chore(lapis-docs): bump axios from 1.8.1 to 1.8.4 in /lapis-docs

[dependabot]

Bumps axios from 1.8.1 to 1.8.4.

Release notes

Sourced from axios's releases.

Release v1.8.4

Release notes:

Bug Fixes

• buildFullPath: handle allowAbsoluteUrls: false without baseURL (#6833) (f10c2e0)

Contributors to this release

• Marc Hassan

Release v1.8.3

Release notes:

Bug Fixes

• add missing type for allowAbsoluteUrls (#6818) (10fa70e)
• xhr/fetch: pass allowAbsoluteUrls to buildFullPath in xhr and fetch adapters (#6814) (ec159e5)

Contributors to this release

• Ashcon Partovi
• StefanBRas
• Marc Hassan

Release v1.8.2

Release notes:

Bug Fixes

• http-adapter: add allowAbsoluteUrls to path building (#6810) (fb8eec2)

Contributors to this release

• Fasoro-Joseph Alexander

Changelog

Sourced from axios's changelog.

1.8.4 (2025-03-19)

Bug Fixes

• buildFullPath: handle allowAbsoluteUrls: false without baseURL (#6833) (f10c2e0)

Contributors to this release

• Marc Hassan

1.8.3 (2025-03-10)

Bug Fixes

• add missing type for allowAbsoluteUrls (#6818) (10fa70e)
• xhr/fetch: pass allowAbsoluteUrls to buildFullPath in xhr and fetch adapters (#6814) (ec159e5)

Contributors to this release

• Ashcon Partovi
• StefanBRas
• Marc Hassan

1.8.2 (2025-03-07)

Bug Fixes

• http-adapter: add allowAbsoluteUrls to path building (#6810) (fb8eec2)

Contributors to this release

• Fasoro-Joseph Alexander

Commits

• 9f6f97b chore(release): v1.8.4 (#6844)
• f10c2e0 fix(buildFullPath): handle allowAbsoluteUrls: false without baseURL (#6833)
• 1e6632c chore(deps): bump tj-actions/changed-files in the github-actions group (#6838)
• 39ec206 chore(release): v1.8.3 (#6819)
• 10fa70e fix: add missing type for allowAbsoluteUrls (#6818)
• 7821ef9 docs: update readme to include bun install (#6811)
• ec159e5 fix(xhr/fetch): pass allowAbsoluteUrls to buildFullPath in xhr and `fet...
• a9f7689 chore(release): v1.8.2 (#6812)
• fb8eec2 fix(http-adapter): add allowAbsoluteUrls to path building (#6810)
• 9812045 chore(sponsor): update sponsor block (#6804)
• Additional commits viewable in compare view

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Name	Status	Preview	Comments	Updated (UTC)
lapis	✅ Ready (Inspect)	Visit Preview	💬 Add feedback	Apr 22, 2025 9:37am

[github-actions]

This is a preview of the changelog of the next release. If this branch is not up-to-date with the current main branch, the changelog may not be accurate. Rebase your branch on the main branch to get the most accurate changelog.

Note that this might contain changes that are on main, but not yet released.

Changelog:

0.5.0 (2025-04-22)

⚠ BREAKING CHANGES

• lapis: No longer support .* wildcard in advanced queries. Use ? syntax instead.
• lapis: use dot symbol as string search regex separator
• lapis2: throw exception on invalid variant query Maybe operator is case sensitive (in contrast to SQL and my naive user expectation) #797
• lapis2: read data from SILO as NDJSON

Features

• add /sample to query paths #501 (7ad9746)
• add access key parameter to /sample/info and remove downloadAsFile (340f2ac)
• add config generator page (45c9827)
• add info controller (78f9c69)
• add info to lapis response (afff4ae)
• add sample to info route (b703a9c)
• add unaligned nucleotide sequence route (adda1dc)
• allow loweer case for mutations (caa8713)
• allow lower case for genes in variant queries (5434e49)
• allow lower case for insertions (79c9f2d)
• allow lower case for segments and genes (74b41bb)
• allow lower case letters for mutations and insertions in variant queries (fe3f8da)
• allow string arrays as filter for string and pango lineage fields #507 (4d06713)
• allow that fields only contains the primary key in protected mode #623 (0ac0709)
• also get database config from info controller as YAML (cd6536d)
• amino acid and nucleotide insertion filters are case-insensitive (667f487)
• change content type to text/plain when asking for csv/tsv without headers #930 (8313996)
• docs: add LAPIS host to query Url #522 (305e91c)
• docs: add more important parts of the arc42 docs #535 (13644e4)
• docs: database config spec #561 (a1c21d9)
• docs: description of references/fields #604 (5b02ca8)
• docs: document how to provide data to the SILO preprocessing #565 (2e0080d)
• docs: document that there is a cache now #137 (88906a4)
• docs: generate correct URLs for nucleotide sequences endpoints in multi-segmented case #521 (6058b99)
• docs: implement order by, limit and offset in query generator #524 (6995d28)
• docs: improve introduction with ChatGPT #561 (e026ccd)
• docs: improve reference/filters #604 (31bb706)
• docs: list valid nucleotide and amino acid symbols #573 (35ccf58)
• docs: move architecture docs to Starlight docs #530 (a663067)
• docs: reference how to start LAPIS and SILO #569 #570 (0cc0d40)
• docs: references/additional-request-properties #604 (837e474)
• docs: separate maintainer docs from user docs #561 (98a9e30)
• docs: transfer ambiguous symbols explanation #551 (066f5b6)
• docs: transfer lapis and silo tutorial #547 (db4932d)
• docs: update mutation filters to reflect the reference genomes (03079d7)
• fix authentication, don't document authentication for now #553 (f593073)
• forward Retry-After header when SILO is not available yet #667 (62bcc7c)
• implement a request cache for mutation and insertion queries #137 (17ff89c)
• implement a request id to trace requests #586 (194e7fd)
• implement compressing the response as zstd and gzip #600 (d6e8d9d)
• implement downloadAsFile #599 (c522296)
• implement leftover variant query parts #498 (556552f)
• implement maybe mutation filters #551 (fab1c72)
• implement the header parameter "headers=false" to disable the header in the returned CSV/TSV #624 (a216e0c)
• include link to GitHub issues in LapisInfo #692 (ea42ac2)
• lapis-docs: document string search feature (ae098a9)
• lapis-docs: mark sections of the docs that are generated from the config (b2009eb), closes #928
• lapis2-docs: document url encoded forms (8c3ba60), closes #765
• lapis2: allow filtering for null (f680305)
• lapis2: clear cache when SILO is restarting (6100bff)
• lapis2: delete insertions metadata types #804 (dd0ecd1)
• lapis2: implement boolean columns (7718b4f), closes #740
• lapis2: make "maybe" mutation queries case-insensitive #797 (0af9c7f)
• lapis2: read data from SILO as NDJSON (767b19d), closes #741
• lapis2: stream data from SILO (8fcf360), closes #744
• lapis2: support url encoded form POST requests (f2f62b1), closes #754
• lapis2: use entrypoint.sh to allow passing JVM_OPTS through env variable (#823) (9b35b8a), closes #821
• lapis: abort on startup when silo url has invalid syntax (373d662), closes #939
• lapis: adapt to new generalized lineage system (508bc8e), closes #961
• lapis: add fields property to mutation endpoints (#1149) (4d8df3a), closes #1092
• lapis: add siloVersion to response info (#1066) (c1edcf3)
• lapis: add healthcheck to Docker containers (0944990), closes #813
• lapis: add instance name to landing page json (6c5f81b)
• lapis: add LAPIS version to info response (#1019) (7d8d713)
• lapis: allow customizable filename for file downloads (817d3f4), closes #869
• lapis: auto remove entries from cache when heap limit is reached (f804004)
• lapis: expose the lineage definition files used by SILO (#1073) (2ac977c), closes #1034
• lapis: hint to which regex syntax is used in Swagger docs (ca4fcdc), closes #903
• lapis: implement landing page when calling / #856 (b886b7d)
• lapis: make it possible to fetch sequences in JSON and NDJSON format (ba18956), closes #971
• lapis: omit sequences with null values in unaligned fasta downloads (f1931a6), closes #912
• lapis: only allow regex search for fields that have lapisAllowsRegexSearch: true configured (d146717), closes #898
• lapis: order CSV/TSV columns of aggregated/details data as specified in the request fields or as in the database config (6cf8704), closes #910
• lapis: pass through coverage from SILO in mutation endpoints (#1094) (ed90514), closes #1091
• lapis: regex filtering for string columns #898 (b3e7775)
• lapis: return empty lineage definitions when SILO returns an empty file (#1126) (64651ad)
• lapis: stream JSON responses (#1053) (bfb5f99), closes #1047
• lapis: throw error when filtering by "equals" and "regex" for the same string field (540d63a), closes #899
• lapis: use dot symbol as regex separator #908 (3728c7e)
• lapis: validate that lapisAllowsRegexSearch-fields are of type string (97b3ce9)
• lapis: validate that metadata fields do not contain the reserved character . (97b3ce9), closes #976
• log to files again (additionally to stdout) #692 (1acedad)
• log whether request was cached #717 (3de90f1)
• make fields case-insensitive #502 (45e931e)
• make headers accessible to browser despite CORS (4877c04)
• pass request id to SILO (901e08a)
• provide full reference genome, and database config to new endpoints (e406023)
• return bad request error when unknown compression format in request #647 (decaea5)
• return structured mutation and insertion responses #718 (af38e93)
• set Content-Type header to application/gzip|zstd when the compression property in the request was set #665 (5592857)
• show instance name on "not found" page (4e444f1)
• support order by random #658 (598b05f)
• try whether also caching aggregated queries makes cov spectrum faster (bbfaf22)
• use multiple access keys (3ecc11a)

Bug Fixes

• add info route to endpoints that server aggregated data to allow access (5b10e2b)
• allow access in authorized mode when fields is specified non-fine-grained (eaa832c)
• allow stop codon symbol for AminoAcidMutations (74cfa74)
• consider context path in Swagger UI link (4b12b53)
• consider only servlet URL when checking auth (0006ac2)
• consider only servlet URL when checking auth behind a proxy (6b1767a)
• details does no longer return insertions (3686658)
• docs: display everything on the mutation filters page (d912f59)
• docs: schema for uploaded config (ecd2f9c)
• docs: some minor improvements (c77bf6f)
• don't set Transfer-Encoding twice #600 (7e49aa5)
• don't store logs in files #405 (1ca90f7)
• e2e tests with new silo ordering of insertions and mutations (4a75342)
• end to end tests failing due to timeout and new pango lineage alias in return (d265809)
• exact n of query with more elements than n (1402019)
• file ending when downloading compressed file #685 (6a51de0)
• import of property (848f4b6)
• lapis-docs: allow all hosts (#1129) (d0ea4e2), closes #1124
• lapis-docs: config generator: dateToSortBy, partitionBy and features is optional (4e905e8)
• lapis-docs: fix link on landing page (d4137b3)
• lapis-docs: mention how arrays must be supplied in form urlencoded requests (#1128) (4f24a76), closes #1089
• lapis-docs: Sequence file naming scheme uses indexes now not names (1e7cd60)
• lapis2-docs: relative links must not end with a / (992210d)
• lapis2-docs: use relative links so that they work when deployed behind a proxy #725 (0cfa8ec)
• lapis2: also log which line of the SILO response failed to parse (d1badea)
• lapis2: bring back request id header in OpenAPI docs (eb75391), closes #627
• lapis2: log request id again (26f83c9)
• lapis2: only accept a single variant query in a request #798 (54df8e5)
• lapis2: prefer zstd over gzip #738 (1fb67ac)
• lapis2: throw exception on invalid variant query #797 (980806a)
• lapis: add missing dataFormat to amino acid mutation GET endpoint in Swagger UI (#1160) (5c4dbe2), closes #1159
• lapis: also return CSV header when there are no data (#1138) (aba1320), closes #1090
• lapis: don't show the single segmented sequence download when there are no nucleotide sequences (#1054) (f27f94b)
• lapis: fix computation of downloaded file ending with multiple accept headers (3b679a8), closes #890
• lapis: fix description of mutation objects in OpenApi spec (#1051) (c6f625e)
• lapis: fix download file ending for csv-without-headers data format (65afba0), closes #871
• lapis: get rid of logger config deprecation warnings in the log (e7c3908), closes #972
• lapis: never show whitelabel error page (eb03345), closes #890
• lapis: nucleotideInsertionContains correctly handles segment (4776a3e)
• lapis: only keep old log files for 30 days (#1111) (66952c5)
• lapis: pass correctly escaped stop codon to SILO (be1bb87), closes #1105
• lapis: reject unknown data formats (#1093) (b1cc7fd), closes #1078
• lapis: return proper error message when lineage definition from SILO is invalid YAML (#1117) (cdf9b63), closes #1104
• make stop codon a valid symbolFrom for amino acid mutations (43e5e9e)
• orderBy is an array (0260036)
• recognition of which endpoint was called to determine the filename of a download (6c1674c)
• reduce log level when unable to read from cached request (6810696)
• remove header output from mutations and insertion endpoints (ffd6b55)
• remove request id header -> make Swagger UI work again #610 (0afa2a5)
• return valid gzip when LAPIS returns an error response #656 (db1c6cb)
• Sending unknown value in fields returns incomprehensible error (107396d)
• set default min proportion (d033b34)
• speed up compressing responses #717 (1624580)
• test #685 (f52d68d)
• update e2e tests: deletions are also mutations (from SILO) (886a8f1)
• use authorization filter before other filters #660 (0dab1e7)
• variant query with nextcladePangolineageQuery (9158575)
• write empty string to CSV/TSV for null values #708 (c8872ba)

[fengelniederhammer]

@dependabot merge