New in SQLite 3.37.0, released a few days ago: https://www.sqlite.org/stricttables.html

• https://github.com/simonw/sqlite-utils/issues/344#issuecomment-982014776

Make table.transform() preserve STRICT mode.

:books: Documentation preview :books:: https://sqlite-utils--604.org.readthedocs.build/en/604/

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.

I keep making this mistake: bash sqlite-utils add-column content.db assets _since int ``` Usage: sqlite-utils add-column [OPTIONS] PATH TABLE COL_NAME [[integer|float|b lob|text|INTEGER|FLOAT|BLOB|TEXT]] Try 'sqlite-utils add-column -h' for help.

Error: Invalid value for '[[integer|float|blob|text|INTEGER|FLOAT|BLOB|TEXT]]': 'int' is not one of 'integer', 'float', 'blob', 'text', 'INTEGER', 'FLOAT', 'BLOB', 'TEXT'. ```

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.

https://dev.to/hugovk/help-test-python-312-beta-1508/

:books: Documentation preview :books:: https://sqlite-utils--591.org.readthedocs.build/en/591/

Currently trying to create a column with Python type datetime.timedelta results in an error:

```

from sqlite_utils import Database db = Database("test.db") test_tbl = db['test'] test_tbl.insert({'col1': datetime.timedelta()}) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/local/lib/python3.10/dist-packages/sqlite_utils/db.py", line 2979, in insert return self.insert_all( File "/usr/local/lib/python3.10/dist-packages/sqlite_utils/db.py", line 3082, in insert_all self.create( File "/usr/local/lib/python3.10/dist-packages/sqlite_utils/db.py", line 1574, in create self.db.create_table( File "/usr/local/lib/python3.10/dist-packages/sqlite_utils/db.py", line 961, in create_table sql = self.create_table_sql( File "/usr/local/lib/python3.10/dist-packages/sqlite_utils/db.py", line 852, in create_table_sql column_type=COLUMN_TYPE_MAPPING[column_type], KeyError: <class 'datetime.timedelta'> ```

The reason this would be useful is that MySQLdb uses timedelta for MySQL TIME columns:

```

import MySQLdb conn = MySQLdb.connect(host='database', user='user', passwd='pw') csr = conn.cursor() csr.execute("SELECT CAST('11:20' AS TIME)") tuple(csr) ((datetime.timedelta(seconds=40800),),) ```

So currently any attempt to convert a MySQL DB with a TIME column using db-to-sqlite will result in the above error.

I was rather surprised that MySQLdb uses timedelta for TIME columns but I see that this column type is intended for time intervals as well as the time of day so it makes sense.

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/

The issue is that underlying iterator is not fully consumed within the body of the with file_progress() block. Instead, that block creates generator expressions like docs = (dict(zip(headers, row)) for row in reader)

These iterables are consumed later, outside the with file_progress() block, which consumes the underlying iterator, and in turn updates the progress bar.

This means that the ProgressBar.__exit__ method gets called before the last time the ProgressBar.update method gets called. The result is that the code to make the cursor invisible (inside the update() method) is called after the cleanup code to make it visible (in the __exit__ method).

The fix is to move consumption of the docs iterators within the progress bar block. (

(An additional fix, to make ProgressBar more robust against this kind of misuse, would to make it refusing to update after its __exit__ method had been called, just like files cannot be read() after they are closed. That requires a in the click library).

Note that Github diff obscures the simplicity of this diff, it's just indenting a block of code.

:books: Documentation preview :books:: https://sqlite-utils--598.org.readthedocs.build/en/598/

I'm not sure why this happens but sqlite-utils makes my terminal cursor disappear after running commands like sqlite-utils insert. I've only noticed this behavior in sqlite-utils, not in any other CLI tools

I can still type commands after it runs but the text cursor is invisible

According to both Debian and Ubuntu, the correct “target triple” for arm64 is aarch64-linux-gnu, so we should be looking in /usr/lib/aarch64-linux-gnu for mod_spatialite.so.

I can confirm that on both of my Debian arm64 SBCs, libsqlite3-mod-spatialite installs to that path.

$ 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

This is a set of before and after snippets of pytest’s output for this PR.

Before

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

After

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

Issue: #599

:books: Documentation preview :books:: https://sqlite-utils--600.org.readthedocs.build/en/600/

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 !

I just spotted a bug when using https://datasette.io/plugins/datasette-configure-fts and https://datasette.io/plugins/datasette-edit-schema at the same time.

Steps to reproduce:

• Configure FTS for a table, then run a test search
• Edit the schema for that table and change the order of columns
• Run the test search again

I got the wrong search results, which I think is because the _fts table pointed to the first table by rowid but those rowid values were entirely rewritten as a consequence of running table.transform() on the table.

Reconfiguring FTS on the table fixed the problem.

I think table.transform() should be able to preserve rowid values.

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/

Extremely detailed story of how I got to this point:

• https://github.com/simonw/llm/issues/162

Steps to reproduce (only if that pragma is on though): bash python -c ' import sqlite_utils db = sqlite_utils.Database(memory=True) db.execute(""" CREATE TABLE "logs" ( [id] INTEGER PRIMARY KEY, [model] TEXT, [prompt] TEXT, [system] TEXT, [prompt_json] TEXT, [options_json] TEXT, [response] TEXT, [response_json] TEXT, [reply_to_id] INTEGER, [chat_id] INTEGER REFERENCES [log]([id]), [duration_ms] INTEGER, [datetime_utc] TEXT ); """) db["logs"].add_foreign_key("reply_to_id", "logs", "id") ' This succeeds in some environments, fails in others.

https://github.com/simonw/sqlite-utils/blob/13ebcc575d2547c45e8d31288b71a3242c16b886/sqlite_utils/db.py#L1165-L1174

This is the only place in the code that attempts to modify sqlite_master directly, which fails on some Python installations.

Could this use the .transform() trick instead?

Or automatically switch to that trick if it hits an error?

The new options added in: - #577 Deserve consideration in the CLI as well.

https://github.com/simonw/sqlite-utils/blob/d2bcdc00c6ecc01a6e8135e775ffdb87572b802b/sqlite_utils/db.py#L1706-L1708

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

Refs: - #577

:books: Documentation preview :books:: https://sqlite-utils--584.org.readthedocs.build/en/584/

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.

Currently the changelog starts at 0.4:

https://sqlite-utils.datasette.io/en/3.34/changelog.html#id115

I want the other releases - according to https://pypi.org/project/sqlite-utils/#history there are three missing:

Plugins affecting the CLI by default makes sense to me.

I'm less confident about them always affecting users of the Python API.

I'm going to have them apply by default, but I'm going to add a mechanism to opt-out on an individual database basis. Basically this:

```python from sqlite_utils import Database db = Database(memory=True, execute_plugins=False)

Anything using db from here on will not execute plugins

``` cc @asg017

Refs: - #567 - #574

Splitting off an issue for prepare_connection() since Alex got the PR in seconds before I shipped 3.34!

Originally posted by @simonw in https://github.com/simonw/sqlite-utils/issues/567#issuecomment-1646686424

I'd like there to be a plugin system for sqlite-utils, similar to the datasette/llm plugins. I'd like to make plugins that would do things like:

• Register SQLite extensions for more SQL functions + virtual tables
• Register new subcommands
• Different input file formats for sqlite-utils memory
• Different output file formats (in addition to --csv --tsv --nl etc.

A few real-world use-cases of plugins I'd like to see in sqlite-utils:

• Register many of my sqlite extensions in sqlite-utils (sqlite-http, sqlite-lines, sqlite-regex, etc.)
• New subcommands to work with sqlite-vss vector tables
• Input/ouput Parquet/Avro/Arrow IPC files with sqlite-arrow

Just like the Datasette prepare_connection hook, this PR adds a similar hook for the sqlite-utils plugin system.

The sole argument is conn, since I don't believe a database or datasette argument would be relevant here.

I want to do this so I can release sqlite-utils plugins for my SQLite extensions, similar to the Datasette plugins I've release for them.

An example plugin: https://gist.github.com/asg017/d7cdf0d56e2be87efda28cebee27fa3c

```bash $ sqlite-utils install https://gist.github.com/asg017/d7cdf0d56e2be87efda28cebee27fa3c/archive/5f5ad549a40860787629c69ca120a08c32519e99.zip

$ sqlite-utils memory 'select hello("alex") as response' [{"response": "Hello, alex!"}] ``` Refs: - #574

:books: Documentation preview :books:: https://sqlite-utils--573.org.readthedocs.build/en/573/

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

Spotted this in the GitHub Actions logs:

... and it turns out running .transform() with no arguments still fixes the format of the schema!

```pycon

db["log"].add_column("foo", str)

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.

I find myself wanting two new features in sqlite-utils: - The ability to have the new transformed table set to a specific name, while keeping the old table around - The ability to rename a table (sqlite-utils doesn't have a table rename function at all right now)

Originally posted by @simonw in https://github.com/simonw/llm/issues/65#issuecomment-1618375042

Found myself using this pattern to quickly prototype a schema:

```python import sqlite_utils db = sqlite_utils.Database(memory=True)

print(db["answers_chunks"].create({ "id": int, "content": str, "embedding_type_id": int, "embedding": bytes, "embedding_content_md5": str, "source": str, }, pk="id", transform=True).schema) ```

Using replace=True to drop and then recreate the table would be neat here, and would be consistent with other places that use replace=True.

I'm going to start by adding the register_command hook using the exact same pattern as Datasette and LLM.

Originally posted by @simonw in https://github.com/simonw/sqlite-utils/issues/567#issuecomment-1646643450

As seen in LLM.

Needed while working on: - #567

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

Refs: - #559

:books: Documentation preview :books:: https://sqlite-utils--560.org.readthedocs.build/en/560/

Thanks for what seems like a truly great suite of libraries. I wanted to try out Datasette, but never got more than half way through your YouTube video with the SF tree dataset. Whenever I try to extract a column, I get a sqlite3.OperationalError: table sqlite_master may not be modified error from Python. This snippet reproduces the error on my system, Python 3.9.1 and sqlite-utils 3.5 on an M1 Macbook Pro running in rosetta mode: curl "https://data.nasa.gov/resource/y77d-th95.json" | \ sqlite-utils insert meteorites.db meteorites - --pk=id sqlite-utils extract meteorites.db meteorites recclass

I have tried googling the problem, but all I've found is that this might be a problem with the sqlite3 database running in defensive mode, but I definitely can't know for sure. Does the problem seem familiar to you?

If sqlean is available, use that.

Refs: - https://github.com/nalgeon/sqlean.py/issues/1#issuecomment-1605707788

This will provide a good workaround for: - #235

It would be nice if the rows subcommand had a flag, perhaps called --transpose which would print in long form instead of wide. Similar to extended display mode in psql (\x)

In other words instead of this:

sqlite-utils rows --limit 5 --fmt github track_metadata.db songs

| track_id | title | song_id | release | artist_id | artist_mbid | artist_name | duration | artist_familiarity | artist_hotttnesss | year | track_7digitalid | shs_perf | shs_work | |--------------------|-------------------|--------------------|--------------------------------------|--------------------|--------------------------------------|------------------|------------|----------------------|---------------------|--------|--------------------|------------|------------| | TRMMMYQ128F932D901 | Silent Night | SOQMMHC12AB0180CB8 | Monster Ballads X-Mas | ARYZTJS1187B98C555 | 357ff05d-848a-44cf-b608-cb34b5701ae5 | Faster Pussy cat | 252.055 | 0.649822 | 0.394032 | 2003 | 7032331 | -1 | 0 | | TRMMMKD128F425225D | Tanssi vaan | SOVFVAK12A8C1350D9 | Karkuteillä | ARMVN3U1187FB3A1EB | 8d7ef530-a6fd-4f8f-b2e2-74aec765e0f9 | Karkkiautomaatti | 156.551 | 0.439604 | 0.356992 | 1995 | 1514808 | -1 | 0 | | TRMMMRX128F93187D9 | No One Could Ever | SOGTUKN12AB017F4F1 | Butter | ARGEKB01187FB50750 | 3d403d44-36ce-465c-ad43-ae877e65adc4 | Hudson Mohawke | 138.971 | 0.643681 | 0.437504 | 2006 | 6945353 | -1 | 0 | | TRMMMCH128F425532C | Si Vos Querés | SOBNYVR12A8C13558C | De Culo | ARNWYLR1187B9B2F9C | 12be7648-7094-495f-90e6-df4189d68615 | Yerba Brava | 145.058 | 0.448501 | 0.372349 | 2003 | 2168257 | -1 | 0 | | TRMMMWA128F426B589 | Tangle Of Aspens | SOHSBXH12A8C13B0DF | Rene Ablaze Presents Winter Sessions | AREQDTE1269FB37231 | | Der Mystic | 514.298 | 0 | 0 | 0 | 2264873 | -1 | 0 |

The output would look something like this:

$ for col in (sqlite-columns track_metadata.db songs) sqlite-utils --fmt github track_metadata.db "select $col from songs order by rowid desc limit 5" end

| track_id | |--------------------| | TRYYYVU12903CD01E3 | | TRYYYDJ128F9310A21 | | TRYYYMG128F4260ECA | | TRYYYJO128F426DA37 | | TRYYYUS12903CD2DF0 | | title | |-------------------------------------| | Fernweh feat. Sektion Kuchikäschtli | | Faraday | | Novemba | | Jago Chhadeo | | O Samba Da Vida | | song_id | |--------------------| | SOWXJXQ12AB0189F43 | | SOLXGOR12A81C21EB7 | | SOHODZI12A8C137BB3 | | SOXQYIQ12A8C137FBB | | SOTXAME12AB018F136 | | release | |---------------------------------| | So Oder So | | The Trance Collection Vol. 2 | | Dub_Connected: electronic music | | Naale Baba Lassi Pee Gya | | Pacha V.I.P. | | artist_id | |--------------------| | AR7PLM21187B990D08 | | ARCMCOK1187B9B1073 | | ARZ3R6M1187B9AF750 | | ART5FZD1187B9A7FCF | | AR7Z4J81187FB3FC59 | | artist_mbid | |--------------------------------------| | 3af2b07e-c91c-4160-9bda-f0b9e3144ed3 | | 4ac5f3de-c5ad-475e-ad50-41f1ef9dba20 | | 8b97e9c8-61f5-4615-9a96-276f24204e34 | | 2357c400-9109-42b6-b3fe-9e2d9f8e3872 | | 9d50cb20-7e42-45cc-b0dd-154c3e92a577 | | artist_name | |----------------| | Texta | | Elude | | Gabriel Le Mar | | Kuldeep Manak | | Kiko Navarro | | duration | |------------| | 295.079 | | 484.519 | | 553.038 | | 244.166 | | 217.443 | | artist_familiarity | |----------------------| | 0.552977 | | 0.403668 | | 0.556918 | | 0.4015 | | 0.528617 | | artist_hotttnesss | |---------------------| | 0.454869 | | 0.256935 | | 0.336914 | | 0.374866 | | 0.411595 | | year | |--------| | 2004 | | 0 | | 0 | | 0 | | 0 | | track_7digitalid | |--------------------| | 8486723 | | 5472456 | | 2219291 | | 1632096 | | 7522478 | | shs_perf | |------------| | -1 | | -1 | | -1 | | -1 | | -1 | | shs_work | |------------| | 0 | | 0 | | 0 | | 0 | | 0 |

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$

If you use INTEGER PRIMARY KEY column, the VACUUM does not change the values of that column. However, if you use unaliased rowid, the VACUUM command will reset the rowid values.

ROWID should never be used with foreign keys but the simple act of aliasing rowid to id (which is what happens when one does id integer primary key DDL) makes it OK.

It would be convenient if there were more options to use a string column (eg. filepath) as the PK, and be able to use it during upserts, but when creating a foreign key, to create an integer column which aliases rowid

I made an attempt to switch to integer primary keys here but it is not going well... In my usecase the path column is a business key. Yes, it should be as simple as including the id column in any select statement where I plan on using upsert but it would be nice if this could be abstracted away somehow https://github.com/chapmanjacobd/library/commit/788cd125be01d76f0fe2153335d9f6b21db1343c

https://github.com/chapmanjacobd/library/actions/runs/5173602136/jobs/9319024777

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.

e.g. in this section:

https://sqlite-utils.datasette.io/en/stable/cli.html#running-queries-directly-against-csv-or-json

The little copy button will also copy the $ which breaks the examples when copied.

Refs: - #551

:books: Documentation preview :books:: https://sqlite-utils--553.org.readthedocs.build/en/553/

https://github.com/Textualize/trogon

https://github.com/simonw/sqlite-utils/actions/runs/5039064797/jobs/9036965488

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.7.16/x64/bin/flake8", line 8, in <module> sys.exit(main()) File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/site-packages/flake8/main/cli.py", line 22, in main app.run(argv) File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/site-packages/flake8/main/application.py", line 363, in run self._run(argv) File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/site-packages/flake8/main/application.py", line 350, in _run self.initialize(argv) File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/site-packages/flake8/main/application.py", line 330, in initialize self.find_plugins(config_finder) File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/site-packages/flake8/main/application.py", line 153, in find_plugins self.check_plugins = plugin_manager.Checkers(local_plugins.extension) File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/site-packages/flake8/plugins/manager.py", line 357, in __init__ self.namespace, local_plugins=local_plugins File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/site-packages/flake8/plugins/manager.py", line 238, in __init__ self._load_entrypoint_plugins() File "/opt/hostedtoolcache/Python/3.7.16/x64/lib/python3.7/site-packages/flake8/plugins/manager.py", line 254, in _load_entrypoint_plugins eps = importlib_metadata.entry_points().get(self.namespace, ()) AttributeError: 'EntryPoints' object has no attribute 'get' Error: Process completed with exit code 1.

Refs: - #545

:books: Documentation preview :books:: https://sqlite-utils--549.org.readthedocs.build/en/549/

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.

The "least common" section is frequently uninteresting, especially for huge tables with a large number of repeated-once values.

sqlite-utils analyze-tables content.db repos --common-limit 20 --no-least

Refs #544

• [x] Documentation for CLI options
• [x] Documentation for new Python API parameters: most_common: bool and least_common: bool
• [x] Tests for CLI
• [x] Tests for Python API

Summary

By design, Table.convert() does not attempt conversion of falsey values (None, "", 0, ...). This is surprising (directly contradicts the docstring) and convert() may quietly skip cells where the user assumed a conversion would take place.

Example

Increment a column of integers by one

``` python from sqlite_utils import Database

db = Database(memory=True) table = db['table'] col = 'x' table.insert_all([{col: 0}, {col:1}]) print(table.get(1)) # 0 print(table.get(2)) # 1 print()

table.convert(col, lambda x: x+1) print(table.get(1)) # got 0, expected 1 ⚠⚠⚠ print(table.get(2)) # got 2, expected 2 ```

Another example might be, say, transforming cells containing empty string to NULL.

Discussion

This was, I think, a pragmatic choice so that consumers can skip writing guard clauses for these falsey values (particularly from the CLI). But this surprising undocumented behavior can lead to incorrect data. I don't think this is a good trade-off between convenience and correctness.

In the absence of this convenience users will either have to write guard clauses into their conversion expressions (or adapt the called function to do the same), so: python fn(value) if value else value instead of: python fn(value) This is more typing and sometimes I will forget, and there will be errors. (But they will be noisy errors, which is a good thing).

Such a change will certainly inconvenience some existing consumers; there will be some breakage. But I think this is worth it to avoid quietly not converting some values by default, which can lead to quietly bad data.

I have a PR that I will attach, please take a look and see what you think.

:books: Documentation preview :books:: https://sqlite-utils--537.org.readthedocs.build/en/537/

https://github.com/simonw/sqlite-utils/actions/runs/4920084038/jobs/8788501314 python sql = 'update [example] set [dt] = lambda_-9223371942137158589([dt]);' From: - #526

I got this error:

File "/Users/simon/Dropbox/Development/openai-to-sqlite/openai_to_sqlite/cli.py", line 27, in embeddings rows, _ = rows_from_file(input) ^^^^^^^^^^^^^^^^^^^^^ File "/Users/simon/.local/share/virtualenvs/openai-to-sqlite-jt4obeb2/lib/python3.11/site-packages/sqlite_utils/utils.py", line 305, in rows_from_file first_bytes = buffered.peek(2048).strip() ^^^^^^^^^^^^^^^^^^^ From this code: ```python

@cli.command() @click.argument( "db_path", type=click.Path(file_okay=True, dir_okay=False, allow_dash=False), ) @click.option( "-i", "--input", type=click.File("r"), default="-", ) def embeddings(db_path, input): "Store embeddings for one or more text documents" click.echo("Here is some output") db = sqlite_utils.Database(db_path) rows, _ = rows_from_file(input) print(list(rows)) `` The error went away when I changed it totype=click.File("rb")`.

This should either be called out in the documentation or rows_from_file() should be fixed to handle text-mode files in addition to binary files.

Attempting to run the example given here (without extra bracket ;-): https://sqlite-utils.datasette.io/en/stable/python-api.html#reading-rows-from-a-file ``` from sqlite_utils.utils import rows_from_file import io

rows, format = rows_from_file(io.StringIO("id,name\n1,Cleo")) print(list(rows), format)

Outputs [{'id': '1', 'name': 'Cleo'}] Format.CSV

```

Gives error ```

"c:\Program Files\Python37\python.exe" test2.py Traceback (most recent call last): File "test2.py", line 4, in <module> rows, format = rows_from_file(io.StringIO("id,name\n1,Cleo")) File "C:\Users\swood\Downloads\sqlite-utils-main-20220621\sqlite-utils-main\sqlite_utils\utils.py", line 300, in rows_from_file first_bytes = buffered.peek(2048).strip() AttributeError: '_io.StringIO' object has no attribute 'readinto' ```

I am running Python on Windows. ```

"c:\Program Files\Python37\python.exe" Python 3.7.4 (tags/v3.7.4:e09359112e, Jul 8 2019, 20:34:20) [MSC v.1916 64 bit (AMD64)] on win32 Type "help", "copyright", "credits" or "license" for more information. ```

Summary

When using the API, repeated calls to Table.convert() do not work correctly since all conversions quietly use the callable (function, lambda) from the first call to convert() only. Subsequent invocations with different callables use the callable from the first invocation only.

Example

```python from sqlite_utils import Database

db = Database(memory=True) table = db['table'] col = 'x' table.insert_all([{col: 1}]) print(table.get(1))

table.convert(col, lambda x: x*2) print(table.get(1))

def zeroize(x): return 0

zeroize = lambda x: 0

zeroize.name = 'zeroize'

table.convert(col, zeroize) print(table.get(1)) ```

Output: {'x': 1} {'x': 2} {'x': 4} Expected: {'x': 1} {'x': 2} {'x': 0}

Explanation

This is some relevant documentation.

• Table.convert() takes a Callable to perform data conversion on a column
• The Callable is passed to Database.register_function()
• Database.register_function() uses the callable's __name__ attribute for registration
• (Aside: all lambdas have a __name__ of <lambda>: I thought this was the problem, and it was close, but not quite)
• However convert() first wraps the callable by local function convert_value()
• Consequently register_function() sees name convert_value for all invocations from convert()
• register_function() silently ignores registrations using the same name, retaining only the first such registration

There's a mismatch between the comments and the code: https://github.com/simonw/sqlite-utils/blob/fc221f9b62ed8624b1d2098e564f525c84497969/sqlite_utils/db.py#L404

but actually the existing function is returned/used instead (as the "registering custom sql functions" doc I linked above says too). Seems like this can be rectified to match the comment?

Suggested fix

I think there are four things: 1. The call to register_function() from convert()should have an explicit name= parameter (to continue using convert_value() and the progress bar). 2. For functions, this name can be the real function name. (I understand the sqlite api needs a name, and it's nice if those are recognizable names where possible). For lambdas would 'lambda-{uuid}' or similar be acceptable? 3. register_function() really should throw an error on repeated attempts to register a duplicate (function, arity)-pair. 4. A test? I haven't looked at the test framework here but seems this should be testable.

See also

• 458

Fixes #525. All tests pass.

There's perhaps a better way to name lambdas? There could be a collision if a caller passes a function with name like lambda_123456.

SQLite documentation is a little, ah, lite on function name specs. If there is a character that can be used in place of underscore in a SQLite function name that is not permitted in a Python function identifier then that could be a good way to prevent accidental collisions. (I tried dash, colon, dot, no joy).

Otherwise, there is little chance of this happening and if it should happen the risk is mitigated by now throwing an exception in the case of a (name, arity) collision without replace=True.

:books: Documentation preview :books:: https://sqlite-utils--526.org.readthedocs.build/en/526/

(I originally opened this in https://github.com/simonw/datasette-insert/issues/20, but I see that that library depends on sqlite-utils)

In the case of a new row, upsert first adds the row, specifying only its pkeys: https://github.com/simonw/sqlite-utils/blob/965ca0d5f5bffe06cc02cd7741344d1ddddf9d56/sqlite_utils/db.py#L2783-L2787

This means that a table with NON NULL (or other constraint) columns that aren't part of the pkey can't have new rows upserted.

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''' ); ```

Very nice library! Our team found sqlite-utils through @simonw's comment on the "Simple declarative schema migration for SQLite" article, and we were excited to use it, but unfortunately sqlite-utils transform seems to break our DB.

Running sqlite-utils transform to modify a column mangles their DEFAULT values:

• Default string values are wrapped in extra single quotes
• Function expressions such as STRFTIME() are turned into strings!

Here are steps to reproduce:

Original database

``` $ 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')) ) ```

Modified database after sqlite-utils

``` $ sqlite3 test.db "INSERT INTO mytable DEFAULT VALUES; SELECT * FROM mytable;" foo|2022-11-02 02:26:58.038

$ 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'')' )

$ sqlite3 test.db "INSERT INTO mytable DEFAULT VALUES; SELECT * FROM mytable;" foo|2022-11-02 02:26:58.038 'foo'|STRFTIME('%Y-%m-%d %H:%M:%f', 'NOW') ```

(Related: #336)

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/

I am currently trying to import the JSON export of my data from Discord, specifically activity/reporting/events-*.json

sqlite-utils.exe insert test.db reporting events-2023-00000-of-00001.json [###################################-] 99% 00:00:00 Error: Invalid JSON - use --csv for CSV or --tsv for TSV files

Please show more information as to why this is invalid, if possible.

I am using version 3.30 with Python 3.10 on Windows 11.

I found an odd bug today, where calls to table.upsert_all don't write rows if you include the not_null kwarg.

Repro Example

```py from sqlite_utils import Database

db = Database("upsert-test.db")

db["comments"].upsert_all( [{"id": 1, "name": "david"}], pk="id", not_null=["name"], )

assert list(db["comments"].rows) # err! ```

The schema is correctly created:

sql CREATE TABLE [comments] ( [id] INTEGER PRIMARY KEY, [name] TEXT NOT NULL )

But no rows are created. Removing either the not_null kwargs works as expected, as does an insert_all call.

Version Info

• Python: 3.11.0
• sqlite-utils: 3.30
• sqlite: 3.39.5 2022-10-14

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

https://readthedocs.org/projects/sqlite-utils/builds/20512693/ ``` Running Sphinx v6.2.1

Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/latest/lib/python3.8/site-packages/sphinx/registry.py", line 442, in load_extension mod = import_module(extname) File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/latest/lib/python3.8/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1014, in _gcd_import File "<frozen importlib._bootstrap>", line 991, in _find_and_load File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 671, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 783, in exec_module File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/latest/lib/python3.8/site-packages/sphinx/builders/linkcheck.py", line 20, in <module> from requests import Response File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/latest/lib/python3.8/site-packages/requests/init.py", line 43, in <module> import urllib3 File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/latest/lib/python3.8/site-packages/urllib3/init.py", line 38, in <module> raise ImportError( ImportError: urllib3 v2.0 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with OpenSSL 1.0.2n 7 Dec 2017. See: https://github.com/urllib3/urllib3/issues/2168

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/latest/lib/python3.8/site-packages/sphinx/cmd/build.py", line 280, in build_main app = Sphinx(args.sourcedir, args.confdir, args.outputdir, File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/latest/lib/python3.8/site-packages/sphinx/application.py", line 225, in init self.setup_extension(extension) File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/latest/lib/python3.8/site-packages/sphinx/application.py", line 404, in setup_extension self.registry.load_extension(self, extname) File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/latest/lib/python3.8/site-packages/sphinx/registry.py", line 445, in load_extension raise ExtensionError(__('Could not import extension %s') % extname, sphinx.errors.ExtensionError: Could not import extension sphinx.builders.linkcheck (exception: urllib3 v2.0 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with OpenSSL 1.0.2n 7 Dec 2017. See: https://github.com/urllib3/urllib3/issues/2168)

Extension error: Could not import extension sphinx.builders.linkcheck (exception: urllib3 v2.0 only supports OpenSSL 1.1.1+, currently the 'ssl' module is compiled with OpenSSL 1.0.2n 7 Dec 2017. See: https://github.com/urllib3/urllib3/issues/2168) ```

I wanted to output newline-separated output of the first column of every row in the results - like --row but for more than one line.

Got this error while investigating: - #421

Even though I was using the LD_PRELOAD trick from https://til.simonwillison.net/sqlite/ld-preload to use a newer version of SQLite.

Originally posted by @simonw in https://github.com/simonw/sqlite-utils/issues/421#issuecomment-1098531354

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/

This also passes in the extension path when specified in GIS methods. Wherever we know an extension path, we use db.init_spatialite(find_spatialite() or load_extension).

:books: Documentation preview :books:: https://sqlite-utils--531.org.readthedocs.build/en/531/

https://sqlite-utils.datasette.io/en/2.14.1/ isn't showing a link to the stable release right now.

I should also apply the same fix I used for Datasette in: - https://github.com/simonw/datasette/issues/1608

TIL: https://til.simonwillison.net/readthedocs/link-from-latest-to-stable

This came up as a failure running tests for: - #531

Traceback on https://readthedocs.org/projects/sqlite-utils/builds/19749348/

``` File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/531/lib/python3.8/site-packages/docutils/parsers/rst/states.py", line 889, in interpreted nodes, messages2 = role_fn(role, rawsource, text, lineno, self) File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/531/lib/python3.8/site-packages/sphinx/ext/extlinks.py", line 103, in role title = caption % part TypeError: not all arguments converted during string formatting

Exception occurred: File "/home/docs/checkouts/readthedocs.org/user_builds/sqlite-utils/envs/531/lib/python3.8/site-packages/sphinx/ext/extlinks.py", line 103, in role title = caption % part TypeError: not all arguments converted during string formatting ```

Hey. Currently i do transformation with the type --type TEXT, but i noticed using the sqlalchemy based library dataset that is reading and writing differ depending on the column types TEXT, DATETIME.

Is it possible to alter a column type to DATETIME somehow using Sqlite-Utils?

Hi,

I needed to extract data in JSON Arrays to normalize data imports. I've quickly hacked the following together based on #241 which refers to #239 where you, @simonw, wrote:

Could this handle lists of objects too? That would be pretty amazing - if the column has a [{...}, {...}] list in it could turn that into a many-to-many.

They way this works in my work is that many-to-many relationships are created for anything that maps to an dictionary in a list, and many-to-one relations for everything else (assumed to be scalar values). Not sure what the best approach here would be? Are many-to-one relationships are at all useful here?

What do you think about this approach? I could try to add it to the cli interface and documentation if wanted.

Thanks for this awesome piece of software in any case! :sun_with_face:

Error code '#' supplied to 'extend-ignore' option does not match '^[A-Z]{1,3}[0-9]{0,3}$'

https://github.com/simonw/sqlite-utils/actions/runs/3662011265/jobs/6190770361

I think from this:

https://github.com/simonw/sqlite-utils/blob/e660635cea6c32f4022818380b1e1ee88e7c93a6/setup.cfg#L1-L3

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.

When I do sqlite-utils enable-fts my.db table_name column_name (with or without --fts5), I get an FTS4 virtual table instead of the expected FTS5.

FTS5 is however available and Python/SQLite versions do not seem to be the issue. I can manually create the FTS5 virtual table, and then Datasette also works with it from this same Python environment.

>>> sqlite3.version 2.6.0 >>> sqlite3.sqlite_version 3.39.4

PRAGMA compile_options; includes ENABLE_FTS5.

sqlite-utils, version 3.30.

Any ideas what's happening and how to fix?

closes #507

https://dwheeler.com/essays/fixing-unix-linux-filenames.html

:books: Documentation preview :books:: https://sqlite-utils--508.org.readthedocs.build/en/508/

https://github.com/simonw/sqlite-utils/actions/runs/3472012235 failed on Python 3.11:

Truncated output: sqlite_utils/db.py:2467: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True sqlite_utils/db.py:2467: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase sqlite_utils/db.py:2530: error: Incompatible default for argument "where" (default has type "None", argument has type "str") [assignment] sqlite_utils/db.py:2530: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True sqlite_utils/db.py:2530: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase sqlite_utils/db.py:2658: error: Argument 1 to "count_where" of "Queryable" has incompatible type "Optional[str]"; expected "str" [arg-type] Found 23 errors in 1 file (checked 51 source files) Best look at https://github.com/hauntsaninja/no_implicit_optional

My understand is that INSERT OR IGNORE will ignore when inserts would cause duplicate keys so I'm not sure exactly why the error is raised from sqlite3.

``` import argparse from pathlib import Path

from xklb import db, utils from xklb.utils import log

def parse_args() -> argparse.Namespace: parser = argparse.ArgumentParser() parser.add_argument("database") parser.add_argument("dbs", nargs="*") parser.add_argument("--upsert") parser.add_argument("--db", "-db", help=argparse.SUPPRESS) parser.add_argument("--verbose", "-v", action="count", default=0) args = parser.parse_args()

if args.db:
    args.database = args.db
Path(args.database).touch()
args.db = db.connect(args)
log.info(utils.dict_filter_bool(args.__dict__))

return args

def merge_db(args, source_db): source_db = str(Path(source_db).resolve())

s_db = db.connect(argparse.Namespace(database=source_db, verbose=args.verbose))
for table in [s for s in s_db.table_names() if not "_fts" in s and not s.startswith("sqlite_")]:
    log.info("[%s]: %s", source_db, table)
    with s_db.conn:
        data = s_db[table].rows

    with args.db.conn:
        if args.upsert:
            args.db[table].upsert_all(data, pk=args.upsert.split(","), alter=True)
        else:
            args.db[table].insert_all(data, alter=True, replace=True)

def merge_dbs(): args = parse_args() for s_db in args.dbs: merge_db(args, s_db)

if name == "main": merge_dbs()

```

``` $ lb-dev merge video.db tube_71.db --upsert path -vv SQL: INSERT OR IGNORE INTO media VALUES(?); - params: ['https://archive.org/details/088ghostofachanceroygetssackedrevengeofthelivinglunchdvdripxvidphz'] ... File ~/.local/lib/python3.10/site-packages/sqlite_utils/db.py:3122, in Table.insert_all(self, records, pk, foreign_keys, column_order, not_null, defaults, batch_size, hash_id, hash_id_columns, alter, ignore, replace, truncate, extracts, conversions, columns, upsert, analyze) 3116 all_columns += [ 3117 column for column in record if column not in all_columns 3118 ] 3120 first = False -> 3122 self.insert_chunk( 3123 alter, 3124 extracts, 3125 chunk, 3126 all_columns, 3127 hash_id, 3128 hash_id_columns, 3129 upsert, 3130 pk, 3131 conversions, 3132 num_records_processed, 3133 replace, 3134 ignore, 3135 ) 3137 if analyze: 3138 self.analyze()

File ~/.local/lib/python3.10/site-packages/sqlite_utils/db.py:2887, in Table.insert_chunk(self, alter, extracts, chunk, all_columns, hash_id, hash_id_columns, upsert, pk, conversions, num_records_processed, replace, ignore) 2885 for query, params in queries_and_params: 2886 try: -> 2887 result = self.db.execute(query, params) 2888 except OperationalError as e: 2889 if alter and (" column" in e.args[0]): 2890 # Attempt to add any missing columns, then try again

File ~/.local/lib/python3.10/site-packages/sqlite_utils/db.py:484, in Database.execute(self, sql, parameters) 482 self._tracer(sql, parameters) 483 if parameters is not None: --> 484 return self.conn.execute(sql, parameters) 485 else: 486 return self.conn.execute(sql)

IntegrityError: constraint failed

/home/xk/.local/lib/python3.10/site-packages/sqlite_utils/db.py(484)execute() 482 self._tracer(sql, parameters) 483 if parameters is not None: --> 484 return self.conn.execute(sql, parameters) 485 else: 486 return self.conn.execute(sql) ```

sqlite3 --version 3.36.0 2021-06-18 18:36:39

Reported here: https://github.com/dogsheep/healthkit-to-sqlite/issues/9

It looks like there's a default limit of 999 variables - we need to be smart about that, maybe dynamically lower the batch size based on the number of columns.

In building this Datasette feature on top of sqlite-utils I thought it might be useful to expose the number of rows that had been affected by a bulk insert or update - the cursor.rowcount:

• https://github.com/simonw/datasette/issues/1866

This isn't currently exposed by sqlite-utils.

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)

```

https://github.com/simonw/sqlite-utils/compare/3.29...defa2974c6d3abc19be28d6b319649b8028dc966

When using the convert function on a JSON column, the result of the conversion function must be a string. If the return value is either a dict (object) or a list (array), the convert call will error out with an unhelpful user defined function exception.

It makes sense that since the original column value was a string and required conversion to data structures, the result should be converted back into a JSON string as well. However, other functions auto-convert to JSON string representation, so the fact that convert doesn't could be surprising.

At least the documentation should note this requirement, because the sqlite error messages won't readily reveal the issue.

Jf only sqlite's JSON column type meant something :)

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.

https://github.com/simonw/sqlite-utils/actions/runs/3323672128/jobs/5494726927

Related: - #502

FAILED tests/test_recreate.py::test_recreate[True-True] - PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\pytest-of-runneradmin\\pytest-0\\test_recreate_True_True_0\\data.db' FAILED tests/test_recreate.py::test_recreate[False-True] - PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\pytest-of-runneradmin\\pytest-0\\test_recreate_False_True_0\\data.db'

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 ? ^^^^^^^ ^^^ ```

Failure here: https://github.com/simonw/sqlite-utils/actions/runs/3275786702/jobs/5391063221

I figured out the problem:

`diff diff --git a/docs/cli-reference.rst b/docs/cli-reference.rst index b88e38a..82b4b6c 100644 --- a/docs/cli-reference.rst +++ b/docs/cli-reference.rst @@ -112,11 +112,15 @@ See :ref:`cli_query`. --tsv Output TSV --no-headers Omit CSV headers -t, --table Output as a formatted table - --fmt TEXT Table format - one of fancy_grid, fancy_outline, - github, grid, html, jira, latex, latex_booktabs, - latex_longtable, latex_raw, mediawiki, moinmoin, - orgtbl, pipe, plain, presto, pretty, psql, rst, - simple, textile, tsv, unsafehtml, youtrack + --fmt TEXT Table format - one of asciidoc, double_grid, + double_outline, fancy_grid, fancy_outline, github, + grid, heavy_grid, heavy_outline, html, jira, + latex, latex_booktabs, latex_longtable, latex_raw, + mediawiki, mixed_grid, mixed_outline, moinmoin, + orgtbl, outline, pipe, plain, presto, pretty, + psql, rounded_grid, rounded_outline, rst, simple, + simple_grid, simple_outline, textile, tsv, + unsafehtml, youtrack --json-cols Detect JSON cols and output them as JSON, not escaped strings -r, --raw Raw output, first column of first row @@ -176,11 +180,15 @@ See :ref:`cli_memory`. --tsv Output TSV --no-headers Omit CSV headers -t, --table Output as a formatted table - --fmt TEXT Table format - one of fancy_grid, fancy_outline, - github, grid, html, jira, latex, latex_booktabs, - latex_longtable, latex_raw, mediawiki, moinmoin, - orgtbl, pipe, plain, presto, pretty, psql, rst, - simple, textile, tsv, unsafehtml, youtrack + --fmt TEXT Table format - one of asciidoc, double_grid, + double_outline, fancy_grid, fancy_outline, github, + grid, heavy_grid, heavy_outline, html, jira, + latex, latex_booktabs, latex_longtable, latex_raw, + mediawiki, mixed_grid, mixed_outline, moinmoin, + orgtbl, outline, pipe, plain, presto, pretty, + psql, rounded_grid, rounded_outline, rst, simple, + simple_grid, simple_outline, textile, tsv, + unsafehtml, youtrack --json-cols Detect JSON cols and output them as JSON, not escaped strings -r, --raw Raw output, first column of first row @@ -401,11 +409,14 @@ See :ref:`cli_search`. --tsv Output TSV --no-headers Omit CSV headers -t, --table Output as a formatted table - --fmt TEXT Table format - one of fancy_grid, fancy_outline, - github, grid, html, jira, latex, latex_booktabs, - latex_longtable, latex_raw, mediawiki, moinmoin, - orgtbl, pipe, plain, presto, pretty, psql, rst, simple, - textile, tsv, unsafehtml, youtrack + --fmt TEXT Table format - one of asciidoc, double_grid, + double_outline, fancy_grid, fancy_outline, github, + grid, heavy_grid, heavy_outline, html, jira, latex, + latex_booktabs, latex_longtable, latex_raw, mediawiki, + mixed_grid, mixed_outline, moinmoin, orgtbl, outline, + pipe, plain, presto, pretty, psql, rounded_grid, + rounded_outline, rst, simple, simple_grid, + simple_outline, textile, tsv, unsafehtml, youtrack --json-cols Detect JSON cols and output them as JSON, not escaped strings --load-extension TEXT Path to SQLite extension, with optional :entrypoint @@ -651,11 +662,14 @@ See :ref:`cli_tables`. --tsv Output TSV --no-headers Omit CSV headers -t, --table Output as a formatted table - --fmt TEXT Table format - one of fancy_grid, fancy_outline, - github, grid, html, jira, latex, latex_booktabs, - latex_longtable, latex_raw, mediawiki, moinmoin, - orgtbl, pipe, plain, presto, pretty, psql, rst, simple, - textile, tsv, unsafehtml, youtrack + --fmt TEXT Table format - one of asciidoc, double_grid, + double_outline, fancy_grid, fancy_outline, github, + grid, heavy_grid, heavy_outline, html, jira, latex, + latex_booktabs, latex_longtable, latex_raw, mediawiki, + mixed_grid, mixed_outline, moinmoin, orgtbl, outline, + pipe, plain, presto, pretty, psql, rounded_grid, + rounded_outline, rst, simple, simple_grid, + simple_outline, textile, tsv, unsafehtml, youtrack --json-cols Detect JSON cols and output them as JSON, not escaped strings --columns Include list of columns for each table @@ -689,11 +703,14 @@ See :ref:`cli_views`. --tsv Output TSV --no-headers Omit CSV headers -t, --table Output as a formatted table - --fmt TEXT Table format - one of fancy_grid, fancy_outline, - github, grid, html, jira, latex, latex_booktabs, - latex_longtable, latex_raw, mediawiki, moinmoin, - orgtbl, pipe, plain, presto, pretty, psql, rst, simple, - textile, tsv, unsafehtml, youtrack + --fmt TEXT Table format - one of asciidoc, double_grid, + double_outline, fancy_grid, fancy_outline, github, + grid, heavy_grid, heavy_outline, html, jira, latex, + latex_booktabs, latex_longtable, latex_raw, mediawiki, + mixed_grid, mixed_outline, moinmoin, orgtbl, outline, + pipe, plain, presto, pretty, psql, rounded_grid, + rounded_outline, rst, simple, simple_grid, + simple_outline, textile, tsv, unsafehtml, youtrack --json-cols Detect JSON cols and output them as JSON, not escaped strings --columns Include list of columns for each view @@ -732,11 +749,15 @@ See :ref:`cli_rows`. --tsv Output TSV --no-headers Omit CSV headers -t, --table Output as a formatted table - --fmt TEXT Table format - one of fancy_grid, fancy_outline, - github, grid, html, jira, latex, latex_booktabs, - latex_longtable, latex_raw, mediawiki, moinmoin, - orgtbl, pipe, plain, presto, pretty, psql, rst, - simple, textile, tsv, unsafehtml, youtrack + --fmt TEXT Table format - one of asciidoc, double_grid, + double_outline, fancy_grid, fancy_outline, github, + grid, heavy_grid, heavy_outline, html, jira, + latex, latex_booktabs, latex_longtable, latex_raw, + mediawiki, mixed_grid, mixed_outline, moinmoin, + orgtbl, outline, pipe, plain, presto, pretty, + psql, rounded_grid, rounded_outline, rst, simple, + simple_grid, simple_outline, textile, tsv, + unsafehtml, youtrack --json-cols Detect JSON cols and output them as JSON, not escaped strings --load-extension TEXT Path to SQLite extension, with optional @@ -768,11 +789,14 @@ See :ref:`cli_triggers`. --tsv Output TSV --no-headers Omit CSV headers -t, --table Output as a formatted table - --fmt TEXT Table format - one of fancy_grid, fancy_outline, - github, grid, html, jira, latex, latex_booktabs, - latex_longtable, latex_raw, mediawiki, moinmoin, - orgtbl, pipe, plain, presto, pretty, psql, rst, simple, - textile, tsv, unsafehtml, youtrack + --fmt TEXT Table format - one of asciidoc, double_grid, + double_outline, fancy_grid, fancy_outline, github, + grid, heavy_grid, heavy_outline, html, jira, latex, + latex_booktabs, latex_longtable, latex_raw, mediawiki, + mixed_grid, mixed_outline, moinmoin, orgtbl, outline, + pipe, plain, presto, pretty, psql, rounded_grid, + rounded_outline, rst, simple, simple_grid, + simple_outline, textile, tsv, unsafehtml, youtrack --json-cols Detect JSON cols and output them as JSON, not escaped strings --load-extension TEXT Path to SQLite extension, with optional :entrypoint @@ -804,11 +828,14 @@ See :ref:`cli_indexes`. --tsv Output TSV --no-headers Omit CSV headers -t, --table Output as a formatted table - --fmt TEXT Table format - one of fancy_grid, fancy_outline, - github, grid, html, jira, latex, latex_booktabs, - latex_longtable, latex_raw, mediawiki, moinmoin, - orgtbl, pipe, plain, presto, pretty, psql, rst, simple, - textile, tsv, unsafehtml, youtrack + --fmt TEXT Table format - one of asciidoc, double_grid, + double_outline, fancy_grid, fancy_outline, github, + grid, heavy_grid, heavy_outline, html, jira, latex, + latex_booktabs, latex_longtable, latex_raw, mediawiki, + mixed_grid, mixed_outline, moinmoin, orgtbl, outline, + pipe, plain, presto, pretty, psql, rounded_grid, + rounded_outline, rst, simple, simple_grid, + simple_outline, textile, tsv, unsafehtml, youtrack --json-cols Detect JSON cols and output them as JSON, not escaped strings --load-extension TEXT Path to SQLite extension, with optional :entrypoint diff --git a/docs/cli.rst b/docs/cli.rst index 8bc4176..1d67e88 100644 --- a/docs/cli.rst +++ b/docs/cli.rst @@ -187,10 +187,15 @@ Available--fmtoptions are: cog.out("\n" + "\n".join('-{}``'.format(t) for t in tabulate.tabulate_formats) + "\n\n") .. ]]]

+- asciidoc +- double_grid +- double_outline - fancy_grid - fancy_outline - github - grid +- heavy_grid +- heavy_outline - html - jira - latex @@ -198,15 +203,22 @@ Available --fmt options are: - latex_longtable - latex_raw - mediawiki +- mixed_grid +- mixed_outline - moinmoin - orgtbl +- outline - pipe - plain - presto - pretty - psql +- rounded_grid +- rounded_outline - rst - simple +- simple_grid +- simple_outline - textile - tsv - unsafehtml ```

The --flatten implementation isn't currently available to Python code - people have to roll their own implementation. Feedback from a conversation at DjangoCon.

I was wondering why my all my databases were giving wild search results. Turns out create_trigger was not sticking!

Running sqlite-utils triggers x.db shows [] after running enable-fts using the python api. Looking at the counts trigger it seems that is the right way to save triggers. triggers show up now

:books: Documentation preview :books:: https://sqlite-utils--498.org.readthedocs.build/en/498/

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])

I'm using just a lot know, based on this file - I should add that to https://sqlite-utils.datasette.io/en/latest/contributing.html

https://github.com/simonw/sqlite-utils/blob/afbd2b2cba45cccb305c3d4638d18db4dd3d4bbd/Justfile#L1-L24

With the addition of --functions in: - #471

In addition to the existing convert command, there are now very good reasons to want to install additional packages into the same virtual environment as sqlite-utils itself, to allow them to be used with those features.

This isn't easy if you installed the tool with pipx or brew install sqlite-utils.

Datasette solved this problem with the datasette install command:

• https://github.com/simonw/datasette/issues/925

sqlite-utils could benefit from the same idea.

I was looking into how to parse application log files that contain multiline text (e.g. Java stack traces) into sqlite. I can see that at the moment --lines helps, but falls short when processing multi-line texts.

I wonder if this functionality would be useful for sqlite-utils. A similar approach to Elastic logstash/filebeat can be adopted: https://www.elastic.co/guide/en/beats/filebeat/current/multiline-examples.html

Potential changes:

• add a --multiline option
• additional properties for
• multiline-pattern (regex expression)
• multiline-negate: true/false
• multiline-what: previous or next

Or if this is achievable in a different way, please share. Thanks!

:books: Documentation preview :books:: https://sqlite-utils--486.org.readthedocs.build/en/486/

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