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AbdouSeck committed Dec 29, 2023
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4 changes: 4 additions & 0 deletions .buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 57dd3c8af315681fbc240f296de95650
tags: 645f666f9bcd5a90fca523b33c5a78b7
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63 changes: 63 additions & 0 deletions _sources/api_intro.rst.txt
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The python API of this tool is divided into the following sections:

- download: Handles the downloading of data files from s3. It matches up with the ``simeon download`` and ``simeon split`` commands

- upload: Handles the uploading of data to GCS and BigQuery. It matches up with the ``simeon push`` command

- report: Handles the generation of secondary tables in BigQuery. It matches up with the ``simeon report`` command


Components of the :class:`~simeon.download` package
----------------------------------------------------
AWS module
^^^^^^^^^^^
.. automodule:: simeon.download.aws
:members:

Email opt-in module
^^^^^^^^^^^^^^^^^^^^
.. automodule:: simeon.download.emails
:members:

Tracking logs module
^^^^^^^^^^^^^^^^^^^^^
.. automodule:: simeon.download.logs
:members:

SQL data files module
^^^^^^^^^^^^^^^^^^^^^^
.. automodule:: simeon.download.sqls
:members:

Utilities module for the download package
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. automodule:: simeon.download.utilities
:members:


Components of the :class:`~simeon.upload` package
----------------------------------------------------
GCP module
^^^^^^^^^^^^
.. automodule:: simeon.upload.gcp
:members:

Utilities module for the upload package
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. automodule:: simeon.upload.utilities
:members:


Components of the :class:`~simeon.report` package
-----------------------------------------------------
Utilities module for the report package
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. automodule:: simeon.report.utilities
:members:

Components of the :class:`~simeon.exceptions` package
-------------------------------------------------------
Exceptions module
^^^^^^^^^^^^^^^^^^
.. automodule:: simeon.exceptions
:members:
329 changes: 329 additions & 0 deletions _sources/cli_intro.rst.txt
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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.
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