chore: release 678-release

[github-actions]

🤖 I have created a release beep boop

0.1.0

0.1.0 (2024-05-06)

⚠ 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 nucleotideInsertions endpoint returning json,csv and tsv (829b8e9)
• add sample to info route (b703a9c)
• add unaligned nucleotide sequence route (adda1dc)
• 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)
• implement maybe mutation filters #551 (fab1c72)
• implement orderBy, limit and offset (0a1dbe7), closes #290
• 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)
• introduce SiloNotImplementedError (4f94a06)
• lapis2: implement boolean columns (7718b4f), closes #740
• 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
• 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)
• make it possible to return data from /details as CSV #284 (151e18f)
• Mention that it's LAPIS' error page. (7c365ce)
• nucleotideMutations ary aminoAcidMutations endpoint return CSV/TSV (cc3926c)
• pass on errors from SILO (7f6153d)
• pass request id to SILO (901e08a)
• provide data for SILO in e2e tests (4f74c62)
• provide default values for file locations in Docker image (e2248ac)
• provide full reference genome, and database config to new endpoints (e406023)
• return a standard problem detail instead of a custom error format (5f89b50)
• return bad request error when unknown compression format in request #647 (decaea5)
• return data version in each header (27ecd70)
• 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)
• stick to the default of having config value keys in camel case (b14c91e)
• support order by random #658 (598b05f)
• throw more specialized exception to handle bad requests (b8b86c2)
• try whether also caching aggregated queries makes cov spectrum faster (bbfaf22)
• use multiple access keys (3ecc11a)
• wrap response data to match LAPIS 1 structure (#324) (e1976cc)

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)
• correct spelling (1971713)
• details does no longer return insertions (3686658)
• don't set Transfer-Encoding twice #600 (7e49aa5)
• don't store logs in files #405 (1ca90f7)
• exact n of query with more elements than n (1402019)
• file ending when downloading compressed file #685 (6a51de0)
• import of property (848f4b6)
• lapis2: prefer zstd over gzip #738 (1fb67ac)
• 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)
• use authorization filter before other filters #660 (0dab1e7)
• use updated config (d9d5a1a)
• variant query with nextcladePangolineageQuery (9158575)
• write empty string to CSV/TSV for null values #708 (c8872ba)

lapis2-docs: 0.1.0

0.1.0 (2024-05-06)

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)

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[fengelniederhammer]

This was only created for testing.