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#398 in Rust patterns

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Aorist

Aorist is a code-generation tool for MLOps. Its aim is to generate legible code for common repetitive tasks in data science, such as data replication, common transformations, as well as machine learning operations.

Table of contents

Installation instructions

Go to aorist.scie.nz for installation instructions and a tutorial. You can find the developer guide below.

Developer Guide

Package organization

Aorist has a Rust core and a Python interface. The project relies on the following sub-projects:

  • aorist_util -- a Rust crate containing small utility functions used across the project.
  • aorist_derive -- Rust crate exporting derive macros (and only those macros) used across the project.
  • aorist_primitives -- Rust crate exporting "primitive" macros (such as register_constraint, define_attribute, etc.) used to abstract away boiler-plate code inside the Rust code base.
  • aorist_concept -- a Rust crate dedicated to the aorist macro. This macro "decorates" structs and enums to make them "constrainable" in the aorist sense.
  • aorist_ast -- a Rust crate implementing a cross-language Abstract Syntax Tree (AST), used for generating code in both Python and R. Aorist AST nodes get compiled into native Python or R AST nodes. More languages can be supported here.
  • aorist_attributes -- this Rust crate exports a taxonomy of data attributes (e.g. KeyStringIdentifier, POSIXTimestamp), which can be used to impose data quality and compliance constraints across table schemas.
  • aorist_core -- This is the core Rust crate for the Aorist project. The main object taxonomy is defined here. New structs and enums can be added here.
  • aorist_constraint -- This Rust crate lists constraints that can be applied to Aorist universes made up of concepts as listed in aorist_core. Multiple aorist_constraint crates can be compiled against the aorist_core crate.
  • aorist -- This Rust crate exports a Python library via a PyO3 binding. This directory also contains the conda recipe used for creating the aorist conda package (which includes the compiled Rust library, as well as a number of Python helpers).
  • aorist_recipes -- This Python package contains recipes (using Python, TrinoSQL, R, or Bash) that can be used to satisfy constraints as defined in aorist_constraint. Multiple aorist_recipes packages can be provided at runtime.
  • scienz -- This Python package contains a set of pre-defined datasets which can be used out-of-the box with the aorist package.

How to build

Because Aorist is a mixed Rust / Python project, building involves two stages:

  • first a set of Rust libraries is built via cargo.
  • then, a Python library is built bia conda.

Rust library

Pre-requisites

You will need to install Rust in order to compile Aorist.

Building

You can build individual Rust libraries directly by running cargo build from within the respective directory listed in the Package Organization section.

To build the entire project run cargo build from the root directory.

Conda library

Pre-requisites

  1. Install Anaconda.

  2. Make sure you use conda-forge, rather than the default conda channel.

conda config --add channels conda-forge
conda config --set channel_priority strict
  1. Create a new environment w/ mamba
conda create -n aorist-build -c conda-forge mamba
conda activate aorist-build
  1. Install boa:
mamba install "conda-build>=3.20" colorama \
    pip ruamel ruamel.yaml rich mamba jsonschema -c conda-forge
cd ~ && git clone git@github.com:mamba-org/boa.git
cd boa ~ && pip install -e .

Building

Build the packages by running:

cd ~/aorist
cd aorist && conda mambabuild . && cd .. 
anaconda upload [ARTIFACT] --label dev
conda search --override -c scienz/label/dev aorist

mamba install aorist dill astor -c conda-forge -c scienz/label/dev

cd aorist_recipes && conda mambabuild . && cd .. 

cd scienz && conda mambabuild . && cd ..

Adding new datasets

You can add new canonical datasets to the scienz package. Once accepted for publication metadata associated with these datasets can be distributed painlessly. To do so, please follow the steps described below:

  1. specify your datasets in a new Python file in the scienz/scienz directory. (You can look at other files in that directory for examples)
  2. make sure to import the datasets in scienz/__init__.py.
  3. Run conda build . from within the scienz subdirectory. The build step will also trigger a test, which ensures that your dataset is correctly specified.
  4. If conda build . succeeds, submit a Pull Request against scienz/aorist.
  5. Once the PR is accepted, the scienz package will be rebuilt and your dataset will be accessible via Anaconda.

How to test

Run the following commands:

pip install astor black dill

Inside aorist:

python build_for_testing.py

Inside aorist/scienz:

PYTHONPATH=$PYTHONPATH:../aorist_recipes:../scienz:../aorist python run_test.py

If no error messages appear, your new dataset has been successfully added.

Overview of an Aorist universe

(note that the code examples below are provided for illustrative purposes and may have occasional bugs)

Let's say we are starting a new project which involves analyzing a number of large graph datasets, such as the ones provided by the SNAP project.

We will conduct our analysis in a mini data-lake, such as the Trino + MinIO solution specified by Walden.

We would like to replicate all these graphs into our data lake before we can start analyzing them. At a very high-level, this is achieved by defining a "universe", the totality of things we care about in our project. One such universe is specified below:

from snap import snap_dataset
from aorist import (
    dag,
    Universe,
    ComplianceConfig,
    HiveTableStorage,
    MinioLocation,
    StaticHiveTableLayout,
    ORCEncoding,
)
from common import DEFAULT_USERS, DEFAULT_GROUPS, DEFAULT_ENDPOINTS

universe = Universe(
    name="my_cluster",
    datasets=[
        snap_dataset,
    ],
    endpoints=DEFAULT_ENDPOINTS,
    users=DEFAULT_USERS,
    groups=DEFAULT_GROUPS,
    compliance=ComplianceConfig(
        description="""
        Testing workflow for data replication of SNAP data to
        local cluster. The SNAP dataset collection is provided
        as open data by Stanford University. The collection contains
        various social and technological network graphs, with
        reasonable and systematic efforts having been made to ensure
        the removal of all Personally Identifiable Information.
        """,
        data_about_human_subjects=True,
        contains_personally_identifiable_information=False,
    ),
)

The universe definition contains a number of things:

  • the datasets we are talking about (more about it in a bit),
  • the endpoints we have available (e.g. the fact that a MinIO server is available for storage, as opposed to HDFS or S3, etc., and where that server is available; what endpoint we should use for Presto / Trino, etc.)
  • who the users and groups are that will access the dataset,
  • some compliance annotations.

Note: Currently users, groups, and compliance annotations are supported as a proof of concept -- these concepts are not essential to an introduction so we will skip them for now.

Generating a DAG

To generate a flow that replicates our data all we have to do is run:

DIALECT = "python"
out = dag(
  universe, [
    "AllAssetsComputed",
  ], DIALECT
)

This will generate a set of Python tasks, which will do the following, for each asset (i.e., each graph) in our dataset:

  • download it from its remote location,
  • decompress it, if necessary
  • remove its header,
  • convert the file to a CSV, if necessary
  • upload the CSV data to MinIO
  • create a Hive table backing the MinIO location
  • convert the CSV-based Hive table to an ORC-based Hive table
  • drop the temporary CSV-based Hive table

This set of tasks is also known as a Directed Acyclic Graph (DAG). The same DAG can be generated as a Jupyter notebook, e.g. by setting:

DIALECT = "jupyter"

Or we can set DIALECT to "airflow" for an Airflow DAG.

Aside: what is actually going on?

What Aorist does is quite complex -- the following is an explanation of the conceptual details, but you can skip this if you'd want something a bit more concrete:

  • first, you describe the universe. This universe is actually a highly-structured hierarchy of concepts, each of which can be "constrained".
  • A constraint is something that "needs to happen". In this example all you declare that needs to happen is the constraint AllAssetsComputed. This constraint is attached to the Universe, which is a singleton object.
  • Constraints attach to specific kinds of objects -- some attach to the entire Universe, others attach to tables, etc.
  • Constraints are considered to be satisfied when their dependent constraints are satisfied. When we populate each constraint's own dependent constraints we follow a set of complex mapping rules that are nonetheless fairly intuitive (but difficult to express without a longer discussion, see the end of this document for that)
  • Programs ("recipes") are attached to this constraint graph by a Driver. The Driver decides which languages are prefered (e.g. maybe the Driver likes Bash scrips more than Presto, etc.). The driver will complain if it can't provide a solution for a particular constraint.
  • Once the recipes are attached, various minutiae are extracted from the concept hierarchy -- e.g., which endpoints to hit, actual schemas of input datasets, etc.
  • Once the various minutiae are filled in, we have a graph of Python code snippets. If these snippets are repetitive (e.g. 100 instances of the same function call but with different arguments) we compress them into for loops over parameter dictionarie.
  • We then take the compressed snippet-graph and further optimize it, for instance by pushing repeated parameters out of parameter dictionaries and into the main body of the for loop.
  • We also compute unique, maximally-descriptive names for the tasks, a combination of the constraint name and the concept's position in the hierarchy. (e.g. wine_table_has_replicated_schema). These names are shortened as much as possible while still being unique (e.g., we may shorten things to wine_schema, a less mouthful of a task name).
  • The driver then adds scaffolding for native Python, Airflow or Jupyter code generation. Other output formats (e.g. Prefect, Dagster, Makefiles, etc.) will be supported in the future.
  • Finally, the driver converts the generated Python AST to a concrete string, which it then formats as a pretty (PEP8-compliant) Python program via Python black.

Describing a dataset

Before we can turn our attention to what we would like to achieve with our data, we need to determine what the data is, to begin with. We do so via a dataset manifest, which is created using Python code.

Here's an example of how we'd create such a manifest for a canonical ML dataset (the Wine dataset, as per example/wine.py).

First, we define our attribute list:

attributes = [
    Categorical("wine_class_identifier"),
    PositiveFloat("alcohol"),
    PositiveFloat("malic_acid"),
    PositiveFloat("ash"),
    PositiveFloat("alcalinity_of_ash"),
    PositiveFloat("magnesium"),
    PositiveFloat("total_phenols"),
    PositiveFloat("non_flavanoid_phenols"),
    PositiveFloat("proanthocyanins"),
    PositiveFloat("color_intensity"),
    PositiveFloat("hue"),
    PositiveFloat("od_280__od_315_diluted_wines"),
    PositiveFloat("proline"),
]

Then, we express the fact that a row corresponds to a struct with the fields defined in the attributes list:

wine_datum = RowStruct(
    name="wine_datum",
    attributes=attributes,
)

Then, we declare that our data can be found somewhere on the Web, in the remote storage. Note that we also record the data being CSV-encoded, and the location corresponding to a single file. This is where we could note compression algorithms, headers, etc.:

remote = RemoteStorage(
    location=RemoteLocation(WebLocation(
        address=("https://archive.ics.uci.edu/ml/"
                 "machine-learning-databases/wine/wine.data"),
    )),
    layout=Layout(SingleFileLayout()),
    encoding=Encoding(CSVEncoding()),
)

We need this data to live locally, in a Hive table in ORC format, backed by a MinIO location with the prefix wine:

local = HiveTableStorage(
    location=Location(MinioLocation(name="wine")),
    layout=Layout(StaticHiveTableLayout()),
    encoding=Encoding(ORCEncoding()),
)

Note a few things:

  • we don't specify the table name, as this is automatically-generated from the asset name (we will define that momentarily)
  • we declare, "this thing needs to be stored in MinIO", but do not concern ourselves with endpoints at this moment. Aorist will find the right endpoints for us and fill in secrets, etc. Or if MinIO is unavailable it will fail.
  • this is also where we can indicate whether our table is static (i.e. there is no time dimension, or dynamic).

We are now ready to define our asset, called wine_table:

wine_table = StaticDataTable(
    name="wine_table",
    schema=default_tabular_schema(wine_datum),
    setup=StorageSetup(RemoteImportStorageSetup(
        tmp_dir="/tmp/wine",
        remote=remote,
        local=[local],
    )),
    tag="wine",
)

Here's what we do here:

  • we define an asset called wine_table. This is also going to be the name of any Hive table that will be created to back this asset (or file, or directory, etc., depending on the dataset storage).
  • we also define a schema. A schema tells us exactly how we can turn a row into a template. For instance, we need the exact order of columns in a row to know unambiguously how to convert it into a struct.
  • default_tabular_schema is a helper function that allows us to derive a schema where columnns in the table are in exactly the same order as fields in the struct.
  • the setup field introduces the notion of a "replicated" remote storage, via RemoteImportStorageSetup. The idea expressed here is that we should make sure the data available at the remote location is replicated exactly in the local locations (either by copying it over, or, if already availalbe, by checking that the remote and target data has the same checksum, etc.)
  • we also use a tag field to help generate legible task names and IDs (e.g., in Airflow)

Finally, let's define our dataset:

wine_dataset = DataSet(
    name="wine",
    description="A DataSet about wine",
    sourcePath=__file__,
    datumTemplates=[DatumTemplate(wine_datum)],
    assets={"wine_table": Asset(wine_table)},
)

This dataset can then be imported into the universe discussed previously.

Aside: The asset / template split

An Aorist dataset is meant to be a collection of two things:

  • data assets -- concrete information, stored in one or multiple locations, remotely, on-premise, or in some sort of hybrid arrangement.
  • datum templates -- information about what an instance of our data (i.e., a datum) represents.

For instance, a table is a data asset. It has rows and columns, and those rows and columns are filled with some values that can be read from some location.

What those rows and columns mean depends on the template. Oftentimes rows in tables translate to structs, for instance in a typical dim_customers table. But if we're talking about graph data, then a row in our table represents a tuple (more specifically a pair), and not a struct.

Other examples of data assets would be:

  • directories with image files,
  • concrete machine learning models,
  • aggregations,
  • scatterplots,

Other examples of data templates could be:

  • a tensor data template corresponding to RGB images,
  • an ML model template that takes a certain set of features (e.g. number of rooms and surface of a house, and produces a prediction, e.g. a valuation),
  • a histogram data template, expressing the meaning of margin columns used for aggregations, as well as the aggregation function (a count for a histogram)
  • a scatterplot template, encoding the meaning of the x and y axis, etc.

This conceptual differentiation allows us to use the same template to refer to multiple assets. For instance, we may have multiple tables with exactly the same schema, some being huge tables with real data, and others being downsampled tables used for development. These tables should be refered to using the same template.

This is also very useful in terms of tracking data lineage, on two levels: semantically (how does template Y follow from template X?) and concretely (how does row A in table T1 follow from row B in table T2?).

Back to the SNAP dataset

The SNAP dataset we discussed initially is a bit different from the simple Wine dataset. For one, it contains many assets -- this is a collection of different graphs used for Machine Learning applications -- each graph is its own asset. But the meaning of a row remains the same: it's a 2-tuple made up of identifiers. We record this by defining the template:

edge_tuple = IdentifierTuple(
    name="edge",
    attributes=[
        NumericIdentifier("from_id"),
        NumericIdentifier("to_id"),
    ],
)

Then we define an asset for each of 12 datasets. Note that the names come from the URL patterns corresponding to each dataset. We need to replace dashes with underscores when creating asset names however (Hive tables don't like dashes in their names):

names = [
    "ca-AstroPh", "ca-CondMat", "ca-GrQc", "ca-HepPh",
    "ca-HepTh", "web-BerkStan", "web-Google", "web-NotreDame",
    "web-Stanford", "amazon0302", "amazon0312", "amazon0505",
]
tables = {}
for name in names:

    name_underscore = name.replace("-", "_").lower()
    remote = Storage(RemoteStorage(
        location=Location(WebLocation(
            address="https://snap.stanford.edu/data/%s.txt.gz" % name,
        )),
        layout=Layout(SingleFileLayout()),
        encoding=Encoding(TSVEncoding(
            compression=Compression(GzipCompression()),
            header=FileHeader(UpperSnakeCaseCSVHeader(num_lines=4)),
        )),
    ))
    local = Storage(HiveTableStorage(
        location=Location(MinioLocation(name=name_underscore)),
        layout=Layout(StaticHiveTableLayout()),
        encoding=Encoding(ORCEncoding()),
    ))
    table = StaticDataTable(
        name=name_underscore,
        schema=default_tabular_schema(edge_tuple),
        setup=StorageSetup(RemoteImportStorageSetup(
            tmp_dir="/tmp/%s" % name_underscore,
            remote=remote,
            local=[local],
        )),
        tag=name_underscore,
    )
    tables[name] = table

snap_dataset = DataSet(
    name="snap",
    description="The Snap DataSet",
    sourcePath=__file__,
    datumTemplates=[edge_tuple],
    assets=tables,
    tag="snap",
)

What if we want to do Machine Learning?

As a proof-of-concept, ML models are not substantively different from tabular-based data assets. Here's an example for how we can declare the existence of an SVM regression model trained on the wine table:

# We will train a classifier and store it in a local file.
classifier_storage = Storage(LocalFileStorage(
    location=Location(MinioLocation(name="wine")),
    layout=Layout(SingleFileLayout()),
    encoding=Encoding(ONNXEncoding()),
))
# We will use these as the features in our classifier.
features = attributes[2:10]
# This is the "recipe" for our classifier.
classifier_template = TrainedFloatMeasure(
    name="predicted_alcohol",
    comment="""
    Predicted alcohol content, based on the following inputs:
    %s
    """ % [x.name for x in features],
    features=features,
    objective=attributes[1],
    source_asset_name="wine_table",
)
# We now augment the dataset with this recipe.
wine_dataset.add_template(classifier_template)
# The classifier is computed from local data
# (note the source_asset_names dictionary)
classifier_setup = ComputedFromLocalData(
    source_asset_names={"training_dataset": "wine_table"},
    target=classifier_storage,
    tmp_dir="/tmp/wine_classifier",
)
# We finally define our regression_model as a concrete
# data asset, following a recipe defined by the template,
# while also connected to concrete storage, as defined
# by classifier_setup
regression_model = SupervisedModel(
    name="wine_alcohol_predictor",
    tag="predictor",
    setup=classifier_setup,
    schema=classifier_template.get_model_storage_tabular_schema(),
    algorithm=Algorithm(SVMRegressionAlgorithm()),
)
wine_dataset.add_asset(regression_model)

Note the use of imperative directives such as wine_dataset.add_asset. This is a small compromise on our mostly-declarative syntax, but it maps well on the following thought pattern common to ML models:

  • we have some "primary sources", datasets external to the project,
  • we then derive other data assets by building, iteratively on the primary sources.

The common development cycle, therefore, is one where, after the original data sources are imported, we add new templates and assets to our dataset, fine-tuning Python code by first running it in Jupyter, then in Native python, then as an Airflow task, etc.

Also note that while currently Aorist only supports generating single files as DAGs, in the future we expect it will support multiple file generation for complex projects.

Dependencies

~4.5–6.5MB
~120K SLoC