This commit introduces/improves the `parseTvsWithDiagnostics`
function to parse the input TSV incrementally, collecting errors
as we go, and eventually reporting them upstream via the newly
added `emitTsvParseWarning` function.

Furthermore, the env var we used to override (in some parts) the logging
level from `LOG_LEVEL`  to `GGTX_LOG_LEVEL`, to avoid the env var
`LOG_LEVEL` clashing with some other service.

This will eventually allow us to properly override the logging level in
the tests, silencing non interesting stuff.

commit be879b1e
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jan 30 18:22:44 2025 +0100

    [ngrams] code fixes according to review

    Related MR:
    !378

commit bf89561b
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jan 22 21:11:47 2025 +0100

    [test] notification on node move

    Also, some small refactorings.

commit 3d5d74ab
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jan 22 20:13:44 2025 +0100

    [tests] add notifications func comment, fix core/notifications indent

commit b8ea3af2
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jan 22 19:13:35 2025 +0100

    [update-project-dependencies]

commit 1217baf4
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jan 22 19:09:17 2025 +0100

    [tests] notifications: test async notifications for update tree

    Related to
    #418

commit 874785e9
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 21 06:06:27 2025 +0100

    [refactor] unify Database & ExternalIDs

    These types are the same, except for Database.Empty

    I managed to have backwards compatibility with the frontend format,
    hence the frontend doesn't need any changes.

commit e7b16520
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 21 06:05:57 2025 +0100

    [cabal] upgrade haskell-bee to fix TSRetry and ESRepeat issues

commit ad045ae0
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Jan 20 06:32:49 2025 +0100

    [cabal] upgrade haskell-bee tag

commit b3910bb4
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 14 10:56:12 2025 +0100

    [test] move some Arbitrary instances to Test/Instances.hs

commit bb282d02
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 14 09:17:23 2025 +0100

    [test] WithQuery offline test (with EPO constructor)

commit c0fe2e51
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 14 06:59:45 2025 +0100

    [query] move EPO user/token into the datafield

    This simplifies the WithQuery structure even more

commit 93586adc
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Jan 13 17:45:42 2025 +0100

    [tests] fix WithQuery frontend serialization test

    Also, add WithQuery pubmed test (with api_key)

commit bc29319c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Jan 13 10:13:15 2025 +0100

    [ngrams] simplify WithQuery json structure

    There is now only a 'datafield' field, no need for duplicated
    'database'.

    Related to #441

commit e6fdbee4
Merge: 95dc32b3 13457ca8
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Jan 10 12:03:59 2025 +0100

    Merge branch 'dev' into 224-dev-understanding-ngrams

commit 95dc32b3
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 7 20:01:11 2025 +0100

    [ngrams] refactor PubMed DB type (to include Maybe APIKey)

commit baa2491f
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 7 18:09:04 2025 +0100

    [refactor] searx search refactoring

commit fcf83bf7
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jan 7 11:14:03 2025 +0100

    [ngrams] more types annotations

commit 0d8a77c4
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 16:15:07 2024 +0100

    [ngrams, test] refactor: Count -> Terms

commit 85f1dffe
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 14:35:05 2024 +0100

    [ngrams] refactor opaque Int into TermsWeight newtype

commit a81ea049
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 14:34:39 2024 +0100

    [CLI] fix limit removal

    It wasn't used anyways.

commit d1dfbf79
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 11:35:41 2024 +0100

    [ngrams] one more simplification in ngramsByDoc'

commit fcb48b8f
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 11:33:33 2024 +0100

    [ngrams] some more simplification of ngramsByDoc'

commit ab7c1766
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 30 11:00:19 2024 +0100

    [ngrams, tests] understanding ngramsByDoc better

commit 35c2d0b0
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 23 21:20:29 2024 +0100

    [ngrams] small simplification to docNgrams function

commit 161ac077
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Mon Dec 23 18:35:59 2024 +0100

    [ngrams] annotate types of ngrams algorithms

commit 08c7c91c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Sat Dec 21 09:45:00 2024 +0100

    [ngrams] improve function documentation, add types, add unit tests

    I want to understand ngrams algorithms better.

Related to
#433

Textual formats often have either encoding or column errors.

This is a common issue, see e.g.
https://duckdb.org/docs/data/csv/reading_faulty_csv_files.html

We just ignore them.

There is now only a 'datafield' field, no need for duplicated
'database'.

Related to #441

Maybe this will fix notifications for job finish

Start worker in tests

commit 27413399
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 15 16:17:10 2024 +0200

    [VERSION] +1 to 0.0.7.3.3

commit f1d6a083
Merge: 0143f243 afdbe31d
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 15 15:45:40 2024 +0200

    Merge remote-tracking branch 'origin/improve-onboarding-experience' into dev

commit 0143f243
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 14 13:45:12 2024 +0200

    Fix step1c again

commit 43901901
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 14 12:39:43 2024 +0200

    Fix bug in GargPorter implementation

commit d44831d0
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 14 10:50:31 2024 +0200

    Introduce SpecContext, replicate search issue

    This commit refactors the test code ever so slightly to add a proper
    type called `SpecContext` rather than anonymous pairs to carry around
    the spec context/data. It also replicates the search problem around #415
    via a test.

commit b4260d9b
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 14 09:11:51 2024 +0200

    Add soysauce docs list to test-data

commit afdbe31d
Author: Grégoire Locqueville <gregoire.locqueville@cnrs.fr>
Date:   Thu Oct 10 18:51:46 2024 +0200

    Improve onboarding experience

    Edited the README to have a linear path to installation.
    Also made scripts to run the executables without having to worry
    whether they are on our path.

commit 3030272d
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Thu Oct 10 18:31:19 2024 +0200

    [VERSION] +1 to 0.0.7.3.2

commit bd33dd6c
Merge: 1d3417d9 592d966c
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Thu Oct 10 18:10:51 2024 +0200

    Merge remote-tracking branch 'origin/dev-websockets-node-update' into dev

commit 592d966c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Oct 10 18:06:20 2024 +0200

    [notifications] add missing test/Test/Core/Notifications.hs

commit 1d3417d9
Merge: 163304df a48fe0c8
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Thu Oct 10 17:54:39 2024 +0200

    Merge remote-tracking branch 'origin/dev-websockets-node-update' into dev

commit a48fe0c8
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Oct 10 10:01:10 2024 +0200

    [ws] rename AsyncUpdates to Notifications

    This is bit more clear

commit cd831db4
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Oct 9 16:00:48 2024 +0200

    [tests] first working notification test

commit 81af005d
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Oct 9 11:05:11 2024 +0200

    Squashed commit of the following:

    commit 163304df
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 18:39:54 2024 +0200

        [FIX] conflict

    commit 82c68074
    Merge: f7b76918 5623161c
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 18:28:55 2024 +0200

        Merge remote-tracking branch 'origin/dev-websockets-node-update' into dev

    commit f7b76918
    Merge: fe7a92cc 88655f68
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 18:28:53 2024 +0200

        [FIX] conflicts

    commit fe7a92cc
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 17:19:53 2024 +0200

        fix: no longer update graphs and phylos on corpus update

    commit f775d4a3
    Merge: 76b557ea d2f4b89d
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 16:27:53 2024 +0200

        Merge remote-tracking branch 'origin/dev-guidelines-update' into dev

    commit 76b557ea
    Merge: 2925d008 50c77ea2
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 16:27:27 2024 +0200

        Merge remote-tracking branch 'origin/304-dev-pubmed-api-not-in-toml' into dev

    commit d2f4b89d
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 15:37:54 2024 +0200

        DEVELOPER_GUIDELINES: update about git amend

        This is the result of Autumn workshop 2024

    commit 50c77ea2
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 15:15:28 2024 +0200

        [notifications] fix for send

        sendNonblocking threw an error initially. I just do a compromise and
        timeout the normal send (which blocks infinitely sometimes)

    commit 025b80b6
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 14:10:56 2024 +0200

        [docker] fix network: host, fix caddyfile

    commit 2925d008
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 10:34:17 2024 +0200

        fix arbitrary instance

    commit e8fb3db6
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 10:13:40 2024 +0200

        fix: re-add lost instances

    commit b86d2e61
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 10:09:18 2024 +0200

        [toml] remove pubmed api key from config

        It's set up in user settings instead and has been for a long time.

    commit c06de5ef
    Merge: ab710337 a0ec337b
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 09:35:55 2024 +0200

        Merge remote-tracking branch 'gitlab/dev' into cm/update-corpus-button

    commit ab710337
    Author: Christian Merten <christian@merten.dev>
    Date:   Fri Apr 26 22:32:33 2024 +0200

        feat: update corpus endpoint

commit d4a9200e
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Oct 9 11:01:43 2024 +0200

    [ws] notification action on node share

commit 163304df
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 18:39:54 2024 +0200

    [FIX] conflict

commit 82c68074
Merge: f7b76918 5623161c
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 18:28:55 2024 +0200

    Merge remote-tracking branch 'origin/dev-websockets-node-update' into dev

commit f7b76918
Merge: fe7a92cc 88655f68
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 18:28:53 2024 +0200

    [FIX] conflicts

commit 5623161c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 18:18:23 2024 +0200

    [ws] implement node update (rename, move) with notifications to parents

commit 88655f68
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 18:05:25 2024 +0200

    Squashed commit of the following:

    commit f775d4a3
    Merge: 76b557ea d2f4b89d
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 16:27:53 2024 +0200

        Merge remote-tracking branch 'origin/dev-guidelines-update' into dev

    commit 76b557ea
    Merge: 2925d008 50c77ea2
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 16:27:27 2024 +0200

        Merge remote-tracking branch 'origin/304-dev-pubmed-api-not-in-toml' into dev

    commit d2f4b89d
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 15:37:54 2024 +0200

        DEVELOPER_GUIDELINES: update about git amend

        This is the result of Autumn workshop 2024

    commit 50c77ea2
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 15:15:28 2024 +0200

        [notifications] fix for send

        sendNonblocking threw an error initially. I just do a compromise and
        timeout the normal send (which blocks infinitely sometimes)

    commit 025b80b6
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 14:10:56 2024 +0200

        [docker] fix network: host, fix caddyfile

    commit 2925d008
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 10:34:17 2024 +0200

        fix arbitrary instance

    commit e8fb3db6
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 10:13:40 2024 +0200

        fix: re-add lost instances

    commit b86d2e61
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 10:09:18 2024 +0200

        [toml] remove pubmed api key from config

        It's set up in user settings instead and has been for a long time.

    commit c06de5ef
    Merge: ab710337 a0ec337b
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 09:35:55 2024 +0200

        Merge remote-tracking branch 'gitlab/dev' into cm/update-corpus-button

    commit ab710337
    Author: Christian Merten <christian@merten.dev>
    Date:   Fri Apr 26 22:32:33 2024 +0200

        feat: update corpus endpoint

commit fe7a92cc
Author: Christian Merten <christian@merten.dev>
Date:   Tue Oct 8 17:19:53 2024 +0200

    fix: no longer update graphs and phylos on corpus update

commit f775d4a3
Merge: 76b557ea d2f4b89d
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 16:27:53 2024 +0200

    Merge remote-tracking branch 'origin/dev-guidelines-update' into dev

commit 76b557ea
Merge: 2925d008 50c77ea2
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 16:27:27 2024 +0200

    Merge remote-tracking branch 'origin/304-dev-pubmed-api-not-in-toml' into dev

commit d2f4b89d
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 15:37:54 2024 +0200

    DEVELOPER_GUIDELINES: update about git amend

    This is the result of Autumn workshop 2024

commit 50c77ea2
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 15:15:28 2024 +0200

    [notifications] fix for send

    sendNonblocking threw an error initially. I just do a compromise and
    timeout the normal send (which blocks infinitely sometimes)

commit 025b80b6
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 14:10:56 2024 +0200

    [docker] fix network: host, fix caddyfile

commit ee0db8c1
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 12:39:12 2024 +0200

    [nix] add nanomsg to nix pkgs

    Also, fix ./start to use gargantext-settings.toml

commit 2925d008
Author: Christian Merten <christian@merten.dev>
Date:   Tue Oct 8 10:34:17 2024 +0200

    fix arbitrary instance

commit e8fb3db6
Author: Christian Merten <christian@merten.dev>
Date:   Tue Oct 8 10:13:40 2024 +0200

    fix: re-add lost instances

commit b86d2e61
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 10:09:18 2024 +0200

    [toml] remove pubmed api key from config

    It's set up in user settings instead and has been for a long time.

commit c06de5ef
Merge: ab710337 a0ec337b
Author: Christian Merten <christian@merten.dev>
Date:   Tue Oct 8 09:35:55 2024 +0200

    Merge remote-tracking branch 'gitlab/dev' into cm/update-corpus-button

commit ab710337
Author: Christian Merten <christian@merten.dev>
Date:   Fri Apr 26 22:32:33 2024 +0200

    feat: update corpus endpoint

This commit refactors the test code ever so slightly to add a proper
type called `SpecContext` rather than anonymous pairs to carry around
the spec context/data. It also replicates the search problem around #415
via a test.

Now everything is in Core/Config

Also, tests pass now, locally

While doing this, I have also fixed a bug in the current implementation
of ThrowAll (formerly named `throwAll'`).