commit 4f25aa65
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Sat Aug 2 13:04:35 2025 +0200

    [CI] sudo with chown at the end of tests

commit a4d26226
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Sat Aug 2 06:55:27 2025 +0200

    [CI] no /root/.config needed

commit 1f8eaa0b
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Aug 1 21:27:01 2025 +0200

    [CI] more permission fixes

commit c4d9b175
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Aug 1 20:43:09 2025 +0200

    [CI] more permission fixes for gitlab-ci

commit f85213fd
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Aug 1 19:34:35 2025 +0200

    [CI] add sudo to dockerfile, change dir owner in CI

commit f14c6246
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Aug 1 08:42:32 2025 +0200

    [CI] modify dockerfile to build with test user

commit 1670cc4a
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 31 19:20:10 2025 +0200

    [CI] add verbose=2 for testing to check what is happening with CI timeouts

commit 210ba723
Merge: 1a213aeb 27192b88
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 31 09:22:52 2025 +0200

    Merge branch 'dev' into 483-dev-corenlp-in-nix-flake

commit 1a213aeb
Merge: d7aa1301 61aac410
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Jul 29 18:58:07 2025 +0200

    Merge branch 'dev' into 483-dev-corenlp-in-nix-flake

commit d7aa1301
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Jul 25 09:57:38 2025 +0200

    [CI] one more try to fix nix permission

commit b45e16eb
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Jul 11 07:24:53 2025 +0200

    [CI] writable permissions for nix db

commit 50f13d32
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 10 16:34:01 2025 +0200

    [CI] attempt at fixing nix db permissions

commit 76c1b9a6
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 10 14:44:55 2025 +0200

    [CI] fix /nix dir permissions

    Apparently, this is needed to run 'nix' inside tests (e.g. start corenlp)

commit 7edb97af
Merge: 19e752b8 64e2a689
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 10 11:56:04 2025 +0200

    Merge branch 'dev' into 483-dev-corenlp-in-nix-flake

commit 19e752b8
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 10 11:47:58 2025 +0200

    [tests] better startup of corenlp

    Take into account the async nature of createProcess. Add proper watch
    so that we monitor that coreNLP is running.

commit bde033f9
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 10 10:47:36 2025 +0200

    [nix] fix stdenv to be gcc 14, not 13

commit 1d4ceb07
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 10 07:03:15 2025 +0200

    [nix] add openblas as a dependency

commit 9dd4ebc3
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jul 9 14:44:28 2025 +0200

    [update-project-dependencie]

commit 120e205c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jul 9 12:50:38 2025 +0200

    [corenlp] some fixes to Dockerfile

commit 3a2b2079
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 3 19:21:37 2025 +0200

    [dockerfile] add fontconfig, to see if this is what causes errors on CI

    E.g.:
    https://gitlab.iscpif.fr/gargantext/haskell-gargantext/-/jobs/18643

    paginating QuantumComputing corpus works (MapTerms):            Fontconfig error: Cannot load default config file: No such file: (null)
    Fontconfig error: No writable cache directories

commit d9d4a09c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Jul 3 14:02:30 2025 +0200

    [nix] don't use experimental features for corenlp nix call

    Also, update Dockerfile with patched `nix.conf`

commit 5ccb44bb
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jul 2 21:05:47 2025 +0200

    [test] fix calling of nix flakes

commit 1adc512e
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Jul 2 19:42:29 2025 +0200

    [nix] move corenlp to separate flake in core-nix repo

    #483

This can be derived from 'url' setting already.

This is used mainly to specify at which port the server will listen.

The 'url' param is the external URL (sometimes it's needed for the
server to know where it is hosted, e.g. when sending out emails).

This commit refactors the flow code to generate the ngrams for
the master docs separately, and then it "commits" them later after such
docs have been associated with a `Node`.

Route implements Ord so no need to import Internal stuff

Now it is required to specify port in `frontend.url`.

The `-p` port flag was removed from CLI server.

Related to
#465

This commit uses the `race` function from the async library to fix a bug
where exceptions raised from the server async wouldn't be caught by the
top-level code.

The bug was stemming from the fact that `runAllWorkers` is **blocking**,
despite its usage of `forConcurrently_`. Therefore we were never
actually running the `wait` function below, but rather we were hanging
waiting on the result of the first function.

As a result the server could die but the workers could keep the main
thread alive, causing the bug we just saw as part of #463.

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.

Related to
#444

The rationale behind this is that we don't want to pollute worker job
queue with large file blobs. Instead, upon API request, we create a
pg_largeobject and use that in worker. After job is finished (with
error or not), the object is removed.

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.

It wasn't used anyways.

Those definitions felt very ad hoc, and were not used a lot in the
codebase, so I simply replaced them with their definition.

Also, removed some old job stuff