v0.2.6

0.2.6 (2024-07-18)

Features

• lapis: auto remove entries from cache when heap limit is reached (f804004)

v0.2.5

0.2.5 (2024-07-11)

Features

• lapis: implement landing page when calling / #856 (b886b7d)

v0.2.4

0.2.4 (2024-06-24)

Bug Fixes

• lapis-docs: config generator: dateToSortBy, partitionBy and features is optional (4e905e8)

v0.2.3

0.2.3 (2024-06-19)

Bug Fixes

• lapis: nucleotideInsertionContains correctly handles segment (4776a3e)

v0.2.2

0.2.2 (2024-05-29)

Features

• lapis2: use entrypoint.sh to allow passing JVM_OPTS through env variable (#823) (9b35b8a), closes #821

v0.2.1

0.2.1 (2024-05-27)

Features

• lapis2: delete insertions metadata types #804 (dd0ecd1)

v0.2.0

0.2.0 (2024-05-23)

⚠ BREAKING CHANGES

• lapis2: throw exception on invalid variant query #797

Features

• lapis2: clear cache when SILO is restarting (6100bff)
• lapis2: make "maybe" mutation queries case-insensitive #797 (0af9c7f)

Bug Fixes

• lapis2-docs: relative links must not end with a / (992210d)
• 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: throw exception on invalid variant query #797 (980806a)

v0.1.1

0.1.1 (2024-05-08)

Features

• lapis2: allow filtering for null (f680305)

v0.1.0

0.1.0 (2024-05-07)

⚠ BREAKING CHANGES

• lapis2: read data from SILO as NDJSON

Features

• adapt to changed SILO response structure (6f58b5c)
• adapt variantFilter to Filters with columns and update tests (88acb65)
• add /sample to query paths #501 (7ad9746)
• add access key parameter to /sample/info and remove downloadAsFile (340f2ac)
• add alignedNucleotideSequence, aminoAcidSequence endpoints (575070a)
• add aminoAcidInsertions endpoint returning json,csv and tsv (bb3358e)
• add dataFormat to swaggerUI for GET requests (1514df7)
• add description to response schema (829448b)
• add feature isSingleSegmentedSequence (a90e331)
• add fields to aggregated endpoint (d183a0f)
• add folder log to gitignore (67a9aa9)
• add info controller (78f9c69)
• add info to lapis response (afff4ae)
• add lineage queries for nextstrain, nextclade and gisaid (e01acda)
• add Maybe and bracket expression (835b9c1)
• add NOf query (217704e)
• add not expression to variantQuery (4b59e14)
• add nucleotideInsertions endpoint returning json,csv and tsv (829b8e9)
• add Or expression to variantQuery (5a0ef38)
• add Pangolineage_query (c159ace)
• add sample to info route (b703a9c)
• add unaligned nucleotide sequence route (adda1dc)
• add variant query to FilterExpressionMapper (64f0c8b)
• allow features to be empty (a5bf1ea)
• 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)
• allow upper and lowercase for queries (b4ce361)
• also enable returning TSV #284 (9597e28)
• also get database config from info controller as YAML (cd6536d)
• also write logs to stdout (a31522c)
• amino acid and nucleotide insertion filters are case-insensitive (667f487)
• base implementation to provide the openness level in the config (aff116c), closes #218
• change content type to text/plain when asking for csv/tsv without headers #930 (8313996)
• configure CORS - allow all origins (a7230f6)
• docs: generate correct URLs for nucleotide sequences endpoints in multi-segmented case #521 (6058b99)
• docs: references/additional-request-properties #604 (837e474)
• docs: transfer ambiguous symbols explanation #551 (066f5b6)
• document access key in swagger docs (0cd3070), closes #218
• e2e tests for filter by insertions (fe8f0b9)
• enable /aggregated to return the data as CSV (893ccca)
• enable for operating behind a proxy that modifies the url (78f0231)
• filter by insertions at all endpoints (3376cb7)
• fix authentication, don't document authentication for now #553 (f593073)
• forward Retry-After header when SILO is not available yet #667 (62bcc7c)
• get access key from request and read valid access keys from file (4e07a6b), closes #218
• handle int and float columns (d978a04)
• handle reverse proxy headers (8b80214)
• implement /aminoAcidMutations (d270104)
• implement /details endpoint (aed93e9), closes #283
• implement a request cache for mutation and insertion queries #137 (17ff89c)
• implement a request id to trace requests #586 (194e7fd)
• implement amino acid mutation filters (f33c0ff)
• implement amino acid mutations in advanced variant queries (85d0d82)
• implement compressing the response as zstd and gzip #600 (d6e8d9d)
• implement downloadAsFile #599 (c522296)
• implement leftover variant query parts #498 ([556552f](https://github.com/GenSpectr...

lapis2-docs: v0.1.0

0.1.0 (2024-05-07)

Features

• add config generator page (45c9827)
• 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)
• implement a request id to trace requests #586 (194e7fd)
• lapis2-docs: configure base to handle links behind reverse proxy (64c3cb7)
• lapis2-docs: configure LAPIS URL via environment variable (2ede4aa)
• lapis2-docs: document url encoded forms (8c3ba60), closes #765
• return structured mutation and insertion responses #718 (af38e93)
• support order by random #658 (598b05f)
• try whether also caching aggregated queries makes cov spectrum faster (bbfaf22)

Bug Fixes

• docs: display everything on the mutation filters page (d912f59)
• docs: schema for uploaded config (ecd2f9c)
• docs: some minor improvements (c77bf6f)
• end to end tests failing due to timeout and new pango lineage alias in return (d265809)
• file ending when downloading compressed file #685 (6a51de0)
• lapis2-docs: tailwind config file name in Docker (28add2b)
• lapis2-docs: typo in link (5943e11)
• lapis2-docs: use relative links so that they work when deployed behind a proxy #725 (0cfa8ec)
• update e2e tests: deletions are also mutations (from SILO) (886a8f1)
• use authorization filter before other filters #660 (0dab1e7)