Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

DuckDB sqlInsert doesn't work #19

Open
edmundmiller opened this issue Dec 21, 2023 · 0 comments · May be fixed by #20
Open

DuckDB sqlInsert doesn't work #19

edmundmiller opened this issue Dec 21, 2023 · 0 comments · May be fixed by #20

Comments

@edmundmiller
Copy link

Example:

include { sqlInsert } from 'plugin/nf-sqldb'
// -- create a table
// CREATE TABLE ducks AS SELECT 3 AS age, 'mandarin' AS breed;
channel
    .of(tuple('3', "mandarin"))
    .sqlInsert( into: 'ducks',
               columns: 'age, breed',
               db: 'playground',
               setup: "CREATE TABLE ducks(age INTEGER, breed VARCHAR);")

Main error via @bentsherman

java.sql.SQLFeatureNotSupportedException: null
    at org.duckdb.DuckDBPreparedStatement.addBatch(DuckDBPreparedStatement.java:606)
    at nextflow.sql.InsertHandler.executeStm(InsertHandler.groovy:189)
    at nextflow.sql.InsertHandler.performAsTuple(InsertHandler.groovy:168)
    at nextflow.sql.InsertHandler.perform(InsertHandler.groovy:144)
    at nextflow.sql.ChannelSqlExtension$_sqlInsert_closure3.doCall(ChannelSqlExtension.groovy:123)

nextflow.log

Then I talked to @abhi18av who hunted down that this line is the issue.

nf-sqldb/plugins/nf-sqldb/src/main/nextflow/sql/InsertHandler.groovy

Line 239 in e9f3da6

preparedStatement.executeBatch()

He then dove into the DuckDB JDBC and found the feature isn't supported 🙃

We thought maybe if the old method without batch was used that might be a quick fix. However we also decided running a ton of queries on the headnode was a anti-pattern.

Regardless, good things come to those who wait, there's a PR to add batch functionality!
@edmundmiller edmundmiller linked a pull request Dec 21, 2023 that will close this issue
Draft
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Bump DuckDB JDBC version edmundmiller/nf-sqldb
1 participant
@edmundmiller