feat: add duckdb as DataSource - Fixes #14563 #19317

rwhaling · 2022-03-22T21:18:47Z

SUMMARY

Adds Duckdb as an embedded, in-process OLAP db engine.
Duckdb can directly query CSV or Parquet files on disk - eventually, we should be able to query Parquet files directly on S3 as well.
Supersedes #19265
Relying on https://github.com/Mause/duckdb_engine for the SQLAlchemy implementation, and building on top of @alitrack's original work.
Since DuckDB is, much like SQLite, an in-process, single-threaded engine, the error handling in TestConnectionDatabaseCommand.run feels a bit weird. Might want to work with @Mause on a narrow exception class for the threading blip.

BEFORE/AFTER SCREENSHOTS OR ANIMATED GIF

TESTING INSTRUCTIONS

install duckdb_engine via pip install duckdb-engine
DuckDB appears in the add a database dropdown
Provide path to a duckdb database on disk in the url, e.g., duckdb:////Users/whoever/path/to/duck.db
in SQL lab, query any tables defined in your on-disk database, tables, schemas, and column defs all appear as normal
have not tested in-memory a ton but duckdb:///:memory: seems to work?
once you are in SQL Lab, you can directly query parquet or CSV files on disk: SELECT * from 'test.parquet' etc.

ADDITIONAL INFORMATION

Has associated issue: duckdb as DataSource #14563
Required feature flags:
Changes UI
Includes DB Migration (follow approval process in SIP-59)
- Migration is atomic, supports rollback & is backwards-compatible
- Confirm DB migration upgrade and downgrade tested
- Runtime estimates and downtime expectations provided
Introduces new feature or API
Removes existing feature or API

needs the forked version of [duckdb-engine](https://github.com/alitrack/duckdb_engine)

update _time_grain_expressions

codecov · 2022-03-22T23:19:24Z

Codecov Report

Merging #19317 (4aa477b) into master (d645579) will decrease coverage by 0.03%.
The diff coverage is 74.77%.

❗ Current head 4aa477b differs from pull request most recent head d1e16c4. Consider uploading reports for the commit d1e16c4 to get more accurate results

@@            Coverage Diff             @@
##           master   #19317      +/-   ##
==========================================
- Coverage   66.53%   66.50%   -0.04%     
==========================================
  Files        1667     1672       +5     
  Lines       64360    64564     +204     
  Branches     6493     6493              
==========================================
+ Hits        42824    42936     +112     
- Misses      19854    19946      +92     
  Partials     1682     1682

Flag	Coverage Δ
hive	`?`
mysql	`81.65% <88.63%> (+0.16%)`	⬆️
postgres	`81.69% <88.63%> (+0.16%)`	⬆️
presto	`?`
python	`81.78% <88.63%> (-0.18%)`	⬇️
sqlite	`81.46% <88.63%> (+0.16%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
...t-ui-chart-controls/src/operators/pivotOperator.ts	`100.00% <ø> (ø)`
...i-chart-controls/src/operators/resampleOperator.ts	`100.00% <ø> (ø)`
.../superset-ui-core/src/query/types/QueryFormData.ts	`100.00% <ø> (ø)`
...tend/packages/superset-ui-core/src/style/index.tsx	`100.00% <ø> (ø)`
...end/plugins/legacy-plugin-chart-chord/src/Chord.js	`0.00% <0.00%> (ø)`
...ns/legacy-plugin-chart-chord/src/transformProps.js	`0.00% <0.00%> (ø)`
.../legacy-plugin-chart-country-map/src/CountryMap.js	`0.00% <0.00%> (ø)`
...acy-plugin-chart-country-map/src/transformProps.js	`0.00% <0.00%> (ø)`
...ns/legacy-plugin-chart-histogram/src/Histogram.jsx	`0.00% <0.00%> (ø)`
...egacy-plugin-chart-histogram/src/transformProps.js	`0.00% <0.00%> (ø)`
... and 258 more

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zhaoyongjie

except for lint error, LGTM. BTW, I was impressed by DuckDB as a column base lite database.

villebro

LGTM - a few non-blocking style related comments

villebro · 2022-03-23T06:59:44Z

superset/databases/commands/test_connection.py

+                except RuntimeError:
+                    # Catches the equivalent single-threading error from duckdb.
+                    alive = engine.dialect.do_ping(conn)


nit: could we have these in the same except:

except (sqlite3.ProgrammingError, RuntimeError): # SQLite can't run on a separate thread, so ``func_timeout`` fails # RuntimeError catches the equivalent single-threading error from duckdb. alive = engine.dialect.do_ping(conn)

villebro · 2022-03-23T07:02:02Z

superset/db_engine_specs/duckdb.py

+
+    @classmethod
+    def get_table_names(
+        cls, database: "Database", inspector: Inspector, schema: Optional[str]


nit: if we add from __future__ import annotations in the beginning of the file, we can remove the quotes. See an example here:

superset/superset/common/query_context.py

Line 17 in b7ecb14

from __future__ import annotations

Suggested change

cls, database: "Database", inspector: Inspector, schema: Optional[str]

cls, database: Database, inspector: Inspector, schema: Optional[str]

rwhaling · 2022-03-23T13:19:13Z

Thanks for the review @villebro @zhaoyongjie - I'll incorporate your feedback and get the linter passing.

rwhaling · 2022-03-24T00:59:42Z

OK - I am about 90% confident that I am running the linter properly on my local and that all the tests will pass now - looks like I cannot trigger the CI myself, but I think if someone kicks that off we'll see the build go green.

zhaoyongjie · 2022-03-24T01:31:53Z

OK - I am about 90% confident that I am running the linter properly on my local and that all the tests will pass now - looks like I cannot trigger the CI myself, but I think if someone kicks that off we'll see the build go green.

@rwhaling, CI looks like waiting to finish other tasks. When the CI is all green, I will merge it. Thanks for the following up!

villebro · 2022-03-24T08:27:57Z

@rwhaling - One thing that I forgot while reviewing was if you would be able to open a PR that adds the relevant documentation for connecting to DuckDB? Something similar to the what this PR did for Trino (there's some unrelated changes, you can ignore those): #13171

rwhaling · 2022-03-24T11:58:41Z

@rwhaling - One thing that I forgot while reviewing was if you would be able to open a PR that adds the relevant documentation for connecting to DuckDB? Something similar to the what this PR did for Trino (there's some unrelated changes, you can ignore those): #13171

absolutely 👍

Alex-Monahan · 2022-03-24T13:30:33Z

Since DuckDB is, much like SQLite, an in-process, single-threaded engine, the error handling in TestConnectionDatabaseCommand.run feels a bit weird. Might want to work with @Mause on a narrow exception class for the

I had one small comment in case it is helpful! DuckDB is indeed embedded in your local process, but it is multi-threaded and can use as many CPU cores as you would like.

Thanks for building this connector!

* + duckdb support needs the forked version of [duckdb-engine](https://github.com/alitrack/duckdb_engine) * Update duckdb.py update _time_grain_expressions * removed superfluous get_all_datasource_names def in duckdb engine spec * added exception handling for duckdb single-threaded RuntimeError * fixed linter blips and other stylistic cleanup in duckdb.py * one last round of linter tweaks in test_connection.py for duckdb support Co-authored-by: Steven Lee <admin@alitrack.com> Co-authored-by: Richard Whaling <richardwhaling@Richards-MacBook-Pro.local> (cherry picked from commit 202e34a)

* + duckdb support needs the forked version of [duckdb-engine](https://github.com/alitrack/duckdb_engine) * Update duckdb.py update _time_grain_expressions * removed superfluous get_all_datasource_names def in duckdb engine spec * added exception handling for duckdb single-threaded RuntimeError * fixed linter blips and other stylistic cleanup in duckdb.py * one last round of linter tweaks in test_connection.py for duckdb support Co-authored-by: Steven Lee <admin@alitrack.com> Co-authored-by: Richard Whaling <richardwhaling@Richards-MacBook-Pro.local>

inakianduaga · 2022-06-21T06:06:02Z

Hi, testing this and Superset doesn't work when installing duckdb-engine, throws a 500 internal error on any page in the UI, backend says

module 'duckdb_engine' has no attribute 'name'
Traceback (most recent call last):                                                                                                                                                                                                                              File "/usr/local/lib/python3.8/site-packages/flask/app.py", line 1516, in full_dispatch_request
    rv = self.dispatch_request()
  File "/usr/local/lib/python3.8/site-packages/flask/app.py", line 1502, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
  File "/app/superset/utils/log.py", line 245, in wrapper
    value = f(*args, **kwargs)
  File "/app/superset/views/core.py", line 2677, in welcome
    "common": common_bootstrap_payload(),
  File "/app/superset/views/base.py", line 368, in common_bootstrap_payload
    available_specs = get_available_engine_specs()
  File "/app/superset/db_engine_specs/__init__.py", line 141, in get_available_engine_specs
    backend = dialect.name

Here's my full Dockerfile

FROM apache/superset

# Switching to root to install the required packages
USER root

# Example: installing the MySQL driver to connect to the metadata database
# if you prefer Postgres, you may want to use `psycopg2-binary` instead
RUN pip install psycopg2-binary

# Example: installing a driver to connect to Redshift
# Find which driver you need based on the analytics database
# you want to connect to here:
# https://superset.apache.org/installation.html#database-dependencies
# RUN pip install sqlalchemy-redshift
RUN pip install pyhive[hive]
RUN pip install pyhive[presto]

# DuckDB support
RUN pip install duckdb-engine

ADD ./config/superset_config.py /app/pythonpath/superset_config.py

# Switching back to using the `superset` user
USER superset

Mause · 2022-06-21T06:46:19Z

@inakianduaga heya, that's on me - unfortunately sqlalchemy doesn't really document what's expected from a dialect, so it's hard to keep up with the changes on their side. I'll push out a fixed version shortly

Mause · 2022-06-21T07:29:12Z

@inakianduaga it should work now if you try with duckdb_engine 0.1.11, sorry about that 😅

inakianduaga · 2022-06-21T11:10:44Z

ok thanks. It actually worked for me by going to the fixed superset:1.5.1 docker image instead of latest. Not sure that made the difference or it was simultaneously your fix. But either way, it works now 🙇

Mageswaran1989 · 2022-07-14T12:55:45Z

I wanted to access the S3 parquet files from Superset/SQL Editor. While I am able to use DuckDB to do the same in my python shell, I am wondering how to do it with the Superset and/or duckdb-engine

My python snippet to load parquet files from S3:

import duckdb
cursor = duckdb.connect()
cursor.execute("INSTALL httpfs;")
cursor.execute("LOAD httpfs;")
cursor.execute("SET s3_region='******'")
cursor.execute("SET s3_access_key_id=''**************")
cursor.execute("SET s3_secret_access_key='*****************************'")
cursor.execute("PRAGMA enable_profiling;")
cursor.execute("SELECT count(*) FROM read_parquet('s3://<bucket>/prefix/*.parquet'")

Mageswaran1989 · 2022-07-14T12:58:12Z

@Mause Could you please help with loading S3 parquet files with your engine?
Reference: https://duckdb.org/docs/guides/import/s3_import

Mause · 2022-07-14T13:01:51Z

@Mageswaran1989

if you're having an issue with

duckdb, please raise it over at https://github.com/duckdb/duckdb
duckdb-engine, please raise it over at https://github.com/Mause/duckdb_engine
superset, raise a new issue in this repo

PS. @zhaoyongjie any chance you could lock this conversation?

alitrack and others added 5 commits October 26, 2021 12:12

+ duckdb support

9129669

needs the forked version of [duckdb-engine](https://github.com/alitrack/duckdb_engine)

Update duckdb.py

fd43c56

update _time_grain_expressions

Merge branch 'apache:master' into master

b9c2199

removed superfluous get_all_datasource_names def in duckdb engine spec

9fa02d7

added exception handling for duckdb single-threaded RuntimeError

1952eaf

pull-request-size bot added the size/M label Mar 22, 2022

zhaoyongjie self-requested a review March 23, 2022 02:06

zhaoyongjie approved these changes Mar 23, 2022

View reviewed changes

villebro approved these changes Mar 23, 2022

View reviewed changes

Richard Whaling added 2 commits March 23, 2022 08:33

fixed linter blips and other stylistic cleanup in duckdb.py

de4792e

one last round of linter tweaks in test_connection.py for duckdb support

d1e16c4

zhaoyongjie closed this Mar 24, 2022

zhaoyongjie reopened this Mar 24, 2022

zhaoyongjie merged commit 202e34a into apache:master Mar 24, 2022

djayatillake mentioned this pull request Mar 24, 2022

feat: add duckdb as DataSource lightdash/lightdash#1585

Closed

villebro added the lts-v1 label Mar 29, 2022

Mause mentioned this pull request Jun 21, 2022

fix: restore name attribute Mause/duckdb_engine#274

Merged

Mageswaran1989 mentioned this pull request Jul 14, 2022

Unable to read S3 parquet files using DuckDB as Database Connector #20708

Closed

apache locked as off-topic and limited conversation to collaborators Jul 15, 2022

apache unlocked this conversation Jul 15, 2022

apache locked as resolved and limited conversation to collaborators Jul 15, 2022

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feat: add duckdb as DataSource - Fixes #14563 #19317

feat: add duckdb as DataSource - Fixes #14563 #19317

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	cls, database: "Database", inspector: Inspector, schema: Optional[str]
	cls, database: Database, inspector: Inspector, schema: Optional[str]

feat: add duckdb as DataSource - Fixes #14563 #19317

feat: add duckdb as DataSource - Fixes #14563 #19317

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rwhaling commented Mar 22, 2022 • edited Loading

SUMMARY

BEFORE/AFTER SCREENSHOTS OR ANIMATED GIF

TESTING INSTRUCTIONS

ADDITIONAL INFORMATION

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