I'm currently working on a new feature for Hypothesis, where we can dump a tidy jsonlines table of all the test cases we tried - including arguments, outcomes, timings, coverage, etc. Exploring this seems like a perfect cases for sqlite-utils and datasette, but I pretty quickly ran into an integer overflow problem and don't want to recommend that experience to my users.

I originally went to report this as a bug... and then found https://github.com/simonw/sqlite-utils/issues/309#issuecomment-895581038 almost exactly matched my repro 😅

https://github.com/simonw/sqlite-utils/issues/110#issuecomment-626391063 suggests that using NUMERIC would avoid this overflow error, although "If the TEXT value is a well-formed integer literal that is too large to fit in a 64-bit signed integer, it is converted to REAL." suggests that this would come at the cost of rounding to the nearest float value. Maybe I should just convert large integers to float before writing out my json?

After a bit more hacking, "manually cast large integers to float" seems like a decent solution for my particular case, but having written it up I thought I might as well post this issue anyway - I hope it's useful feedback, and won't mind at all if you close as wontfix if it's not.

Initially, I found an issue in datasette where it wouldn’t find spatialite when running on my Radxa Rock 5B - an RK3588 powered SBC, running the arm64 build of Debian Bullseye. I confirmed the same behaviour on my Raspberry Pi 4 - a BCM2711 powered SBC, running the arm64 build of Debian Bookworm.

$ datasette --load-extension=spatialite example.db Error: Could not find SpatiaLite extension

I did some digging and realised the issue originates in this project. Even with the libsqlite3-mod-spatialite package installed, pytest skips all of the GIS tests in the project.

``` $ apt list --installed | grep spatial […] libsqlite3-mod-spatialite/stable,now 5.0.1-3 arm64 [installed]

$ ls -l /usr/lib//spatial* lrwxrwxrwx 1 root root 23 Dec 1 2022 /usr/lib/aarch64-linux-gnu/mod_spatialite.so -> mod_spatialite.so.7.1.0 lrwxrwxrwx 1 root root 23 Dec 1 2022 /usr/lib/aarch64-linux-gnu/mod_spatialite.so.7 -> mod_spatialite.so.7.1.0 -rw-r--r-- 1 root root 7348584 Dec 1 2022 /usr/lib/aarch64-linux-gnu/mod_spatialite.so.7.1.0 ```

$ pytest tests/test_get.py ...... [ 73%] tests/test_gis.py ssssssssssss [ 75%] tests/test_hypothesis.py .... [ 75%]

I tracked the issue down to the find_sqlite() function in the utils.py file. The SPATIALITE_PATHS array doesn’t have an entry for the location of this module on arm64 linux.

Adds COLUMN_TYPE_MAPPING for TIME fields that are mapped as datetime.timedelta for MySQL and json represantation for datetime.timedelta in order to fix #522

:books: Documentation preview :books:: https://sqlite-utils--596.org.readthedocs.build/en/596/

Hi ! I noticed that when I am trying to use the delete method of the Table object, the record get properly deleted from the table, but the cascading delete triggers on foreign keys do not activate.

self.db["contact"].delete(contact_id)

I tried querying the database directly via DB Browser and the triggers work without any issue. Looked up the source code and behind the scene this method is just querying the database normally so I'm not exactly sure where this behavior comes from.

Thank you in advance for your time !

Refs: - #592

• [x] Tests against weird shaped tables

I need to test that this works against:

• rowid tables
• Tables that have a column called rowid even though they are not rowid tables

:books: Documentation preview :books:: https://sqlite-utils--593.org.readthedocs.build/en/593/

I have a neater pattern for this now - instead of: https://github.com/simonw/sqlite-utils/blob/1dc6b5aa644a92d3654f7068110ed7930989ce71/tests/test_create.py#L472-L475

I now prefer:

https://github.com/simonw/sqlite-utils/blob/1dc6b5aa644a92d3654f7068110ed7930989ce71/tests/test_create.py#L1163-L1171

While using sqlite-utils convert I realized it would be handy if you could pass --pdb to have it open the debugger at the first instance of a failed conversion.

Also need a design for an option for the .transform() method to indicate that the new table should be created with a new name without dropping the old one.

I think keep_table="name_of_table" is good for this.

Originally posted by @simonw in https://github.com/simonw/sqlite-utils/issues/565#issuecomment-1646657324

For every command/API method there should be a link to the equivalent in the other form factor.

Maybe also link to the API and CLI reference pages too.

CSV files with empty cells in (which come through as the empty string) are common and a bit gross.

Having an option that means "and if it's an empty string store null instead) would be cool.

I brainstormed name options here https://chat.openai.com/share/c947b738-ee7d-419c-af90-bc84e90987da

I found myself wanting to insert rows from a 849MB CSV file without processing the whole thing: https://huggingface.co/datasets/jerpint-org/HackAPrompt-Playground-Submissions/tree/main

sqlite-utils prints \r\n but it should probably print \n (unless the platform is detected as Windows?)

It has tripped me up a few times when piping the output of sqlite-utils to other programs:

$ sqlite-utils --no-headers --csv ~/lb/fs/d.db 'select path from media limit 1' | cat -A /mnt/d7/file^M$ $ sqlite-utils --no-headers --csv ~/lb/fs/d.db 'select path from media limit 1' | tr -d '\r' | cat -A /mnt/d7/file$

https://click.palletsprojects.com/en/8.1.x/shell-completion/

This works for zsh:

eval "$(_SQLITE_UTILS_COMPLETE=zsh_source sqlite-utils)"

This will probably work for bash:

eval "$(_SQLITE_UTILS_COMPLETE=bash_source sqlite-utils)"

Need to add this to the installation docs here: https://sqlite-utils.datasette.io/en/stable/installation.html - along with the pattern for adding that to .zshrc or whatever.

Noticed this while testing: - #547

If you pass a non-existent column to -c/--column you don't get an error message.

Noticed this:

``` % sqlite-utils analyze-tables content.db repos -c delete_branch_on_merge --common-limit 20 --no-least repos.delete_branch_on_merge: (1/1)

Total rows: 158 Null rows: 158 Blank rows: 0

Distinct values: 0

Most common: 158: None ```

The 158: None there is duplicate information considering we already know there are 158/158 null rows.

This fixes #514 by making the initial insert for upserts include all columns, so that new rows can be added to tables with non-pkey columns that have constraints.

(aside: I'm not a python programmer. pip? pipenv? venv? These are mystical incantations to me. The process to set up this repo for local development and testing was so easy. Thank you for the excellent contributing documentation!)

:books: Documentation preview :books:: https://sqlite-utils--515.org.readthedocs.build/en/515/

Reproducible code below:

```bash

echo 'create table bar (baz text, created_at timestamp default CURRENT_TIMESTAMP)' | sqlite3 foo.db sqlite3 foo.db SQLite version 3.36.0 2021-06-18 18:36:39 Enter ".help" for usage hints. sqlite> .schema bar CREATE TABLE bar (baz text, created_at timestamp default CURRENT_TIMESTAMP); sqlite> .exit sqlite-utils transform foo.db bar --column-order baz sqlite3 foo.db SQLite version 3.36.0 2021-06-18 18:36:39 Enter ".help" for usage hints. sqlite> .schema bar CREATE TABLE IF NOT EXISTS "bar" ( [baz] TEXT, [created_at] FLOAT DEFAULT 'CURRENT_TIMESTAMP' ); sqlite> .exit sqlite-utils transform foo.db bar --column-order baz sqlite3 foo.db SQLite version 3.36.0 2021-06-18 18:36:39 Enter ".help" for usage hints. sqlite> .schema bar CREATE TABLE IF NOT EXISTS "bar" ( [baz] TEXT, [created_at] FLOAT DEFAULT '''CURRENT_TIMESTAMP''' ); ```

Fixes #509, Fixes #336

Thanks for the great library! I fixed a bug that sqlite-utils transform breaks DEFAULT values. All tests already present passed with no changes, and I added some tests for this PR.

In #509 case, fixed here.

```shell $ sqlite3 test.db << EOF CREATE TABLE mytable ( col1 TEXT DEFAULT 'foo', col2 TEXT DEFAULT (STRFTIME('%Y-%m-%d %H:%M:%f', 'NOW')) ) EOF

$ sqlite3 test.db "SELECT sql FROM sqlite_master WHERE name = 'mytable';" CREATE TABLE mytable ( col1 TEXT DEFAULT 'foo', col2 TEXT DEFAULT (STRFTIME('%Y-%m-%d %H:%M:%f', 'NOW')) )

$ sqlite3 test.db "INSERT INTO mytable DEFAULT VALUES; SELECT * FROM mytable;" foo|2022-12-21 01:15:39.669

$ sqlite-utils transform test.db mytable --rename col1 renamedcol1 $ sqlite3 test.db "SELECT sql FROM sqlite_master WHERE name = 'mytable';" CREATE TABLE "mytable" ( [renamedcol1] TEXT DEFAULT 'foo', [col2] TEXT DEFAULT (STRFTIME('%Y-%m-%d %H:%M:%f', 'NOW')) # ← Non-String Value )

$ sqlite3 test.db "INSERT INTO mytable DEFAULT VALUES; SELECT * FROM mytable;" foo|2022-12-21 01:15:39.669 foo|2022-12-21 01:15:56.432 ```

And #336 case also fixed. Special values are described here.

3.2. The DEFAULT clause ... A default value may also be one of the special case-independent keywords CURRENT_TIME, CURRENT_DATE or CURRENT_TIMESTAMP.

```shell $ echo 'create table bar (baz text, created_at timestamp default CURRENT_TIMESTAMP)' | sqlite3 foo.db $ sqlite3 foo.db SQLite version 3.39.5 2022-10-14 20:58:05 Enter ".help" for usage hints. sqlite> .schema bar CREATE TABLE bar (baz text, created_at timestamp default CURRENT_TIMESTAMP); sqlite> .exit

$ sqlite-utils transform foo.db bar --column-order baz $ sqlite3 foo.db SQLite version 3.39.5 2022-10-14 20:58:05 Enter ".help" for usage hints. sqlite> .schema bar CREATE TABLE IF NOT EXISTS "bar" ( [baz] TEXT, [created_at] FLOAT DEFAULT CURRENT_TIMESTAMP ); sqlite> .exit

$ sqlite-utils transform foo.db bar --column-order baz $ sqlite3 foo.db SQLite version 3.39.5 2022-10-14 20:58:05 Enter ".help" for usage hints. sqlite> .schema bar CREATE TABLE IF NOT EXISTS "bar" ( [baz] TEXT, [created_at] FLOAT DEFAULT CURRENT_TIMESTAMP # ← Non-String Value ); ```

:books: Documentation preview :books:: https://sqlite-utils--519.org.readthedocs.build/en/519/

Fixes #527

:books: Documentation preview :books:: https://sqlite-utils--528.org.readthedocs.build/en/528/

Issuing either

py -Wdefault -m sqlite_utils insert dogs.db dogs dogs0.csv --csv [#############-----------------------] 36% [####################################] 100%C:\Users\Doug\AppData\Local\Programs\Python\Python311\Lib\site-packages\sqlite_utils\cli.py:1187: ResourceWarning: unclosed file <_io.TextIOWrapper name='dogs0.csv' encoding='utf-8-sig'> insert_upsert_implementation( ResourceWarning: Enable tracemalloc to get the object allocation traceback or set pythonwarnings=default sqlite-utils insert dogs.db dogs dogs0.csv --csv [#############-----------------------] 36% [####################################] 100%C:\Users\Doug\AppData\Local\Programs\Python\Python311\Lib\site-packages\sqlite_utils\cli.py:1187: ResourceWarning: unclosed file <_io.TextIOWrapper name='dogs0.csv' encoding='utf-8-sig'> insert_upsert_implementation( ResourceWarning: Enable tracemalloc to get the object allocation traceback

exhibits a ResourceWarning indicating that the CSV file being loaded is not closed.

sqlite-utils --version sqlite-utils, version 3.30 py --version Python 3.11.2 Windows Version 10.0.19045 Build 19045 SQLite version 3.41.0 2023-02-21 18:09:37

Does what it says and nothing else. This is the same set of paths as Datasette uses.

:books: Documentation preview :books:: https://sqlite-utils--536.org.readthedocs.build/en/536/

CI has started failing for Python 3.6: https://github.com/simonw/sqlite-utils/actions/runs/3576322798

It's fixable by swiching away from ubuntu-latest according to:

• https://github.com/actions/setup-python/issues/355#issuecomment-1335042510

But https://endoflife.date/python says that 3.6 end of life was almost 6 years ago, and end of security support nearly 1 year ago.

So I'm OK dropping support entirely - Python 3.6 users will still be able to install version 3.30, just not any releases that come next.

I'm not really sure what caused this and it happened in the middle of my program (after running for 35775 seconds).

Extracting metadata 49.9% (chunk 9893 of 19831) ... File "/home/xk/.local/lib/python3.10/site-packages/xklb/fs_extract.py", line 90, in extract_chunk args.db["media"].insert_all(utils.list_dict_filter_bool(media), pk="path", alter=True, replace=True) File "/home/xk/.local/lib/python3.10/site-packages/sqlite_utils/db.py", line 3107, in insert_all self.insert_chunk( File "/home/xk/.local/lib/python3.10/site-packages/sqlite_utils/db.py", line 2872, in insert_chunk result = self.db.execute(query, params) File "/home/xk/.local/lib/python3.10/site-packages/sqlite_utils/db.py", line 483, in execute return self.conn.execute(sql, parameters) UnicodeEncodeError: 'utf-8' codec can't encode character '\udcc3' in position 62: surrogates not allowed

This might be relevant: https://stackoverflow.com/questions/31898353/python-cant-encode-with-surrogateescape

I'm going to try re-running with

`py def execute( self, sql: str, parameters: Optional[Union[Iterable, dict]] = None ) -> sqlite3.Cursor: """ Execute SQL query and return asqlite3.Cursor``.

    :param sql: SQL query to execute
    :param parameters: Parameters to use in that query - an iterable for ``where id = ?``
      parameters, or a dictionary for ``where id = :id``
    """
    try:
        if self._tracer:
            self._tracer(sql, parameters)
        if parameters is not None:
            return self.conn.execute(sql, parameters)
        else:
            return self.conn.execute(sql)
    except UnicodeEncodeError:
        sql = sql.encode('utf-8', 'surrogatepass').decode('utf-8')
        if parameters is not None:
            parameters = parameters.encode('utf-8', 'surrogatepass').decode('utf-8')
        return self.execute(sql, parameters)

```

It would be nice to have a column_names. Similar to table_names.

Or if you could get one or all of the following syntax to work for both Database and Table that might be even better:

Style 1 - if 'table1' in db - if 'col1' in db['table1']

Style 2 - if 'table1' in db.tables - if 'col1' in db['table1'].columns

maybe the table ones actually work but I'm too lazy to check. I just know that I have to do:

[c.name for c in db['table1'].columns]

Edit: This is possible with columns_dict. I have actually used that before but I forgot about it. Feel free to close, but I do think accessing this data could be more consistent and intuitive.

I ended up needing to use db.conn.close() to fix this issue: - #503

I think .close() should be a method on Database itself.

The way errors are represented has changed: https://github.com/simonw/sqlite-utils/actions/runs/3323588047/jobs/5494127154 ``` ____ testquery_invalid_function ______

db_path = '/tmp/pytest-of-runner/pytest-0/test_query_invalid_function0/test.db'

def test_query_invalid_function(db_path):
    result = CliRunner().invoke(
        cli.cli, [db_path, "select bad()", "--functions", "def invalid_python"]
    )
    assert result.exit_code == 1

  assert (
        result.output.strip()
        == "Error: Error in functions definition: invalid syntax (<string>, line 1)"
    )

E AssertionError: assert 'Error: Error...ing>, line 1)' == 'Error: Error...ing>, line 1)' E - Error: Error in functions definition: invalid syntax (<string>, line 1) E ? ^^^^^^ ^^^^^^ E + Error: Error in functions definition: expected '(' (<string>, line 1) E ? ^^^^^^^ ^^^ ```

Is there any performance or size difference with column order in SQLITE ? similar to this https://www.cybertec-postgresql.com/en/column-order-in-postgresql-does-matter/

It might be interesting to have an option to create with an optimized column order. I'm assuming this would look something like INTEGER columns, REAL columns, BLOB columns, TEXT columns, NULL columns. NULL columns at the end because they are more likely to be TEXT and it is impossible to know if they will become INTEGER

(Of course, any schema evolution would reduce optimization but maybe column order could also be re-evaluated when schema changes)

edit:

this is easy to accomplish with the existing transform method:

int_columns = [k for k, v in table_columns.items() if v == int] db[table].transform(column_order=[*int_columns])

When inserting or upserting a jsonlines file, no progressbar is shown. Expected behavior is that, just like with .csv/.tsv files, also for a jsonlines file (--nl), unless --silent is provided, a progressbar is shown.

bash sql-utils upsert mydb.db posts posts.jl --nl --pk post_id (silence)

Currently file_progress is only called within the tsv/csv logic, however I think it can be safely wrapped around all the all the input formats that use decoded: https://github.com/simonw/sqlite-utils/blob/main/sqlite_utils/cli.py#L963

Interesting challenge with default_value: I need to be able to tell if the default values passed to .create() differ from those in the database already.

Introspecting that is a bit tricky:

```pycon

import sqlite_utils db = sqlite_utils.Database(memory=True) db["blah"].create({"id": int, "name": str}, not_null=("name",), defaults={"name": "bob"}) <Table blah (id, name)> db["blah"].columns [Column(cid=0, name='id', type='INTEGER', notnull=0, default_value=None, is_pk=0), Column(cid=1, name='name', type='TEXT', notnull=1, default_value="'bob'", is_pk=0)] `` Note how a default value of the Python stringbobis represented in the results ofPRAGMA table_info()asdefault_value="'bob'"` - it's got single quotes added to it!

So comparing default values from introspecting the database needs me to first parse that syntax. This may require a new table introspection method.

Originally posted by @simonw in https://github.com/simonw/sqlite-utils/issues/468#issuecomment-1229279539

I've run into an issue with extract and I don't believe this is the intended behaviour.

I'm working with a database with music listening information. Currently it has one large table listens that contains all information. I'm trying to normalize the database by extracting relevant columns to separate tables (artists, tracks, albums). Not every track has an album.

A simplified demonstration with just track_title and album_title columns: ```ipython In [1]: import sqlite_utils

In [2]: db = sqlite_utils.Database(memory=True)

In [3]: db["listens"].insert_all([ ...: {"id": 1, "track_title": "foo", "album_title": "bar"}, ...: {"id": 2, "track_title": "baz", "album_title": None} ...: ], pk="id") Out[3]: <Table listens (id, track_title, album_title)> ```

The track in the first row has an album, the second track doesn't. Now I extract album information into a separate column: ```ipython In [4]: db["listens"].extract(columns=["album_title"], table="albums", fk_column="album_id") Out[4]: <Table listens (id, track_title, album_id)>

In [5]: list(db["albums"].rows) Out[5]: [{'id': 1, 'album_title': 'bar'}, {'id': 2, 'album_title': None}]

In [6]: list(db["listens"].rows) Out[6]: [{'id': 1, 'track_title': 'foo', 'album_id': 1}, {'id': 2, 'track_title': 'baz', 'album_id': None}] ```

This behaves as expected -- the album table contains entries for both the existing album and the NULL album. The listens table has a foreign key only for the first row (since the album in the second row was empty).

Now I want to extract the track information as well. Album information belongs to the track so I want to extract both columns to a new table. ```ipython In [7]: db["listens"].extract(columns=["track_title", "album_id"], table="tracks", fk_column="track_id") Out[7]: <Table listens (id, track_id)>

In [8]: list(db["tracks"].rows) Out[8]: [{'id': 1, 'track_title': 'foo', 'album_id': 1}, {'id': 2, 'track_title': 'baz', 'album_id': None}]

In [9]: list(db["listens"].rows) Out[9]: [{'id': 1, 'track_id': 1}, {'id': 2, 'track_id': None}] ```

Extracting to the tracks table worked fine (both tracks are present with correct columns). However, the listens table only has a foreign key to the newly created tracks for the first row, the foreign key in the second row is NULL.

Changing the order of extracts doesn't help.

I poked around in the source a bit and I believe this line (essentially comparing NULL = NULL) is the problem, but I don't know enough about SQL to create a reliable fix myself.

Refs #470

:books: Documentation preview :books:: https://sqlite-utils--473.org.readthedocs.build/en/473/

For consistency with search: https://sqlite-utils.datasette.io/en/stable/cli-reference.html#search

-o, --order TEXT Order by ('column' or 'column desc')

I wanted to run sqlite-utils rows db.db mytable --order 'rowid desc' to see the most recently imported rows.

In this example:

```python @db.register_function def reverse_string(s): return "".join(reversed(list(s)))

print(db.execute('select reverse_string("hello")').fetchone()[0])

``` There's currently no way to over-ride the automatically selected name for the SQL function.

Read the Docs repository was renamed from readthedocs/readthedocs-preview to readthedocs/actions/. Now, the preview action is under readthedocs/actions/preview and is tagged as v1

:books: Documentation preview :books:: https://sqlite-utils--463.org.readthedocs.build/en/463/

I'm using the [insert_upsert_implementation](https://github.com/simonw/sqlite-utils/blob/main/sqlite_utils/cli.py) function directly in my Python code to import a csv file with all the bells and whistles sqlite-utils provides, but I'm getting a resource warning that a io.TextWrapper object is not closed.

The warning goes away when wrapping the code from this line in a try/finally block like:

try: ... ... finally: decoded.close() (might be that sniff_buffer must also be closed if non null, but I might be wrong)

I suspect Python closes the reference automatically when the sqlite-utils cli run is done, but since my code doesn't exit, I'm getting the warning.

Alternatively, it'd be cool if the 'import csv/tsv' functionality could be added directly to the Database class.

CLI equivalent of: - #449

This PR addresses a feature request raised in issue #449. Specifically this PR adds a functionality that lets users duplicate a table via:

python table_new = db["my_table"].duplicate("new_table")

Test added in file tests/test_duplicate.py.

Happy to make changes to meet maintainers' feedback, if any.

Missing values in my dataset are denoted by a single asterisk. I am trying to parse string dates into dates. This works fine for columns without missing values, but, when the column contains "*", I get the following:

``` $ sqlite-utils convert ${dbfile} details dob 'r.parsedate(value)' [------------------------------------] 0%Traceback (most recent call last): File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/sqlite_utils/db.py", line 2508, in convert_value return fn(v) File "<string>", line 2, in fn File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/sqlite_utils/recipes.py", line 8, in parsedate parser.parse(value, dayfirst=dayfirst, yearfirst=yearfirst).date().isoformat() File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/dateutil/parser/_parser.py", line 1368, in parse return DEFAULTPARSER.parse(timestr, **kwargs) File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/dateutil/parser/_parser.py", line 643, in parse raise ParserError("Unknown string format: %s", timestr) dateutil.parser._parser.ParserError: Unknown string format: *

Traceback (most recent call last): File "/usr/local/bin/sqlite-utils", line 33, in <module> sys.exit(load_entry_point('sqlite-utils==3.25.1', 'console_scripts', 'sqlite-utils')()) File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/click/core.py", line 1128, in call return self.main(args, kwargs) File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/click/core.py", line 1053, in main rv = self.invoke(ctx) File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/click/core.py", line 1659, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/click/core.py", line 1395, in invoke return ctx.invoke(self.callback, ctx.params) File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/click/core.py", line 754, in invoke return __callback(args, **kwargs) File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/sqlite_utils/cli.py", line 2698, in convert db[table].convert( File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/sqlite_utils/db.py", line 2524, in convert self.db.execute(sql, where_args or []) File "/usr/local/Cellar/sqlite-utils/3.25.1/libexec/lib/python3.9/site-packages/sqlite_utils/db.py", line 458, in execute return self.conn.execute(sql, parameters) sqlite3.OperationalError: user-defined function raised exception ```

Fixes a typo.

Seen here:

• https://github.com/simonw/geojson-to-sqlite/issues/30

Attempting to create a table with no columns produced this confusing error:

File "/Users/simon/.local/pipx/venvs/geojson-to-sqlite/lib/python3.9/site-packages/geojson_to_sqlite/utils.py", line 69, in import_features db[table].create(column_types, pk=pk) File "/Users/simon/.local/pipx/venvs/geojson-to-sqlite/lib/python3.9/site-packages/sqlite_utils/db.py", line 863, in create self.db.create_table( File "/Users/simon/.local/pipx/venvs/geojson-to-sqlite/lib/python3.9/site-packages/sqlite_utils/db.py", line 517, in create_table self.execute(sql) File "/Users/simon/.local/pipx/venvs/geojson-to-sqlite/lib/python3.9/site-packages/sqlite_utils/db.py", line 236, in execute return self.conn.execute(sql) sqlite3.OperationalError: near ")": syntax error

Closes #418

This adds four files to .gitignore:

.hypothesis/
Pipfile
Pipfile.lock
pyproject.toml

Those are all generated in the course of development and testing.

HI, when dealing with large json file (~170GB) i got the following error Traceback (most recent call last): File "/usr/local/bin/sqlite-utils", line 8, in <module> sys.exit(cli()) File "/usr/lib/python3/dist-packages/click/core.py", line 1126, in __call__ return self.main(*args, **kwargs) File "/usr/lib/python3/dist-packages/click/core.py", line 1051, in main rv = self.invoke(ctx) File "/usr/lib/python3/dist-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/lib/python3/dist-packages/click/core.py", line 1393, in invoke return ctx.invoke(self.callback, **ctx.params) File "/usr/lib/python3/dist-packages/click/core.py", line 752, in invoke return __callback(*args, **kwargs) File "/usr/local/lib/python3.9/dist-packages/sqlite_utils/cli.py", line 1300, in memory rows, format_used = rows_from_file(csv_fp, format=format, encoding=encoding) File "/usr/local/lib/python3.9/dist-packages/sqlite_utils/utils.py", line 185, in rows_from_file return rows_from_file(buffered, format=Format.JSON) File "/usr/local/lib/python3.9/dist-packages/sqlite_utils/utils.py", line 156, in rows_from_file decoded = json.load(fp) File "/usr/lib/python3.9/json/__init__.py", line 293, in load return loads(fp.read(), MemoryError

Inspired by: - #397

To match the option on create-index: https://sqlite-utils.datasette.io/en/stable/cli-reference.html#create-index

--if-not-exists Ignore if index already exists

Hi @simonw , If I run

sqlite3 .load /usr/local/lib/mod_spatialite.so select spatialite_version();

I have 5.0.0.

If I run

sqlite-utils :memory: "select spatialite_version()" --load-extension=spatialite

I have

Traceback (most recent call last): File "/home/aborruso/.local/bin/sqlite-utils", line 8, in <module> sys.exit(cli()) File "/home/aborruso/.local/lib/python3.8/site-packages/click/core.py", line 829, in __call__ return self.main(*args, **kwargs) File "/home/aborruso/.local/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/home/aborruso/.local/lib/python3.8/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/aborruso/.local/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/aborruso/.local/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/home/aborruso/.local/lib/python3.8/site-packages/sqlite_utils/cli.py", line 936, in query _load_extensions(db, load_extension) File "/home/aborruso/.local/lib/python3.8/site-packages/sqlite_utils/cli.py", line 1326, in _load_extensions db.conn.load_extension(ext) TypeError: argument 1 must be str, not None

How to load properly spatialite extension in sqlite-utils?

Thank you very muc

Yeah, apt-get isn't a thing on macOS so 4a2a3e2fd0d5534f446b3f1fee34cb165e4d86d2 (to test #79 against real SpatiaLite) broke.

Currently: https://sqlite-utils.datasette.io/en/stable/python-api.html#insert-replacing-data

If you want to insert a record or replace an existing record with the same primary key, using the replace=True argument to .insert() or .insert_all():

Should describe the exception you get first, then how to use replace to avoid it.

Currently throws an ugly traceback: % echo '[ {"id": 1, "name": "Lila"}, {"id": 1, "name": "Lila"} ]' | sqlite-utils upsert data.db chickens - Traceback (most recent call last): File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/bin/sqlite-utils", line 33, in <module> sys.exit(load_entry_point('sqlite-utils', 'console_scripts', 'sqlite-utils')()) File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.8/site-packages/click/core.py", line 1137, in __call__ return self.main(*args, **kwargs) File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.8/site-packages/click/core.py", line 1062, in main rv = self.invoke(ctx) File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.8/site-packages/click/core.py", line 1668, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.8/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/Users/simon/.local/share/virtualenvs/sqlite-utils-C4Ilevlm/lib/python3.8/site-packages/click/core.py", line 763, in invoke return __callback(*args, **kwargs) File "/Users/simon/Dropbox/Development/sqlite-utils/sqlite_utils/cli.py", line 1104, in upsert insert_upsert_implementation( File "/Users/simon/Dropbox/Development/sqlite-utils/sqlite_utils/cli.py", line 906, in insert_upsert_implementation db[table].insert_all( File "/Users/simon/Dropbox/Development/sqlite-utils/sqlite_utils/db.py", line 2615, in insert_all raise PrimaryKeyRequired("upsert() requires a pk") sqlite_utils.db.PrimaryKeyRequired: upsert() requires a pk

You have to read a lot of stuff in a lot of different places to get started with the Python library. Add a getting started introduction to https://sqlite-utils.datasette.io/en/stable/python-api.html

CLI equivalent of table.rows_where() - should accept parameters too. Work on this at the same time as #381.

For these commits: https://github.com/simonw/sqlite-utils/compare/3.20...129141572f249ea290e2a075437e2ebaad215859

For https://sqlite-utils.datasette.io/en/stable/cli.html#inserting-data-from-files

Given a file called dogs.jpg stem would be dogs and ext would be jpg.

Need to decide what happens for dogs.and.cats.jpg.gz.

Deprecated pytest-runner is not necessary for running the testsuite.

It's not possible to use a module that requires a nested import, such as xml.etree.ElementTree, at the moment. I found and fixed this bug in git-history, I should replicate that fix (and accompanying documentation) here: https://github.com/simonw/git-history/issues/39

the library deal with Postgres type jsonb as dictionary, add dict type as a TEXT for mapping to sqlite

While working on updating sqlite-utils for NixOS/Nixpkgs, I came a cross the following:

In 5ec6686153e29ae10d4921a1ad4c841f192f20e2, a new dependency was added on dateutils (https://pypi.org/project/dateutils/).

I believe this is unintentional, and instead python-dateutil (https://pypi.org/project/python-dateutil/) was intended.

My reasoning is: - python-dateutil is imported here in recipes.py - The mypy type-python-dateutil dependency in setup.py - python-dateutil is a dependency of dateutils as seen in the output in docs/tutorial.ipynb

Seems like the trailing "s" seems to be the source of confusion 😅

I've swapped the dependencies out, hope this helps.

currently --flatten option works only for insert command, it would be cool if it worked for memory as well to query nested json

It seems that click 8.x uses None as the default value for multiple=True options.

This change makes the code forward-compatible with click 8.x.

See this build failure for more info: https://hydra.nixos.org/build/156926608

It currently works like this: https://github.com/simonw/sqlite-utils/blob/77c240df56068341561e95e4a412cbfa24dc5bc7/sqlite_utils/db.py#L2177-L2195

It's registering a function called convert_value() and then failing to de-register that function once it has finished.

It might even be possible for two queries running against the same connection to clobber each other's convert_value() functions, leading to incorrect behaviour.

So two fixes: firstly it should register the function with a unique name (maybe add a random suffix). Secondly, it should de-register that function once it has finished.

Not quite sure if this is a bug, or just an assumption I made but I thought --tsv and --no-headers would work together when inserting from a file, and currently they seem not to (sqlite-utils, version 3.12, installed on Mac OS X via brew)

Instead it says:

Error: Use just one of --nl, --csv or --tsv

As if it has interpreted the --no-headers as --nl.

The --help does specifically say CSV: --no-headers CSV file has no header row

And this heading in the documentation also only refers to CSV, but the text does mention TSV in passing, and I'd generally expect them to behave the same in most cases. https://sqlite-utils.datasette.io/en/stable/cli.html#csv-files-without-a-header-row

https://github.com/simonw/sqlite-utils/blob/7a19822ac9ee24be2fbb4c2326a0bf2f3d2d9c4d/docs/index.rst#L39 Is a very old example

https://sqlite-utils.datasette.io/en/latest/reference.html

Search for backtick to reveal various minor markup bugs.

If the table doesn't exist it should still return self, not []:

https://github.com/simonw/sqlite-utils/blob/ee469e3122d6f5973ec2584c1580d930daca2e7c/sqlite_utils/db.py#L1676-L1683

Spotted with mypy while working on #312.

The sqlite3 client takes user defined functions and replaces the text with "user-defined function raised exception`" so it's not apparent what's gone wrong:

Unexpected error: user-defined function raised exception

As mentioned in https://code.djangoproject.com/ticket/29500 and https://stackoverflow.com/questions/45824209/how-to-get-an-error-kind-from-sqlite-create-function/45834923#45834923 the workaround for this is to enable callback tracebacks:

sqlite3.enable_callback_tracebacks(True)

It would be nice if https://sqlite-utils.datasette.io/en/stable/python-api.html#registering-custom-sql-functions either included a reference to enable_callback_tracebacks or if registering a user defined function set this flag automatically.

I need this for #304. I'll probably add this to the .execute_count() method as where= and where_args=.

Refs #251, #302.

• [x] Get recipes working
• [x] Document recipes
• [x] Implement db[table].convert(...) method
• [x] Add tests for recipes that use the new Python method
• [x] Implement db[table].convert(..., multi=True) mechanism
• [x] Documentation for db[table].convert(...)
• [x] Refactor sqlite-utils convert to use the new method

Spin off from #251. The ability to execute Python functions to convert and split columns should be part of the library too, not just the CLI.

It currently accepts no arguments. Allowing for optional arguments specifying tables would be useful:

sqlite-utils schema fixtures.db facetable searchable

pip install sqlite-utils, pipx install sqlite-utils and brew install sqlite-utils

https://github.com/simonw/sqlite-utils/blob/ec5174ed40fa283cb06f25ee0c0136297ec313ae/sqlite_utils/cli.py#L1244-L1251

This runs against JSON as well as CSV/TSV - which isn't necessary and In fact throws errors if there is any nested data.

• Implement filename.json:json and -:nl and suchlike options for specifying the format rather than guessing it - see https://github.com/simonw/sqlite-utils/issues/272#issuecomment-861985944

Follows #272

https://app.codecov.io/gh/simonw/sqlite-utils

Same mechanism as Datasette. Need to copy across the token from that page and add an equivalent of this workflow: https://github.com/simonw/datasette/blob/main/.github/workflows/test-coverage.yml

This works: ```pycon

db['foo'].insert_all([{"name": "hello"}], pk="name")

The description for create-table was duplicated from create-index.

Refs #256.

Remove extra [

Noticed a typo in the docs and followed that up with a spellcheck. Had to bite my tongue at some of the British spellings.

…are escaped aps unicode for lists, tuples, dicts

Fix of #257

It's common for many processes to create flat files where each line is a JSON object.

So the file isn't a json array.

Many tools (like jq) support this natively, it'd be great for sqlite-utils to also!

I ran this:

db["Reports"].add_foreign_key("Reported by ID", "Reporters", "id")

And got this:

``` ~/jupyter-venv/lib/python3.9/site-packages/sqlite_utils/db.py in add_foreign_keys(self, foreign_keys) 616 # Have to VACUUM outside the transaction to ensure .foreign_keys property 617 # can see the newly created foreign key. --> 618 self.vacuum() 619 620 def index_foreign_keys(self):

~/jupyter-venv/lib/python3.9/site-packages/sqlite_utils/db.py in vacuum(self) 629 630 def vacuum(self): --> 631 self.execute("VACUUM;") 632 633

~/jupyter-venv/lib/python3.9/site-packages/sqlite_utils/db.py in execute(self, sql, parameters) 234 return self.conn.execute(sql, parameters) 235 else: --> 236 return self.conn.execute(sql) 237 238 def executescript(self, sql):

DatabaseError: database disk image is malformed ```

This will enable cross-database joins, as seen in https://github.com/simonw/datasette/issues/283

Also refs #113

Reported by @nieuwenhoven in #225 along with a proposed fix.

Following #211

A command to list the triggers in the database.

sqlite-utils triggers my.db

Can optionally take one or more tables:

sqlite-utils triggers my.db table1 table2

Counting all of the rows in a large table is expensive - this is one of the main causes of performance problems in Datasette when running against large databases.

Carefully constructed SQL triggers could be used to maintain accurate cached counts for a table, by incrementing and decrementing a counter every time a row is inserted or deleted.

sqlite-utils already has a mechanism for creating triggers for FTS - the table.enable_fts(..., create_triggers=True) method. How about a similar mechanism for setting up triggers to maintain a count of table rows?

Hi Simon,

Would be great if you could ingest RData files!

I could do this in a few lines of code but I am too lazy - sorry!

Peter

pytest output: ... ============================== short test summary info =============================== FAILED tests/test_cli.py::test_optimize[tables0] - assert 1662976 < 1662976 FAILED tests/test_cli.py::test_optimize[tables1] - assert 1667072 < 1662976 ===================== 2 failed, 538 passed, 3 skipped in 34.32s ======================

Came across this while packaging sqlite-utils for NixOS, but it can be recreated it using the alpine:edge docker image as well as follows:

``` docker run --rm -it alpine:edge /bin/sh

apk update && apk add git sqlite python3 gcc python3-dev musl-dev && python3 -m ensurepip

git clone https://github.com/simonw/sqlite-utils.git

cd sqlite-utils/

pip3 install -e .[test]

pytest

```

This definitely works on sqlite v3.33.

Both table.search(columns=) and the sqlite-utils search -c option do not work as expected - they always return both the rowid and the rank columns even if those have not been requested.

This should be fixed before the 3.0 non-alpha release.

To let you specify the exact columns you want. Based on the -c option to sqlite-utils search in #192.

According to https://www.sqlite.org/fts5.html (not sure about FTS4) results can be sorted by relevance. At the moment results are returned by default by rowid. Perhaps a flag can be added to the search method?

I'd like a mechanism to optionally avoid registering a custom function if it has already been registered.

SQLite doesn't seem to offer a way to introspect registered custom functions so I'll need to track what has already been registered in sqlite-utils instead.

Should I register the custom rank_bm25 SQLite function for every connection, or should I register it against the connection just the first time the user attempts an FTS4 search? I think I'd rather register it only if it is needed.

Originally posted by @simonw in https://github.com/simonw/sqlite-utils/issues/198#issuecomment-723145383

Inspired by this Twitter conversation: https://twitter.com/simonw/status/1310386009465479168

e.g. for this: calands-datasette % sqlite-utils tables calands.db --counts [{"table": "spatial_ref_sys", "count": 4924}, {"table": "spatialite_history", "count": 14}, {"table": "sqlite_sequence", "count": 1}, {"table": "geometry_columns", "count": 2}, {"table": "spatial_ref_sys_aux", "count": 4873}, {"table": "views_geometry_columns", "count": 0}, {"table": "virts_geometry_columns", "count": 0}, {"table": "geometry_columns_statistics", "count": 2}, {"table": "views_geometry_columns_statistics", "count": 0}, {"table": "virts_geometry_columns_statistics", "count": 0}, {"table": "geometry_columns_field_infos", "count": 0}, {"table": "views_geometry_columns_field_infos", "count": 0}, {"table": "virts_geometry_columns_field_infos", "count": 0}, {"table": "geometry_columns_time", "count": 2}, {"table": "geometry_columns_auth", "count": 2}, {"table": "views_geometry_columns_auth", "count": 0}, {"table": "virts_geometry_columns_auth", "count": 0}, Traceback (most recent call last): File "/usr/local/bin/sqlite-utils", line 8, in <module> sys.exit(cli()) File "/usr/local/Cellar/sqlite-utils/2.15.1/libexec/lib/python3.8/site-packages/click/core.py", line 829, in __call__ return self.main(*args, **kwargs) File "/usr/local/Cellar/sqlite-utils/2.15.1/libexec/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/usr/local/Cellar/sqlite-utils/2.15.1/libexec/lib/python3.8/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/Cellar/sqlite-utils/2.15.1/libexec/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/usr/local/Cellar/sqlite-utils/2.15.1/libexec/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/usr/local/Cellar/sqlite-utils/2.15.1/libexec/lib/python3.8/site-packages/sqlite_utils/cli.py", line 143, in tables for line in output_rows(_iter(), headers, nl, arrays, json_cols): File "/usr/local/Cellar/sqlite-utils/2.15.1/libexec/lib/python3.8/site-packages/sqlite_utils/cli.py", line 922, in output_rows for row, next_row in itertools.zip_longest(current_iter, next_iter): File "/usr/local/Cellar/sqlite-utils/2.15.1/libexec/lib/python3.8/site-packages/sqlite_utils/cli.py", line 123, in _iter row.append(db[name].count) File "/usr/local/Cellar/sqlite-utils/2.15.1/libexec/lib/python3.8/site-packages/sqlite_utils/db.py", line 458, in count return self.db.conn.execute( sqlite3.OperationalError: no such module: VirtualSpatialIndex The tables command could take --load-extension too - as could rows and other similar commands.

Follow-on from #134

Right now enable_fts() is only implemented for Table(). Technically sqlite supports enabling fts on views. But it requires deeper thought since views don't have rowid and the current implementation of enable_fts() relies on the presence of rowid column.

It is possible to provide an alternative rowid using the content_rowid option to the FTS5() function.

Ref: https://sqlite.org/fts5.html#fts5_table_creation_and_initialization

The "content_rowid" option, used to set the rowid field of an external content table.

This will further complicate enable_fts() function by adding an extra argument. I'm wondering if that is outside the scope of this tool or should I work on that feature and send a PR?

``` In [11]: db['one'].insert({"id": 1, "name": "oentuh"}, pk="id") Out[11]: <Table one (id, name)>

In [12]: db['two'].insert({"id": 1, "name": "oentuh"}, pk=["id"]) Out[12]: <Table two (id, name)>

In [13]: db['one'].schema Out[13]: 'CREATE TABLE [one] (\n [id] INTEGER PRIMARY KEY,\n [name] TEXT\n)'

In [14]: db['two'].schema Out[14]: 'CREATE TABLE [two] (\n [id] INTEGER,\n [name] TEXT\n)' ```

The sqlite-utils insert releases.db releases - --pk is missing the pk field name, added "id" to fix it.

https://github.blog/2020-09-30-code-scanning-is-now-available/

I noticed that https://til.simonwillison.net/ search doesn't use porter stemming. I'd like to add that, but since the build script always operates on an existing database (to avoid re-rendering markdown and re-building image thumbnails) I'd like it to only add porter stemming if it's not there already.

So I'd like to be able to say "set up FTS to look like this, and fix it if it doesn't".

I think the neatest way to do that is with a replace=True argument to .enable_fts(), for consistency with def .create_view(self, name, sql, replace=True).

So the replace=True argument would check and see if the configured FTS exists already with the correct options (columns, stemming, triggers) - and if any of those are incorrect it would call .disable_fts() and then create a new FTS configuration with the correct options.