diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 7c649ad2..731c89c6 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -7,7 +7,8 @@ name: Building Pipeline Containers on: push: branches: - 'dev' + - 'dev' + - 'python-update' jobs: starting-notification: @@ -34,10 +35,10 @@ jobs: run: docker login -u $DOCKER_USER -p $DOCKER_PASSWORD - name: docker build - run: docker build -f Dockerfile -t rnacentral/rnacentral-import-pipeline . + run: docker build -f Dockerfile -t rnacentral/rnacentral-import-pipeline:experimental . - name: docker push - run: docker push rnacentral/rnacentral-import-pipeline + run: docker push rnacentral/rnacentral-import-pipeline:experimental finished-notification: needs: @@ -53,23 +54,23 @@ jobs: SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} MSG_MINIMAL: true - singularity-conversion: - needs: - - create-docker-image - uses: rnacentral/rnacentral-import-pipeline/.github/workflows/singularity.yaml@dev - secrets: inherit + # singularity-conversion: + # needs: + # - create-docker-image + # uses: rnacentral/rnacentral-import-pipeline/.github/workflows/singularity.yaml@dev + # secrets: inherit - finished-singularity: - needs: - - singularity-conversion - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 + # finished-singularity: + # needs: + # - singularity-conversion + # runs-on: ubuntu-latest + # steps: + # - uses: actions/checkout@v2 - - name: Finished notification - uses: rtCamp/action-slack-notify@v2 - env: - SLACK_MESSAGE: 'New singularity image pushed to ghcr' - SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} - MSG_MINIMAL: true + # - name: Finished notification + # uses: rtCamp/action-slack-notify@v2 + # env: + # SLACK_MESSAGE: 'New singularity image pushed to ghcr' + # SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} + # MSG_MINIMAL: true diff --git a/.github/workflows/version-tag.yaml b/.github/workflows/version-tag.yaml new file mode 100644 index 00000000..e3788a1b --- /dev/null +++ b/.github/workflows/version-tag.yaml @@ -0,0 +1,23 @@ +# This workflow will create a version tag when a pull request is merged into main +# It only fires if the commit message starts Release: +name: Automatic version tagging + +on: + pull_request: + types: + - closed + branches: + - main +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Bump version and push tag + id: tag_version + uses: mathieudutour/github-tag-action@v6.1 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + default_bump: false + tag_prefix: release_ + custom_release_rules: Release:major diff --git a/Cargo.lock b/Cargo.lock index bd0fb648..ad51c965 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -2,11 +2,22 @@ # It is not intended for manual editing. version = 3 +[[package]] +name = "ahash" +version = "0.7.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47" +dependencies = [ + "getrandom 0.2.8", + "once_cell", + "version_check", +] + [[package]] name = "aho-corasick" -version = "0.7.15" +version = "0.7.19" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7404febffaa47dac81aa44dba71523c9d069b1bdc50a77db41195149e17f68e5" +checksum = "b4f55bd91a0978cbfd91c457a164bab8b4001c833b7f323132c0a4e1922dd44e" dependencies = [ "memchr", ] @@ -42,16 +53,27 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "06e97b4e522f9e55523001238ac59d13a8603af57f69980de5d8de4bbbe8ada6" [[package]] -name = "arrayref" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a4c527152e37cf757a3f78aae5a06fbeefdb07ccc535c980a3208ee3060dd544" - -[[package]] -name = "arrayvec" -version = "0.5.2" +name = "arrow2" +version = "0.11.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "23b62fc65de8e4e7f52534fb52b0f3ed04746ae267519eef2a83941e8085068b" +checksum = "b040061368d1314b0fd8b8f1fde0671eba1afc63a1c61a4dafaf2d4fc10c96f9" +dependencies = [ + "bytemuck", + "chrono", + "csv-core", + "either", + "fallible-streaming-iterator", + "hash_hasher", + "indexmap", + "lexical-core", + "multiversion", + "num-traits", + "serde", + "serde_json", + "simdutf8", + "streaming-iterator", + "strength_reduce", +] [[package]] name = "atty" @@ -76,12 +98,6 @@ version = "1.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "cdb031dd78e28731d87d56cc8ffef4a8f36ca26c38fe2de700543e627f8a464a" -[[package]] -name = "base64" -version = "0.13.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "904dfeac50f3cdaba28fc6f57fdcddb75f49ed61346676a78c4ffe55877802fd" - [[package]] name = "bio" version = "0.32.0" @@ -151,20 +167,9 @@ checksum = "349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb" [[package]] name = "bitflags" -version = "1.2.1" +version = "1.3.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cf1de2fe8c75bc145a2f577add951f8134889b4795d47466a54a5c846d691693" - -[[package]] -name = "blake2b_simd" -version = "0.5.11" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "afa748e348ad3be8263be728124b24a24f268266f6f5d58af9d75f6a40b5c587" -dependencies = [ - "arrayref", - "arrayvec", - "constant_time_eq", -] +checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" [[package]] name = "block-buffer" @@ -203,6 +208,26 @@ version = "0.6.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "72feb31ffc86498dacdbd0fcebb56138e7177a8cc5cea4516031d15ae85a742e" +[[package]] +name = "bytemuck" +version = "1.12.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2f5715e491b5a1598fc2bef5a606847b5dc1d48ea625bd3c02c00de8285591da" +dependencies = [ + "bytemuck_derive", +] + +[[package]] +name = "bytemuck_derive" +version = "1.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1b9e1f5fa78f69496407a27ae9ed989e3c3b072310286f5ef385525e4cbc24a9" +dependencies = [ + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", +] + [[package]] name = "byteorder" version = "1.4.2" @@ -244,11 +269,50 @@ dependencies = [ "atty", "bitflags", "strsim 0.8.0", - "textwrap", + "textwrap 0.11.0", "unicode-width", "vec_map", ] +[[package]] +name = "clap" +version = "3.2.23" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "71655c45cb9845d3270c9d6df84ebe72b4dad3c2ba3f7023ad47c144e4e473a5" +dependencies = [ + "atty", + "bitflags", + "clap_derive", + "clap_lex", + "indexmap", + "once_cell", + "strsim 0.10.0", + "termcolor", + "textwrap 0.16.0", +] + +[[package]] +name = "clap_derive" +version = "3.2.18" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ea0c8bce528c4be4da13ea6fead8965e95b6073585a2f05204bd8f4119f82a65" +dependencies = [ + "heck 0.4.0", + "proc-macro-error", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", +] + +[[package]] +name = "clap_lex" +version = "0.2.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2850f2f5a82cbf437dd5af4d49848fbdfc27c157c3d010345776f952765261c5" +dependencies = [ + "os_str_bytes", +] + [[package]] name = "cloudabi" version = "0.0.3" @@ -259,20 +323,83 @@ dependencies = [ ] [[package]] -name = "constant_time_eq" -version = "0.1.5" +name = "comfy-table" +version = "5.0.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "245097e9a4535ee1e3e3931fcfcd55a796a44c643e8596ff6566d68f09b87bbc" +checksum = "b103d85ca6e209388771bfb7aa6b68a7aeec4afbf6f0a0264bfbf50360e5212e" +dependencies = [ + "crossterm", + "strum 0.23.0", + "strum_macros 0.23.1", + "unicode-width", +] [[package]] -name = "crossbeam-utils" -version = "0.8.1" +name = "crossbeam-channel" +version = "0.5.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c2dd04ddaf88237dc3b8d8f9a3c1004b506b54b3313403944054d23c0870c521" +dependencies = [ + "cfg-if 1.0.0", + "crossbeam-utils", +] + +[[package]] +name = "crossbeam-deque" +version = "0.8.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "715e8152b692bba2d374b53d4875445368fdf21a94751410af607a5ac677d1fc" +dependencies = [ + "cfg-if 1.0.0", + "crossbeam-epoch", + "crossbeam-utils", +] + +[[package]] +name = "crossbeam-epoch" +version = "0.9.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "02d96d1e189ef58269ebe5b97953da3274d83a93af647c2ddd6f9dab28cedb8d" +checksum = "f916dfc5d356b0ed9dae65f1db9fc9770aa2851d2662b988ccf4fe3516e86348" dependencies = [ "autocfg 1.0.1", "cfg-if 1.0.0", - "lazy_static", + "crossbeam-utils", + "memoffset", + "scopeguard", +] + +[[package]] +name = "crossbeam-utils" +version = "0.8.12" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "edbafec5fa1f196ca66527c1b12c2ec4745ca14b50f1ad8f9f6f720b55d11fac" +dependencies = [ + "cfg-if 1.0.0", +] + +[[package]] +name = "crossterm" +version = "0.23.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a2102ea4f781910f8a5b98dd061f4c2023f479ce7bb1236330099ceb5a93cf17" +dependencies = [ + "bitflags", + "crossterm_winapi", + "libc", + "mio", + "parking_lot", + "signal-hook", + "signal-hook-mio", + "winapi", +] + +[[package]] +name = "crossterm_winapi" +version = "0.9.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2ae1b35a484aa10e07fe0638d02301c5ad24de82d310ccbd2f3693da5f09bf1c" +dependencies = [ + "winapi", ] [[package]] @@ -321,10 +448,10 @@ checksum = "f0c960ae2da4de88a91b2d920c2a7233b400bc33cb28453a2987822d8392519b" dependencies = [ "fnv", "ident_case", - "proc-macro2 1.0.28", - "quote 1.0.8", + "proc-macro2 1.0.47", + "quote 1.0.21", "strsim 0.9.3", - "syn 1.0.75", + "syn 1.0.103", ] [[package]] @@ -334,8 +461,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d9b5a2f4ac4969822c62224815d069952656cadc7084fdca9751e6d959189b72" dependencies = [ "darling_core", - "quote 1.0.8", - "syn 1.0.75", + "quote 1.0.21", + "syn 1.0.103", ] [[package]] @@ -344,9 +471,9 @@ version = "0.5.8" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "71f31892cd5c62e414316f2963c5689242c43d8e7bbcaaeca97e5e28c95d91d9" dependencies = [ - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", ] [[package]] @@ -368,11 +495,20 @@ dependencies = [ "dirs-sys", ] +[[package]] +name = "dirs" +version = "4.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ca3aa72a6f96ea37bbc5aa912f6788242832f75369bdfdadcb0e38423f100059" +dependencies = [ + "dirs-sys", +] + [[package]] name = "dirs-sys" -version = "0.3.5" +version = "0.3.7" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8e93d7f5705de3e49895a2b5e0b8855a1c27f080192ae9c32a6432d50741a57a" +checksum = "1b1d1d91c932ef41c0f2663aa8b0ca0342d444d842c06914aa0a7e352d0bada6" dependencies = [ "libc", "redox_users", @@ -407,9 +543,22 @@ version = "0.4.6" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e5c450cf304c9e18d45db562025a14fb1ca0f5c769b6f609309f81d4c31de455" dependencies = [ - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", +] + +[[package]] +name = "env_logger" +version = "0.9.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c90bf5f19754d10198ccb95b70664fc925bd1fc090a0fd9a6ebc54acc8cd6272" +dependencies = [ + "atty", + "humantime", + "log", + "regex", + "termcolor", ] [[package]] @@ -427,12 +576,33 @@ dependencies = [ "test_bin", ] +[[package]] +name = "expression-parse" +version = "0.1.0" +dependencies = [ + "anyhow", + "clap 3.2.23", + "env_logger", + "log", + "multimap", + "polars", + "quick-xml 0.22.0", + "regex", + "serde", +] + [[package]] name = "fallible-iterator" version = "0.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "4443176a9f2c162692bd3d352d745ef9413eec5782a80d8fd6f8a1ac692a07f7" +[[package]] +name = "fallible-streaming-iterator" +version = "0.1.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7360491ce676a36bf9bb3c56c1aa791658183a54d2744120f27285738d90465a" + [[package]] name = "feature-probe" version = "0.1.1" @@ -501,13 +671,13 @@ dependencies = [ [[package]] name = "getrandom" -version = "0.2.1" +version = "0.2.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4060f4657be78b8e766215b02b18a2e862d83745545de804638e2b545e81aee6" +checksum = "c05aeb6a22b8f62540c194aac980f2115af067bfe15a0734d7277a768d396b31" dependencies = [ "cfg-if 1.0.0", "libc", - "wasi 0.10.1+wasi-snapshot-preview1", + "wasi 0.11.0+wasi-snapshot-preview1", ] [[package]] @@ -516,17 +686,39 @@ version = "0.0.9" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5bb3f5b7d8d70c9bd23cf29b2b38094661418fb0ea79f1b0cc2019a11d6f5429" dependencies = [ - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", ] +[[package]] +name = "glob" +version = "0.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9b919933a397b79c37e33b77bb2aa3dc8eb6e165ad809e58ff75bc7db2e34574" + +[[package]] +name = "hash_hasher" +version = "2.0.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "74721d007512d0cb3338cd20f0654ac913920061a4c4d0d8708edb3f2a698c0c" + [[package]] name = "hashbrown" version = "0.9.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d7afe4a420e3fe79967a00898cc1f4db7c8a49a9333a29f8a4bd76a253d5cd04" +[[package]] +name = "hashbrown" +version = "0.12.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888" +dependencies = [ + "ahash", + "rayon", +] + [[package]] name = "heck" version = "0.3.2" @@ -536,6 +728,12 @@ dependencies = [ "unicode-segmentation", ] +[[package]] +name = "heck" +version = "0.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2540771e65fc8cb83cd6e8a237f70c319bd5c29f78ed1084ba5d50eeac86f7f9" + [[package]] name = "hermit-abi" version = "0.1.18" @@ -545,6 +743,12 @@ dependencies = [ "libc", ] +[[package]] +name = "humantime" +version = "2.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4" + [[package]] name = "ident_case" version = "1.0.1" @@ -558,7 +762,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "4fb1fa934250de4de8aef298d81c729a7d33d8c239daa3a7575e6b92bfc7313b" dependencies = [ "autocfg 1.0.1", - "hashbrown", + "hashbrown 0.9.1", ] [[package]] @@ -625,11 +829,99 @@ version = "1.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646" +[[package]] +name = "lexical" +version = "6.1.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c7aefb36fd43fef7003334742cbf77b243fcd36418a1d1bdd480d613a67968f6" +dependencies = [ + "lexical-core", +] + +[[package]] +name = "lexical-core" +version = "0.8.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2cde5de06e8d4c2faabc400238f9ae1c74d5412d03a7bd067645ccbc47070e46" +dependencies = [ + "lexical-parse-float", + "lexical-parse-integer", + "lexical-util", + "lexical-write-float", + "lexical-write-integer", +] + +[[package]] +name = "lexical-parse-float" +version = "0.8.5" +source = 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"4fceb2595057b6891a4ee808f70054bd2d12f0e97f1cbb78689b59f676df325a" dependencies = [ + "indexmap", "itoa", "ryu", "serde", @@ -1304,11 +1901,47 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1197ff7de45494f290c1e3e1a6f80e108974681984c87a3e480991ef3d0f1950" dependencies = [ "darling", - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", +] + +[[package]] +name = "signal-hook" +version = "0.3.14" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a253b5e89e2698464fc26b545c9edceb338e18a89effeeecfea192c3025be29d" +dependencies = [ + "libc", + "signal-hook-registry", +] + +[[package]] +name = "signal-hook-mio" +version = "0.2.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "29ad2e15f37ec9a6cc544097b78a1ec90001e9f71b81338ca39f430adaca99af" +dependencies = [ + "libc", + "mio", + "signal-hook", +] + +[[package]] +name = "signal-hook-registry" +version = "1.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e51e73328dc4ac0c7ccbda3a494dfa03df1de2f46018127f60c693f2648455b0" +dependencies = [ + "libc", ] +[[package]] +name = "simdutf8" +version = "0.1.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f27f6278552951f1f2b8cf9da965d10969b2efdea95a6ec47987ab46edfe263a" + [[package]] name = "simplelog" version = "0.7.6" @@ -1326,6 +1959,12 @@ version = "0.2.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0b8de496cf83d4ed58b6be86c3a275b8602f6ffe98d3024a869e124147a9a3ac" +[[package]] +name = "smallvec" +version = "1.10.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0" + [[package]] name = "snafu" version = "0.6.10" @@ -1342,9 +1981,9 @@ version = "0.6.10" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "1508efa03c362e23817f96cde18abed596a25219a8b2c66e8db33c03543d315b" dependencies = [ - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", ] [[package]] @@ -1360,6 +1999,12 @@ dependencies = [ "structopt", ] +[[package]] +name = "static_assertions" +version = "1.1.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a2eb9349b6444b326872e140eb1cf5e7c522154d69e7a0ffb0fb81c06b37543f" + [[package]] name = "statrs" version = "0.12.0" @@ -1369,6 +2014,18 @@ dependencies = [ "rand 0.7.3", ] +[[package]] +name = "streaming-iterator" +version = "0.1.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d55dd09aaa2f85ef8767cc9177294d63c30d62c8533329e75aa51d8b94976e22" + +[[package]] +name = "strength_reduce" +version = "0.2.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a3ff2f71c82567c565ba4b3009a9350a96a7269eaa4001ebedae926230bc2254" + [[package]] name = "strsim" version = "0.8.0" @@ -1381,13 +2038,19 @@ version = "0.9.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "6446ced80d6c486436db5c078dde11a9f73d42b57fb273121e160b84f63d894c" +[[package]] +name = "strsim" +version = "0.10.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623" + [[package]] name = "structopt" version = "0.3.21" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5277acd7ee46e63e5168a80734c9f6ee81b1367a7d8772a2d765df2a3705d28c" dependencies = [ - "clap", + "clap 2.33.3", "lazy_static", "structopt-derive", ] @@ -1398,11 +2061,11 @@ version = "0.4.14" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "5ba9cdfda491b814720b6b06e0cac513d922fc407582032e8706e9f137976f90" dependencies = [ - "heck", + "heck 0.3.2", "proc-macro-error", - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", ] [[package]] @@ -1417,16 +2080,22 @@ version = "0.21.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "aaf86bbcfd1fa9670b7a129f64fc0c9fcbbfe4f1bc4210e9e98fe71ffc12cde2" +[[package]] +name = "strum" +version = "0.23.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cae14b91c7d11c9a851d3fbc80a963198998c2a64eec840477fa92d8ce9b70bb" + [[package]] name = "strum_macros" version = "0.18.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "87c85aa3f8ea653bfd3ddf25f7ee357ee4d204731f6aa9ad04002306f6e2774c" dependencies = [ - "heck", - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "heck 0.3.2", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", ] [[package]] @@ -1435,10 +2104,10 @@ version = "0.20.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ee8bc6b87a5112aeeab1f4a9f7ab634fe6cbefc4850006df31267f4cfb9e3149" dependencies = [ - "heck", - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "heck 0.3.2", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", ] [[package]] @@ -1447,10 +2116,23 @@ version = "0.21.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d06aaeeee809dbc59eb4556183dd927df67db1540de5be8d3ec0b6636358a5ec" dependencies = [ - "heck", - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "heck 0.3.2", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", +] + +[[package]] +name = "strum_macros" +version = "0.23.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5bb0dc7ee9c15cea6199cde9a127fa16a4c5819af85395457ad72d68edc85a38" +dependencies = [ + "heck 0.3.2", + "proc-macro2 1.0.47", + "quote 1.0.21", + "rustversion", + "syn 1.0.103", ] [[package]] @@ -1461,18 +2143,18 @@ checksum = "9ca4b3b69a77cbe1ffc9e198781b7acb0c7365a883670e8f1c1bc66fba79a5c5" dependencies = [ "proc-macro2 0.4.30", "quote 0.6.13", - "unicode-xid 0.1.0", + "unicode-xid", ] [[package]] name = "syn" -version = "1.0.75" +version = "1.0.103" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b7f58f7e8eaa0009c5fec437aabf511bd9933e4b2d7407bd05273c01a8906ea7" +checksum = "a864042229133ada95abf3b54fdc62ef5ccabe9515b64717bcb9a1919e59445d" dependencies = [ - "proc-macro2 1.0.28", - "quote 1.0.8", - "unicode-xid 0.2.1", + "proc-macro2 1.0.47", + "quote 1.0.21", + "unicode-ident", ] [[package]] @@ -1484,7 +2166,7 @@ dependencies = [ "cfg-if 1.0.0", "libc", "rand 0.8.2", - "redox_syscall 0.2.4", + "redox_syscall", "remove_dir_all", "winapi", ] @@ -1495,10 +2177,19 @@ version = "0.6.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "c0863a3345e70f61d613eab32ee046ccd1bcc5f9105fe402c61fcd0c13eeb8b5" dependencies = [ - "dirs", + "dirs 2.0.2", "winapi", ] +[[package]] +name = "termcolor" +version = "1.1.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bab24d30b911b2376f3a13cc2cd443142f0c81dda04c118693e35b3835757755" +dependencies = [ + "winapi-util", +] + [[package]] name = "test_bin" version = "0.3.0" @@ -1514,6 +2205,12 @@ dependencies = [ "unicode-width", ] +[[package]] +name = "textwrap" +version = "0.16.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "222a222a5bfe1bba4a77b45ec488a741b3cb8872e5e499451fd7d0129c9c7c3d" + [[package]] name = "thiserror" version = "1.0.23" @@ -1529,18 +2226,9 @@ version = "1.0.23" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9be73a2caec27583d0046ef3796c3794f868a5bc813db689eed00c7631275cd1" dependencies = [ - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", -] - -[[package]] -name = "thread_local" -version = "1.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bb9bc092d0d51e76b2b19d9d85534ffc9ec2db959a2523cdae0697e2972cd447" -dependencies = [ - "lazy_static", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", ] [[package]] @@ -1565,9 +2253,9 @@ version = "0.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "345426c7406aa355b60c5007c79a2d1f5b605540072795222f17f6443e6a9c6f" dependencies = [ - "proc-macro2 1.0.28", - "quote 1.0.8", - "syn 1.0.75", + "proc-macro2 1.0.47", + "quote 1.0.21", + "syn 1.0.103", ] [[package]] @@ -1576,6 +2264,12 @@ version = "1.12.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "373c8a200f9e67a0c95e62a4f52fbf80c23b4381c05a17845531982fa99e6b33" +[[package]] +name = "unicode-ident" +version = "1.0.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6ceab39d59e4c9499d4e5a8ee0e2735b891bb7308ac83dfb4e80cad195c9f6f3" + [[package]] name = "unicode-segmentation" version = "1.7.1" @@ -1594,12 +2288,6 @@ version = "0.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "fc72304796d0818e357ead4e000d19c9c174ab23dc11093ac919054d20a6a7fc" -[[package]] -name = "unicode-xid" -version = "0.2.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f7fe0bb3479651439c9112f72b6c505038574c9fbb575ed1bf3b797fa39dd564" - [[package]] name = "vec_map" version = "0.8.2" @@ -1623,9 +2311,9 @@ checksum = "cccddf32554fecc6acb585f82a32a72e28b48f8c4c1883ddfeeeaa96f7d8e519" [[package]] name = "wasi" -version = "0.10.1+wasi-snapshot-preview1" +version = "0.11.0+wasi-snapshot-preview1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "93c6c3420963c5c64bca373b25e77acb562081b9bb4dd5bb864187742186cea9" +checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423" [[package]] name = "winapi" @@ -1643,8 +2331,74 @@ version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6" +[[package]] +name = "winapi-util" +version = "0.1.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178" +dependencies = [ + "winapi", +] + [[package]] name = "winapi-x86_64-pc-windows-gnu" version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f" + +[[package]] +name = "windows-sys" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5a3e1820f08b8513f676f7ab6c1f99ff312fb97b553d30ff4dd86f9f15728aa7" +dependencies = [ + "windows_aarch64_gnullvm", + "windows_aarch64_msvc", + "windows_i686_gnu", + "windows_i686_msvc", + "windows_x86_64_gnu", + "windows_x86_64_gnullvm", + "windows_x86_64_msvc", +] + +[[package]] +name = "windows_aarch64_gnullvm" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "41d2aa71f6f0cbe00ae5167d90ef3cfe66527d6f613ca78ac8024c3ccab9a19e" + +[[package]] +name = "windows_aarch64_msvc" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "dd0f252f5a35cac83d6311b2e795981f5ee6e67eb1f9a7f64eb4500fbc4dcdb4" + +[[package]] +name = "windows_i686_gnu" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fbeae19f6716841636c28d695375df17562ca208b2b7d0dc47635a50ae6c5de7" + +[[package]] +name = "windows_i686_msvc" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "84c12f65daa39dd2babe6e442988fc329d6243fdce47d7d2d155b8d874862246" + +[[package]] +name = "windows_x86_64_gnu" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bf7b1b21b5362cbc318f686150e5bcea75ecedc74dd157d874d754a2ca44b0ed" + +[[package]] +name = "windows_x86_64_gnullvm" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "09d525d2ba30eeb3297665bd434a54297e4170c7f1a44cad4ef58095b4cd2028" + +[[package]] +name = "windows_x86_64_msvc" +version = "0.42.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "f40009d85759725a34da6d89a94e63d7bdc50a862acf0dbc7c8e488f1edcb6f5" diff --git a/Dockerfile b/Dockerfile index d223fba7..d6d9b309 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,14 +1,14 @@ -FROM python:3.8-buster +FROM python:3.11.0-buster ENV RNA /rna WORKDIR $RNA -RUN apt-get update -RUN apt-get upgrade -y +RUN apt update +RUN apt upgrade -y # Install all required packages -RUN apt-get install -y \ +RUN apt install -y \ bedtools \ ca-certificates \ curl \ @@ -25,6 +25,7 @@ RUN apt-get install -y \ libsqlite3-dev \ libssl1.1 \ libxml2-utils \ + libxml2-dev \ libzip-dev \ moreutils \ mysql-common \ @@ -102,6 +103,9 @@ COPY openssl/openssl.cnf /etc/ssl/ WORKDIR $RNA +# Install rust build system +RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y + # Setup environmental variables ENV PERL5LIB="/usr/bin/env:$PERL5LIB" diff --git a/files/search-export/query.sql b/files/search-export/query.sql index 2cbffec6..f3287705 100644 --- a/files/search-export/query.sql +++ b/files/search-export/query.sql @@ -19,7 +19,8 @@ COPY ( 'description', array_agg(pre.description), 'deleted', array_agg(xref.deleted), 'length', array_agg(rna.len), - 'species', array_agg(acc.species), + -- 'species', array_agg(acc.species), + 'species', array_agg(tax.name) 'organelles', array_agg(acc.organelle), 'expert_dbs', array_agg(db.display_name), 'rna_type', array_agg(pre.rna_type), @@ -42,11 +43,13 @@ COPY ( 'incomplete_sequence', bool_or(qa.incomplete_sequence), 'missing_rfam_match', bool_or(qa.missing_rfam_match) ), - 'tax_strings', array_agg(acc.classification), + -- 'tax_strings', array_agg(acc.classification), + 'tax_strings', array_agg(tax.lineage), 'functions', array_agg(acc.function), 'genes', array_agg(acc.gene), 'gene_synonyms', array_agg(acc.gene_synonym), - 'common_name', array_agg(acc.common_name), + -- 'common_name', array_agg(acc.common_name), + 'common_name', array_agg(tax.common_name), 'notes', array_agg(acc.note), 'locus_tags', array_agg(acc.locus_tag), 'standard_names', array_agg(acc.standard_name), @@ -56,6 +59,7 @@ FROM rna rna join xref xref ON xref.upi = rna.upi JOIN rnc_rna_precomputed pre ON xref.upi = pre.upi AND xref.taxid = pre.taxid JOIN rnc_accessions acc ON xref.ac = acc.accession +JOIN rnc_taxonomy tax ON tax.id = xref.taxid JOIN rnc_database db ON xref.dbid = db.id JOIN rnc_release release1 ON xref.created = release1.id JOIN rnc_release release2 ON xref.last = release2.id diff --git a/import-data.nf b/import-data.nf index eff12365..1b7e5113 100644 --- a/import-data.nf +++ b/import-data.nf @@ -11,6 +11,7 @@ include { slack_message } from './workflows/utils/slack' include { slack_closure } from './workflows/utils/slack' workflow import_data { + take: _flag emit: post_release main: Channel.of("Starting data import pipeline") | slack_message diff --git a/main.nf b/main.nf new file mode 100644 index 00000000..6d4a0901 --- /dev/null +++ b/main.nf @@ -0,0 +1,20 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { select } from './workflows/databases/select.nf' +include { import_data } from './import-data' +include { precompute } from './precompute' +include { analyze } from './analyze' +include { export } from './export' + +workflow { + select \ + | import_data \ + | ifEmpty('no import') \ + | analyze \ + | ifEmpty('no analysis') \ + | precompute \ + | ifEmpty('no precompute') \ + | export +} diff --git a/poetry.lock b/poetry.lock index 4f456847..66e52319 100644 --- a/poetry.lock +++ b/poetry.lock @@ -34,10 +34,10 @@ optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.extras] -dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope-interface"] -docs = ["furo", "sphinx", "sphinx-notfound-page", "zope-interface"] -tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope-interface"] -tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope.interface"] +docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] +tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope.interface"] +tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"] [[package]] name = "beautifulsoup4" @@ -82,7 +82,7 @@ optional = false python-versions = ">=3.6.0" [package.extras] -unicode_backport = ["unicodedata2"] +unicode-backport = ["unicodedata2"] [[package]] name = "click" @@ -250,7 +250,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, != 3.4.*" [package.extras] cssselect = ["cssselect (>=0.7)"] html5 = ["html5lib"] -htmlsoup = ["beautifulsoup4"] +htmlsoup = ["BeautifulSoup4"] source = ["Cython (>=0.29.7)"] [[package]] @@ -501,7 +501,7 @@ urllib3 = ">=1.21.1,<1.27" [package.extras] socks = ["PySocks (>=1.5.6,!=1.5.7)"] -use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] +use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "retry" @@ -547,7 +547,7 @@ python-versions = ">=3.8" numpy = ">=1.18.5,<1.26.0" [package.extras] -dev = ["flake8", "mypy", "pycodestyle", "typing-extensions"] +dev = 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requirements.in scikit-learn==1.1.1 # via -r requirements.in -scipy==1.8.1 +scipy==1.9.3 # via scikit-learn semver==2.13.0 # via -r requirements.in diff --git a/rnacentral_pipeline/databases/data/entry.py b/rnacentral_pipeline/databases/data/entry.py index 4e87519c..864c9453 100644 --- a/rnacentral_pipeline/databases/data/entry.py +++ b/rnacentral_pipeline/databases/data/entry.py @@ -276,10 +276,10 @@ def write_ac_info(self) -> ty.Iterable[ty.List[ty.Optional[str]]]: None, # self.division, self.keywords, self.description, - self.species, - self.common_name, + None, # self.species, + None, # self.common_name, self.organelle, - self.lineage, + None, # self.lineage, None, # This was self.allele, self.anticodon, self.chromosome, diff --git a/select_databases.nf b/select_databases.nf index baa06bff..1d2a28b8 100644 --- a/select_databases.nf +++ b/select_databases.nf @@ -6,7 +6,8 @@ include { select } from './workflows/databases/select.nf' workflow { + emit: done - select() + select() | set { done } } diff --git a/utils/expression-atlas/Cargo.toml b/utils/expression-atlas/Cargo.toml index 156e976d..d573d703 100644 --- a/utils/expression-atlas/Cargo.toml +++ b/utils/expression-atlas/Cargo.toml @@ -6,7 +6,7 @@ edition = "2021" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [dependencies] -regex = "1.0" +regex = "1.5" anyhow = "1.0" log = "0.4" env_logger = "0.9.0"