          -S ${SAFILE} data/TRACKING_LOGS/MITx__12_3x__1T2021

-  If you already have downloaded SQL bundles or tracking log files, you
   can use ``simeon split`` them up.

Make secondary/aggregated tables
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

``simeon`` can generate secondary tables based on already loaded data.
Call ``simeon report --help`` for the expected positional and optional
arguments.

-  Example: Make ``person_course`` for course ID ``MITx/12.3x/1T2021``

   .. code:: sh

      # Make a person course table for course ID MITx/12.3x/1T2021
      # Provide the -g option to give a geolocation BigQuery table
      # to fill the ip-to-location details in the generated person course table
      COURSE=MITx/12.3x/1T2021
      simeon report -w -g "${GCP_PROJECT_ID}.geocode.geoip" -t "person_course" \
          -p ${GCP_PROJECT_ID} -S ${SAFILE} ${COURSE}

Notes:
~~~~~~

1. Please note that SQL bundles are quite large when split up, so
   consider using the ``-c`` or ``--courses`` option when invoking
   ``simeon download -S`` or ``simeon split`` to make sure that you
   limit the splitting to a set of course IDs. You may also use the
   ``--clistings-file`` option, which expects a txt file of course IDs;
   one ID per line. If the aforementioned options are not used,
   ``simeon`` may end up failing to complete the split operation due to
   exhausted system resources (storage to be specific).

2. ``simeon download`` with file types ``log`` and ``email`` will both
   download and decrypt the files matching the given criteria. If the
   latter operations are successful, then the encrypted files are
   deleted by default. This is to make sure that you don’t exhaust
   storage resources. If you wish to keep those files, you can always
   use the ``--keep-encrypted`` option that comes with
   ``simeon download`` and ``simeon split``. SQL bundles are only
   downloaded (not decrypted). Their decryption is done during a
   ``split`` operation.

3. Unless there is an unhandled exception (which should be reported as a
   bug), ``simeon`` should, by default, print to the standard output
   both information and errors encountered while processing your files.
   You can capture those logs in a file by using the global option
   ``--log-file`` and providing a destination file for the logs.

4. When using multi argument options like ``--tables`` or ``--courses``,
   you should try not to place them right before the expected positional
   arguments. This will help the CLI parser not confuse your positional
   arguments with table names (in the case of ``--tables``) or course
   IDs (when ``--courses`` is used).

5. Splitting tracking logs is a resource intensive process. The routine
   that splits the logs generates a file for each course ID encountered.
   If you happen to have more course IDs in your logs than the running
   process can open operating system file descriptors, then ``simeon``
   will put away records it can’t save to disk for a second pass.
   Putting away the records involves using more memory than normally
   required. The second pass will only require one file descriptor at a
   time, so it should be safe in terms of file descriptor limits. To
   help ``simeon`` not have to do a second pass, you may increase the
   file descriptor limits of processes from your shell by running
   something like ``ulimit -n 2000`` before calling ``simeon split`` on
   Unix machines. For Windows users, you may have to dig into the
   Windows Registries for a corresponding setting. This should tell your
   OS kernel to allow OS processes to open up to 2000 file handles.

6. Care must be taken when using ``simeon split`` and ``simeon push`` to
   make sure that the number of positional arguments passed does not
   lead to the invoked command exceeding the maximum command-line length
   allowed for arguments in a command. To avoid errors along those
   lines, please consider passing the positional arguments as UNIX glob
   patterns. For instance,
   ``simeon split --file-type log 'data/TRACKING-LOGS/*/*.log.gz'``
   tells ``simeon`` to expand the given glob pattern, instead of relying
   on the shell to do it.

7. The ``report`` subcommand relies on the presence of SQL query files
   to parse and send to BigQuery to execute. Any errors arising from
   executing the parsed queries will be shown to the end user through
   the given log stream. While the ``simeon`` tool ships with query
   files for most secondary/reporting tables that are based on the
   ``edx2bigquery`` tool, an end user should be able to point ``simeon``
   to a different location with SQL query files by using the
   ``--query-dir`` option that comes with ``simeon report``.
   Additionally, these query files can contain `jinja2
   templated <https://jinja.palletsprojects.com/en/latest/>`__ SQL code.
   Any mentioned variables within these templated queries can be passed
   to ``simeon report`` by using the ``--extra-args`` option and passing
   key-value pair items in the format
   ``var1=value1,var2=value2,var3=value3,...,var_n=value_n``. Further,
   these key-value pair items can also be typed by using the format
   ``var1:i=value1,var2:s=value2,var3:f=value3,...,var_n:s=value_n``. In
   this format, the type is appended to the key, separated by a colon.
   The only supported scalar types, so far, are ``s`` for ``str``, ``i``
   for ``int``, and ``f`` for ``float``. If any conversion errors occur
   during value parsing, then those are shown to the end user, and the
   query won’t get executed. Finally, if you wish to pass an ``array``
   or ``list`` to the template, you will need to repeat a key multiple
   times. For instance, if you want to pass a list named ``mylist``
   containing the integers, you could write something like
   ``--extra-args mylist:i=1,mylist:i=2,mylist:i=3``. This means that
   you’ll have a python ``list`` named ``mylist`` within your template,
   and it should contain ``[1, 2, 3]``. You can also pass a JSON file
   whose top-level objects are parsed as variables. Use a leading ``@``
   when passing a JSON file.