Work out using rusqlite and migrations.
This is a big commit where I learned how to do proper error tracking, including handling From properly, and deriving it in some cases. The record subcommand still is not implemented but will be easier now that I decided to use SQLite temp tables as my data structure. This means I can simply implement a few loops in the fs submodule in order to scan directories, and dump entries into temp tables. When finished, I'll drop the tables. This is nice because SQLite already contains a very efficient BTree implementation that we can use with indices on these temp tables. It also means we don't have to hold possibly millions of directory entries in memory, and most importantly, we don't have to figure out a bidirectional tree structure in rust.
This commit is contained in:
Jacob Hinkle
parent
afb2fae01b
commit
3556590f7b
218
Cargo.lock
generated
218
Cargo.lock
generated
@ -2,6 +2,17 @@
|
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# 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",
|
||||
"once_cell",
|
||||
"version_check",
|
||||
]
|
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[[package]]
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name = "aho-corasick"
|
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version = "0.7.19"
|
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@ -29,10 +40,13 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
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||||
checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a"
|
||||
|
||||
[[package]]
|
||||
name = "cc"
|
||||
version = "1.0.73"
|
||||
name = "block-buffer"
|
||||
version = "0.10.3"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "2fff2a6927b3bb87f9595d67196a70493f627687a71d87a0d692242c33f58c11"
|
||||
checksum = "69cce20737498f97b993470a6e536b8523f0af7892a4f928cceb1ac5e52ebe7e"
|
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dependencies = [
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"generic-array",
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]
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[[package]]
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name = "cfg-if"
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@ -77,6 +91,54 @@ dependencies = [
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"os_str_bytes",
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]
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[[package]]
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name = "convert_case"
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version = "0.4.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "6245d59a3e82a7fc217c5828a6692dbc6dfb63a0c8c90495621f7b9d79704a0e"
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[[package]]
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name = "cpufeatures"
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version = "0.2.5"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "28d997bd5e24a5928dd43e46dc529867e207907fe0b239c3477d924f7f2ca320"
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dependencies = [
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"libc",
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]
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[[package]]
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name = "crypto-common"
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version = "0.1.6"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3"
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dependencies = [
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"generic-array",
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"typenum",
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]
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[[package]]
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name = "derive_more"
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version = "0.99.17"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "4fb810d30a7c1953f91334de7244731fc3f3c10d7fe163338a35b9f640960321"
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dependencies = [
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"convert_case",
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"proc-macro2",
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"quote",
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"rustc_version",
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"syn",
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]
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[[package]]
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name = "digest"
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version = "0.10.5"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "adfbc57365a37acbd2ebf2b64d7e69bb766e2fea813521ed536f5d0520dcf86c"
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dependencies = [
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"block-buffer",
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"crypto-common",
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]
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[[package]]
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name = "env_logger"
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version = "0.9.1"
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@ -90,6 +152,57 @@ dependencies = [
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"termcolor",
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]
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[[package]]
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name = "fallible-iterator"
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version = "0.2.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "4443176a9f2c162692bd3d352d745ef9413eec5782a80d8fd6f8a1ac692a07f7"
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[[package]]
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name = "fallible-streaming-iterator"
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version = "0.1.9"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "7360491ce676a36bf9bb3c56c1aa791658183a54d2744120f27285738d90465a"
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[[package]]
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name = "generic-array"
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||||
version = "0.14.6"
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||||
source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "bff49e947297f3312447abdca79f45f4738097cc82b06e72054d2223f601f1b9"
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dependencies = [
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"typenum",
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"version_check",
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]
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[[package]]
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name = "getrandom"
|
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version = "0.2.7"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "4eb1a864a501629691edf6c15a593b7a51eebaa1e8468e9ddc623de7c9b58ec6"
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dependencies = [
|
||||
"cfg-if",
|
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"libc",
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"wasi",
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]
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[[package]]
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name = "hashbrown"
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version = "0.12.3"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888"
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dependencies = [
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"ahash",
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]
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[[package]]
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name = "hashlink"
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version = "0.8.1"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "69fe1fcf8b4278d860ad0548329f892a3631fb63f82574df68275f34cdbe0ffa"
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dependencies = [
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"hashbrown",
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]
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[[package]]
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name = "heck"
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version = "0.4.0"
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@ -117,6 +230,16 @@ version = "0.2.135"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "68783febc7782c6c5cb401fbda4de5a9898be1762314da0bb2c10ced61f18b0c"
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[[package]]
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name = "libsqlite3-sys"
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version = "0.25.1"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "9f0455f2c1bc9a7caa792907026e469c1d91761fb0ea37cbb16427c77280cf35"
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dependencies = [
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"pkg-config",
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"vcpkg",
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]
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[[package]]
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name = "log"
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version = "0.4.17"
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@ -137,9 +260,14 @@ name = "nancy"
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version = "0.1.0"
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dependencies = [
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"clap",
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"derive_more",
|
||||
"env_logger",
|
||||
"log",
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||||
"sqlite",
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"once_cell",
|
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"rusqlite",
|
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"rusqlite_migration",
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"sha2",
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||||
"uuid",
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||||
]
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||||
|
||||
[[package]]
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||||
@ -220,35 +348,62 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
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||||
checksum = "a3f87b73ce11b1619a3c6332f45341e0047173771e8b8b73f87bfeefb7b56244"
|
||||
|
||||
[[package]]
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||||
name = "sqlite"
|
||||
version = "0.27.0"
|
||||
name = "rusqlite"
|
||||
version = "0.28.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "e2df8edd55685048550daaaf2be9024182f3523086cc86f7d50c136e55173e8c"
|
||||
checksum = "01e213bc3ecb39ac32e81e51ebe31fd888a940515173e3a18a35f8c6e896422a"
|
||||
dependencies = [
|
||||
"libc",
|
||||
"sqlite3-sys",
|
||||
"bitflags",
|
||||
"fallible-iterator",
|
||||
"fallible-streaming-iterator",
|
||||
"hashlink",
|
||||
"libsqlite3-sys",
|
||||
"smallvec",
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||||
"uuid",
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||||
]
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||||
|
||||
[[package]]
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||||
name = "sqlite3-src"
|
||||
name = "rusqlite_migration"
|
||||
version = "1.0.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "eda44233be97aea786691f9f6f7ef230bcf905061f4012e90f4f39e6dcf31163"
|
||||
dependencies = [
|
||||
"log",
|
||||
"rusqlite",
|
||||
]
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||||
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||||
[[package]]
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||||
name = "rustc_version"
|
||||
version = "0.4.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "d1815a7a02c996eb8e5c64f61fcb6fd9b12e593ce265c512c5853b2513635691"
|
||||
checksum = "bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366"
|
||||
dependencies = [
|
||||
"cc",
|
||||
"pkg-config",
|
||||
"semver",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "sqlite3-sys"
|
||||
version = "0.14.0"
|
||||
name = "semver"
|
||||
version = "1.0.14"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "d47c99824fc55360ba00caf28de0b8a0458369b832e016a64c13af0ad9fbb9ee"
|
||||
checksum = "e25dfac463d778e353db5be2449d1cce89bd6fd23c9f1ea21310ce6e5a1b29c4"
|
||||
|
||||
[[package]]
|
||||
name = "sha2"
|
||||
version = "0.10.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "82e6b795fe2e3b1e845bafcb27aa35405c4d47cdfc92af5fc8d3002f76cebdc0"
|
||||
dependencies = [
|
||||
"libc",
|
||||
"sqlite3-src",
|
||||
"cfg-if",
|
||||
"cpufeatures",
|
||||
"digest",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "smallvec"
|
||||
version = "1.10.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0"
|
||||
|
||||
[[package]]
|
||||
name = "strsim"
|
||||
version = "0.10.0"
|
||||
@ -275,18 +430,45 @@ dependencies = [
|
||||
"winapi-util",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "typenum"
|
||||
version = "1.15.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "dcf81ac59edc17cc8697ff311e8f5ef2d99fcbd9817b34cec66f90b6c3dfd987"
|
||||
|
||||
[[package]]
|
||||
name = "unicode-ident"
|
||||
version = "1.0.5"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "6ceab39d59e4c9499d4e5a8ee0e2735b891bb7308ac83dfb4e80cad195c9f6f3"
|
||||
|
||||
[[package]]
|
||||
name = "uuid"
|
||||
version = "1.2.1"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "feb41e78f93363bb2df8b0e86a2ca30eed7806ea16ea0c790d757cf93f79be83"
|
||||
dependencies = [
|
||||
"getrandom",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "vcpkg"
|
||||
version = "0.2.15"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426"
|
||||
|
||||
[[package]]
|
||||
name = "version_check"
|
||||
version = "0.9.4"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f"
|
||||
|
||||
[[package]]
|
||||
name = "wasi"
|
||||
version = "0.11.0+wasi-snapshot-preview1"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
|
||||
|
||||
[[package]]
|
||||
name = "winapi"
|
||||
version = "0.3.9"
|
||||
|
||||
11
Cargo.toml
11
Cargo.toml
@ -11,14 +11,19 @@ readme = "README.md"
|
||||
|
||||
[lib]
|
||||
name = "nancy"
|
||||
path = "src/lib/main.rs"
|
||||
path = "src/lib.rs"
|
||||
|
||||
[[bin]]
|
||||
name = "nancy"
|
||||
path = "src/cli/main.rs"
|
||||
path = "src/main.rs"
|
||||
|
||||
[dependencies]
|
||||
clap = { version = "4.0.14", features = ["derive"] }
|
||||
derive_more = "0.99.17"
|
||||
env_logger = "0.9.1"
|
||||
log = "0.4.17"
|
||||
sqlite = "0.27.0"
|
||||
once_cell = "1.15.0"
|
||||
rusqlite = { version = "0.28.0", features = ["uuid"] }
|
||||
rusqlite_migration = "1.0.0"
|
||||
sha2 = "0.10.6"
|
||||
uuid = { version = "1.2.1", features = ["v4"] }
|
||||
|
||||
@ -33,7 +33,12 @@
|
||||
#defaultPackage = naersk-lib.buildPackage ./.;
|
||||
devShell = with pkgs; mkShell {
|
||||
inputsFrom = builtins.attrValues self.packages.${system};
|
||||
buildInputs = [ cargo rust-analyzer clippy rustfmt ];
|
||||
buildInputs = [
|
||||
cargo
|
||||
rust-analyzer clippy rustfmt # linting
|
||||
sqlite
|
||||
openssl pkgconfig # for openssl-sys dep that gets pulled in
|
||||
];
|
||||
};
|
||||
});
|
||||
}
|
||||
|
||||
@ -1,45 +0,0 @@
|
||||
use clap::{Parser, Subcommand};
|
||||
use env_logger;
|
||||
use nancy;
|
||||
|
||||
// Composable provenance tracking for scientific data analysis
|
||||
#[derive(Parser)]
|
||||
#[command(author, version, about, long_about = None, arg_required_else_help=true)]
|
||||
struct Cli {
|
||||
#[command(subcommand)]
|
||||
command: Option<Commands>,
|
||||
}
|
||||
|
||||
#[derive(Subcommand)]
|
||||
enum Commands {
|
||||
/// Record changes to a store directory (or a new store)
|
||||
Record {},
|
||||
/// Check for changes in store and print basic statistics
|
||||
Status {},
|
||||
/// Just say hello
|
||||
Hello {
|
||||
#[arg(short, long)]
|
||||
fromlib: bool,
|
||||
},
|
||||
}
|
||||
|
||||
fn main() {
|
||||
env_logger::init();
|
||||
let cli = Cli::parse();
|
||||
|
||||
match &cli.command {
|
||||
Some(Commands::Hello { fromlib }) => {
|
||||
println!("Hello from nancy (binary)!");
|
||||
if *fromlib {
|
||||
nancy::say_hello();
|
||||
}
|
||||
}
|
||||
Some(Commands::Record {}) => {
|
||||
println!("Record not yet implemented");
|
||||
}
|
||||
Some(Commands::Status {}) => {
|
||||
println!("Status not yet implemented");
|
||||
}
|
||||
None => {}
|
||||
}
|
||||
}
|
||||
104
src/db.rs
Normal file
104
src/db.rs
Normal file
@ -0,0 +1,104 @@
|
||||
//! # Database housekeeping methods
|
||||
//!
|
||||
//! This module is mostly for managing migrations. This does not encapsulate all database accesses.
|
||||
//!
|
||||
|
||||
extern crate derive_more;
|
||||
use derive_more::{Display,Error,From};
|
||||
|
||||
use once_cell::sync::Lazy;
|
||||
use rusqlite;
|
||||
use rusqlite::Connection;
|
||||
use rusqlite_migration::{Error as RMError, Migrations, M, SchemaVersion};
|
||||
use uuid;
|
||||
|
||||
use std::num::{NonZeroUsize}; // for describing schema versions
|
||||
|
||||
// NOTE: apply pragmas outside of migrations, using e.g.
|
||||
// conn.pragma_update(None, "foreign_keys", &"ON").unwrap();
|
||||
static MIGRATIONS: Lazy<Migrations<'static>> = Lazy::new(||
|
||||
Migrations::new(
|
||||
vec![
|
||||
M::up(include_str!("migrations/20221024_initial_schema.sql")),
|
||||
]
|
||||
));
|
||||
/// The current schema version as it will appear in the SQLite user_version
|
||||
pub static CURRENT_SCHEMA_VERSION: usize = 1;
|
||||
|
||||
/// Error type for checking schema version of a Connection
|
||||
#[derive(Debug,Display)]
|
||||
pub enum SchemaError {
|
||||
CurrentVersionError(RMError),
|
||||
NoSchemaVersionSet,
|
||||
OldSchema(NonZeroUsize),
|
||||
OutsideSchema(NonZeroUsize),
|
||||
}
|
||||
impl From<RMError> for SchemaError {
|
||||
fn from(cve: RMError) -> Self {
|
||||
Self::CurrentVersionError(cve)
|
||||
}
|
||||
}
|
||||
|
||||
/// Get schema version in connected database
|
||||
pub fn schema_version(conn: &Connection) -> Result<NonZeroUsize, SchemaError> {
|
||||
match MIGRATIONS.current_version(conn)? {
|
||||
SchemaVersion::NoneSet => Err(SchemaError::NoSchemaVersionSet),
|
||||
SchemaVersion::Inside(v) => // A known version is set. Check if it is current
|
||||
if v.get() == CURRENT_SCHEMA_VERSION {
|
||||
Ok(v)
|
||||
} else {
|
||||
Err(SchemaError::OldSchema(v))
|
||||
},
|
||||
SchemaVersion::Outside(v) => Err(SchemaError::OutsideSchema(v)),
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/// Initialize the database starting with an empty schema.
|
||||
///
|
||||
/// This function initializes a database to the latest schema, and also generates a new random UUID
|
||||
/// and associates that with this dataset. The generated uuid is returned.
|
||||
pub fn init(conn: &mut Connection) -> Result<uuid::Uuid, RMError> {
|
||||
MIGRATIONS.to_latest(conn)?;
|
||||
let u = uuid::Uuid::new_v4();
|
||||
conn.execute(
|
||||
"INSERT INTO local_metadata (key, value) VALUES ('dataset_uuid', ?)",
|
||||
[u.to_string()],
|
||||
)?;
|
||||
Ok(u)
|
||||
}
|
||||
|
||||
|
||||
#[derive(Debug)]
|
||||
pub struct SchemaUpdateResult {
|
||||
pub old_version: Option<NonZeroUsize>,
|
||||
pub current_version: NonZeroUsize,
|
||||
pub updated: bool,
|
||||
}
|
||||
/// Ensure that the schema in conn is current.
|
||||
///
|
||||
/// If migrate is true, migrate the schema and return.
|
||||
///
|
||||
/// If migrate is false, throw an Error if schema is not current.
|
||||
pub fn ensure_schema(conn: &mut Connection, migrate: bool)
|
||||
-> Result<SchemaUpdateResult, SchemaError> {
|
||||
let old_version = schema_version(conn)?;
|
||||
let current_version = unsafe { NonZeroUsize::new_unchecked(CURRENT_SCHEMA_VERSION) };
|
||||
Ok(SchemaUpdateResult {
|
||||
old_version: None,
|
||||
current_version: current_version,
|
||||
updated: old_version == current_version,
|
||||
})
|
||||
}
|
||||
|
||||
#[derive(Debug,Display,Error,From)]
|
||||
pub enum LocalUuidError {
|
||||
StatementPrepareError(rusqlite::Error),
|
||||
UuidError(uuid::Error),
|
||||
}
|
||||
/// Find the UUID of the dataset representing the directory containing the connected 'nancy.db'
|
||||
pub fn local_uuid(conn: &Connection) -> Result<uuid::Uuid, LocalUuidError> {
|
||||
let uuid = conn.prepare("SELECT value FROM local_metadata WHERE key = 'dataset_uuid' LIMIT 1")?
|
||||
.query_row([], |row| row.get(0))?;
|
||||
Ok(uuid)
|
||||
}
|
||||
15
src/fs.rs
Normal file
15
src/fs.rs
Normal file
@ -0,0 +1,15 @@
|
||||
//use jwalk;
|
||||
use log;
|
||||
use sha2::{Sha256, Digest, digest::FixedOutput};
|
||||
use std::path::{Path};
|
||||
|
||||
|
||||
#[derive(Debug)]
|
||||
pub enum RecordError {
|
||||
NotImplemented,
|
||||
}
|
||||
|
||||
pub fn record(path: &Path, message: &String) -> Result<(), RecordError> {
|
||||
log::info!("Recording path {:?} using message \"{}\"", path, message);
|
||||
Err(RecordError::NotImplemented)
|
||||
}
|
||||
23
src/lib.rs
Normal file
23
src/lib.rs
Normal file
@ -0,0 +1,23 @@
|
||||
use std::io;
|
||||
|
||||
use rusqlite::{Connection};
|
||||
use uuid::{Uuid};
|
||||
|
||||
//pub mod data;
|
||||
pub mod db;
|
||||
pub mod fs;
|
||||
pub mod program;
|
||||
pub mod timing;
|
||||
|
||||
pub fn print_uuid() -> io::Result<Uuid> {
|
||||
let db_path = "nancy.db";
|
||||
|
||||
let conn = Connection::open(db_path).expect("Couldn't open database");
|
||||
conn.pragma_update(None, "foreign_keys", &"ON").unwrap();
|
||||
|
||||
let uuid = db::local_uuid(&conn).expect("Error when extracting local dataset UUID");
|
||||
|
||||
println!("UUID is {}", uuid);
|
||||
|
||||
Ok(uuid)
|
||||
}
|
||||
@ -1,47 +0,0 @@
|
||||
use log;
|
||||
use sqlite;
|
||||
|
||||
pub struct Store<'a> {
|
||||
conn: &'a sqlite::Connection,
|
||||
uuid: &'a str,
|
||||
}
|
||||
|
||||
#[derive(Debug)]
|
||||
pub enum DBError {
|
||||
NoRowsReturned,
|
||||
NoneValue,
|
||||
}
|
||||
|
||||
pub fn get_uuid(conn: &sqlite::Connection) -> Result<String, DBError> {
|
||||
let mut uuid = Err(DBError::NoRowsReturned);
|
||||
conn.iterate(
|
||||
"
|
||||
SELECT value FROM local_metadata WHERE key = 'store_uuid';
|
||||
",
|
||||
|pairs| {
|
||||
uuid = match (*pairs)[0].1 {
|
||||
Some(u) => Ok(u.to_string()),
|
||||
None => Err(DBError::NoneValue),
|
||||
};
|
||||
|
||||
false // only process the first row
|
||||
},
|
||||
);
|
||||
uuid
|
||||
}
|
||||
|
||||
pub fn say_hello() {
|
||||
log::trace!("enter say_hello()");
|
||||
println!("If you see nothing in the next line, set RUST_LOG to info or lower");
|
||||
log::info!("Hello from libnancy.rlib!!!");
|
||||
|
||||
let store_path = "nancy.db";
|
||||
let conn = sqlite::open(store_path).unwrap();
|
||||
let uuid = get_uuid(&conn).unwrap();
|
||||
let this_store = Store {
|
||||
conn: &conn,
|
||||
uuid: &uuid,
|
||||
};
|
||||
|
||||
println!("Store UUID: {}", this_store.uuid);
|
||||
}
|
||||
@ -1,3 +0,0 @@
|
||||
struct Store{
|
||||
};
|
||||
|
||||
106
src/main.rs
Normal file
106
src/main.rs
Normal file
@ -0,0 +1,106 @@
|
||||
use clap::{Parser, Subcommand};
|
||||
use env_logger;
|
||||
use log;
|
||||
use rusqlite::{Connection};
|
||||
|
||||
use nancy;
|
||||
|
||||
use std::{process};
|
||||
use std::path::{PathBuf};
|
||||
|
||||
// Composable provenance tracking for scientific data analysis
|
||||
#[derive(Parser)]
|
||||
#[command(author, version, about, long_about = None, arg_required_else_help=true)]
|
||||
struct Cli {
|
||||
#[command(subcommand)]
|
||||
command: Option<Commands>,
|
||||
}
|
||||
|
||||
#[derive(Subcommand)]
|
||||
enum Commands {
|
||||
/// Record changes to files/directories within a dataset (or create a new dataset)
|
||||
#[command()]
|
||||
Record {
|
||||
/// If not within an existing dataset, create one
|
||||
#[arg(short, long)]
|
||||
initialize: bool,
|
||||
/// Use
|
||||
#[arg(short, long)]
|
||||
message: String,
|
||||
#[arg()]
|
||||
record_paths: Vec<PathBuf>,
|
||||
},
|
||||
/// Check for changes in dataset and print basic statistics
|
||||
Status {},
|
||||
/// Just say hello
|
||||
Hello {
|
||||
//#[arg(short, long)]
|
||||
//fromlib: bool,
|
||||
},
|
||||
}
|
||||
|
||||
fn main() {
|
||||
env_logger::init();
|
||||
let args = Cli::parse();
|
||||
|
||||
match &args.command {
|
||||
Some(Commands::Hello {}) => {
|
||||
println!("Hello from nancy (binary)!");
|
||||
match nancy::print_uuid() {
|
||||
Ok(_) => {
|
||||
println!("OK");
|
||||
},
|
||||
Err(e) => {
|
||||
println!("SQLite error: {}", e);
|
||||
},
|
||||
};
|
||||
}
|
||||
Some(Commands::Record { initialize, message, record_paths }) => {
|
||||
// Determine dataset dir (ds_dir)
|
||||
// If no paths given, use ["."] for the following steps.
|
||||
// First, for each requested record_path, find whether it exists within a dataset dir
|
||||
// Ensure that all paths are in the same dataset dir, or none belong to a dataset dir
|
||||
// If no dataset dirs found, get top directory containing them all and set this as ds_dir
|
||||
let mut conn = Connection::open_in_memory().expect("Could not create in-memory db");
|
||||
// If initializing:
|
||||
match nancy::db::init(&mut conn) {
|
||||
Err(e) => {
|
||||
log::error!("Encountered error in initializing schema: {:?}", e);
|
||||
process::exit(1);
|
||||
}
|
||||
Ok(dataset_uuid) => {
|
||||
log::trace!("Init OK");
|
||||
log::info!("Dataset UUID is {dataset_uuid}");
|
||||
nancy::program::with_program(
|
||||
&mut conn,
|
||||
"INIT",
|
||||
"Initialize dataset",
|
||||
|prog| {
|
||||
let okres: Result<(), ()> = Ok(());
|
||||
okres
|
||||
}
|
||||
).expect("Empty program should not throw error");
|
||||
}
|
||||
}
|
||||
match nancy::program::with_program(&mut conn, "RECORD", message, |prog| {
|
||||
let dataset_path = PathBuf::from(".");
|
||||
// Note that this may fail, in which case we should roll back only this program
|
||||
// but keep the dataset initialized.
|
||||
nancy::fs::record(
|
||||
&dataset_path,
|
||||
message,
|
||||
)
|
||||
}) {
|
||||
Err(e) => {
|
||||
log::error!("Encountered error in RECORD program: {:?}", e);
|
||||
process::exit(3);
|
||||
},
|
||||
Ok(()) => (),
|
||||
}
|
||||
}
|
||||
Some(Commands::Status {}) => {
|
||||
println!("status not yet implemented");
|
||||
}
|
||||
None => {}
|
||||
}
|
||||
}
|
||||
300
src/migrations/20221024_initial_schema.sql
Normal file
300
src/migrations/20221024_initial_schema.sql
Normal file
@ -0,0 +1,300 @@
|
||||
-- Simple key/value table describing _this_ store (not imported ones).
|
||||
-- In particular, the key "local_store" should be the UUID of the store in this
|
||||
-- directory.
|
||||
CREATE TABLE local_metadata(
|
||||
key TEXT PRIMARY KEY NOT NULL,
|
||||
value TEXT
|
||||
);
|
||||
|
||||
|
||||
-- This lets us enable or disable triggers. For example, when importing we need
|
||||
-- to update some tables to account for changing primary keys using ON UPDATE
|
||||
-- CASCADE. However, some dependent tables like filedir may have a trigger that
|
||||
-- prevents all updates: e.g. for deleted files. In this case, we need to be
|
||||
-- able to disable that one specific trigger during imports, then re-enable it.
|
||||
-- We would do so by updating this table and setting enabled=False/True.
|
||||
--
|
||||
-- Note that entries in this table only need to be inserted when we know we have
|
||||
-- a need to disable the trigger. Otherwise, this table can be ignored.
|
||||
CREATE TABLE triggers(
|
||||
name TEXT PRIMARY KEY NOT NULL,
|
||||
enabled BOOL
|
||||
);
|
||||
|
||||
|
||||
-- We track host machines, so that we can give better information about file
|
||||
-- locations. This also allows us to see whether platform-dependent behavior may
|
||||
-- come into play.
|
||||
-- A row of this table should describe the aspects of a node that are unlikely
|
||||
-- to change during regular software updates. For example, the hostname and CPU
|
||||
-- type are included but not the kernel version. Software that changes due to
|
||||
-- updates should be included in the "environment" table instead.
|
||||
CREATE TABLE machine(
|
||||
sha256 BLOB PRIMARY KEY NOT NULL,
|
||||
machine_id TEXT, -- platform-dependent unique hardware id
|
||||
-- Linux: open('/etc/machine-id', 'r').read() (assumes systemd)
|
||||
-- OSX: `ioreg -rd1 -c IOPlatformExpertDevice | grep IOPlatformUUID | awk '{$print $3}' | tr -d \"`
|
||||
-- Windows: `reg query HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Cryptography /v MachineGuid`
|
||||
|
||||
hostname TEXT, -- platform.node(): 'lucky'
|
||||
system TEXT, -- platform.system(): 'Linux'
|
||||
cpu_type TEXT, -- platform.machine(): 'x86_64'
|
||||
processor TEXT -- platform.processor():
|
||||
);
|
||||
-- Programs are run by users on machines
|
||||
CREATE TABLE user(
|
||||
sha256 BLOB PRIMARY KEY NOT NULL,
|
||||
username TEXT NOT NULL, -- getpass.getuser()
|
||||
userid INTEGER, -- os.getuid()
|
||||
fullname TEXT, -- on Linux/OSX: pwd.getpwuid(os.getuid()).pw_gecos
|
||||
-- on Windows: see https://stackoverflow.com/questions/21766954/how-to-get-windows-users-full-name-in-python
|
||||
machine BLOB NOT NULL REFERENCES machine ON UPDATE CASCADE
|
||||
);
|
||||
CREATE INDEX FK_user_machine ON user (machine);
|
||||
|
||||
-- Stores and files (and directories)
|
||||
-- These are the primary objects tracked by nancy.
|
||||
-- A store is a directory containing a file called nancy.db (e.g. the dir holding this database)
|
||||
-- In order to reliably merge store entries (like when we have converging
|
||||
-- dependencies), we need to deduplicate. The machine and path could match, for
|
||||
-- example if a database is created in one location then copied elsewhere,
|
||||
-- followed by regenerating the original database. In these cases, we would want
|
||||
-- to distinguish the new database from the copied one while still being able to
|
||||
-- equate two simple copies of a db.
|
||||
-- For this we use a UUID generated randomly
|
||||
-- by the client. SQLite does not natively support UUIDs but it is stored here
|
||||
-- as a string.
|
||||
-- Client code should generate random UUIDs in the RFC 4122 variant layout.
|
||||
-- https://datatracker.ietf.org/doc/html/rfc4122.html
|
||||
-- This is possible in Python by simply calling uuid.uuid4() with no arguments
|
||||
CREATE TABLE store (
|
||||
uuid BLOB PRIMARY KEY NOT NULL -- UUID generated by uuid.uuid4()
|
||||
);
|
||||
|
||||
|
||||
-- The filedir table holds all files and directories that are tracked by the
|
||||
-- store. This table also holds tracked files and directories that have been
|
||||
-- imported and live outside the current store.
|
||||
-- We do not support renaming files.
|
||||
CREATE TABLE filedir (
|
||||
sha256 BLOB PRIMARY KEY NOT NULL,
|
||||
store BLOB NOT NULL REFERENCES store ON UPDATE CASCADE,
|
||||
name TEXT, -- only a filename, not a path
|
||||
parent BLOB REFERENCES filedir ON UPDATE CASCADE,
|
||||
UNIQUE(store, name, parent)
|
||||
);
|
||||
CREATE INDEX FK_filedir_store ON filedir (store);
|
||||
CREATE INDEX FK_filedir_parent ON filedir (parent);
|
||||
-- Detect cross-store references
|
||||
CREATE TRIGGER insert_filedir BEFORE INSERT ON filedir
|
||||
BEGIN SELECT CASE
|
||||
WHEN NEW.parent IS NOT NULL AND NEW.store != (SELECT store FROM filedir WHERE sha256 = NEW.parent)
|
||||
THEN RAISE (ABORT, 'Parent resides in different store')
|
||||
END; END;
|
||||
CREATE TRIGGER update_filedir BEFORE UPDATE ON filedir
|
||||
BEGIN
|
||||
SELECT RAISE (ABORT, 'No updates to filedir allowed');
|
||||
END;
|
||||
|
||||
|
||||
-- This table holds _versions_ of files and directories. This table holds
|
||||
-- information that is independent of the location within the filesystem and
|
||||
-- merely indicates a version of the content in a format that is nearly
|
||||
-- independent of filetype (though the computation of content hashes is of
|
||||
-- course dependent on filetype). Each version has a number, and was provided by
|
||||
-- some program (and potentially a datum).
|
||||
CREATE TABLE filedir_version (
|
||||
uuid BLOB PRIMARY KEY NOT NULL,
|
||||
filedir BLOB NOT NULL
|
||||
REFERENCES filedir ON UPDATE CASCADE, -- parent filedir entry
|
||||
|
||||
recorded_time REAL, -- When was this version recorded?
|
||||
|
||||
-- Note that changing filetype (e.g. directory becomes file) or deleting a
|
||||
-- file are simply just new versions of a filedir.
|
||||
filetype TEXT, -- One of 'LNK', 'DIR', 'REG', etc. See store.FSEntry.from_path for details
|
||||
deleted BOOL NOT NULL, -- set True when recording a deleted file
|
||||
|
||||
-- We record the permissions on each file to enable fixing if needed
|
||||
perms TEXT, -- stat.filemode(os.stat(path).st_mode): '-rw-rw-r--'
|
||||
|
||||
symlink_target TEXT, -- if this is a symlink, this is the (read but not fully resolved) target. i.e. this is the "content" of the symlink.
|
||||
|
||||
-- The following hash can be NULL if the file was deleted. It could also be
|
||||
-- null if hashing is deferred. Hash deferring would be preferred in cases
|
||||
-- where a program must use a file or directory for multiple tasks, and each
|
||||
-- task might mutate the directory. In these cases, each task will add an
|
||||
-- additional version, but we do not want to hash every version since that
|
||||
-- would needlessly slow down execution, for very little benefit since we
|
||||
-- would be recording hashes for versions that may not be final. Instead, we
|
||||
-- can defer by only hashing files and directories at the end of a program.
|
||||
sha256 BLOB,
|
||||
|
||||
source_task BLOB REFERENCES task ON UPDATE CASCADE
|
||||
);
|
||||
CREATE INDEX FK_filedir_version_filedir ON filedir_version (filedir);
|
||||
CREATE INDEX FK_filedir_version_source_task ON filedir_version (source_task);
|
||||
-- Disallow UPDATING filedir_version. Instead, new version should be created.
|
||||
-- One exception is during importing, in which case we can disable the trigger
|
||||
INSERT INTO triggers VALUES('update_filedir_version', TRUE);
|
||||
CREATE TRIGGER update_filedir_version BEFORE UPDATE ON filedir_version
|
||||
BEGIN SELECT CASE
|
||||
WHEN (SELECT enabled FROM triggers WHERE name = 'update_filedir_version')
|
||||
THEN RAISE (ABORT, 'Updating filedir versions is prohibited')
|
||||
END; END;
|
||||
-- TODO: check for inserting inconsistent version info re. deleted flag/filetype
|
||||
|
||||
|
||||
|
||||
-- A computational environment which can execute "programs". Note that the
|
||||
-- python executable being used, and environment variables are recorded here.
|
||||
-- Other info is available in the parent "machine" table.
|
||||
CREATE TABLE environment (
|
||||
sha256 BLOB PRIMARY KEY NOT NULL,
|
||||
|
||||
envvars_json TEXT, -- json.dumps(dict(os.environ), sort_keys=True)
|
||||
python_implementation TEXT, -- platform.python_implementation(): 'cpython'
|
||||
python_strversion TEXT, -- sys.version: '3.9.7 (default, Sep 16 2021, 13:09:58) \n[GCC 7.5.0]'
|
||||
python_hexversion INTEGER, -- sys.hexversion: 50923504
|
||||
user TEXT REFERENCES user ON UPDATE CASCADE,
|
||||
timezone TEXT, -- timezone, for interpreting event times
|
||||
platform_release TEXT, -- platform.release(): '5.15.64'
|
||||
freedesktop_os_release TEXT, -- requires python 3.10
|
||||
-- platform.freedesktop_os_release() as JSON
|
||||
-- "{'NAME': 'NixOS', 'ID': 'nixos',
|
||||
-- 'PRETTY_NAME': 'NixOS 22.05 (Quokka)', 'BUG_REPORT_URL':
|
||||
-- 'https://github.com/NixOS/nixpkgs/issues', 'BUILD_ID':
|
||||
-- '22.05.20220902.67e4507', 'DOCUMENTATION_URL':
|
||||
-- 'https://nixos.org/learn.html', 'HOME_URL': 'https://nixos.org/', 'LOGO':
|
||||
-- 'nix-snowflake', 'SUPPORT_URL': 'https://nixos.org/community.html',
|
||||
-- 'VERSION': '22.05 (Quokka)', 'VERSION_CODENAME': 'quokka', 'VERSION_ID':
|
||||
-- '22.05'}"
|
||||
win32_ver TEXT, -- platform.win32_ver() as JSON
|
||||
mac_ver TEXT -- platform.mac_ver() as JSON
|
||||
);
|
||||
|
||||
|
||||
-- A "program" is an execution of a single graph, starting from a number of roots
|
||||
-- Note that if multiple calls to nancy.run() are provided within a single
|
||||
-- python script, multiple "programs" may be created. Also note that historical
|
||||
-- programs are automatically imported and merged when possible when loading a
|
||||
-- "datum" from disk.
|
||||
CREATE TABLE program (
|
||||
uuid BLOB PRIMARY KEY NOT NULL,
|
||||
name TEXT, -- name of the program, usually written lowercase by calling code e.g. cnn_crossval
|
||||
-- Names of built-in operations will be shown in upper case: e.g. 'FREEZE'
|
||||
|
||||
-- we use POSIX timestamps for time recording.
|
||||
-- e.g. datetime.datetime.now().timestamp()
|
||||
start_time REAL,
|
||||
end_time REAL,
|
||||
|
||||
process_id INTEGER, -- host PID of python process on host OS
|
||||
environment BLOB NOT NULL REFERENCES environment ON UPDATE CASCADE,
|
||||
message TEXT NOT NULL -- user-defined message to help distinguish similar runs
|
||||
);
|
||||
CREATE INDEX FK_program_environment ON program (environment);
|
||||
|
||||
|
||||
-- We try to track all python packages that impact execution by traversing a
|
||||
-- copy of sys.modules. This is done once before a "program" and once after in
|
||||
-- case some calling code winds up calling a previously-unloaded module.
|
||||
CREATE TABLE package (
|
||||
sha256 BLOB PRIMARY KEY NOT NULL,
|
||||
name TEXT NOT NULL,
|
||||
version TEXT,
|
||||
|
||||
UNIQUE (name, version)
|
||||
);
|
||||
-- A module describes any python module file containing decorated Functions.
|
||||
-- Modules are tracked since they impact the global scope of function calls.
|
||||
CREATE TABLE module(
|
||||
sha256 BLOB PRIMARY KEY NOT NULL,
|
||||
name TEXT NOT NULL,
|
||||
code TEXT, -- code doesn't have to be included, but should be used to create sha256
|
||||
package BLOB REFERENCES package ON UPDATE CASCADE
|
||||
);
|
||||
CREATE INDEX FK_module_package ON module (package);
|
||||
-- A func just describes a function, without reference to its arguments.
|
||||
-- It can have inputs and outputs, which are described in the func_inputs and
|
||||
-- func_outputs children tables.
|
||||
CREATE TABLE func(
|
||||
sha256 BLOB PRIMARY KEY NOT NULL,
|
||||
name TEXT NOT NULL,
|
||||
module BLOB NOT NULL REFERENCES module ON UPDATE CASCADE
|
||||
);
|
||||
CREATE INDEX FK_func_module ON func (module);
|
||||
CREATE TABLE func_input(
|
||||
uuid BLOB PRIMARY KEY NOT NULL,
|
||||
name TEXT NOT NULL,
|
||||
typename TEXT NOT NULL,
|
||||
func BLOB NOT NULL REFERENCES func ON UPDATE CASCADE,
|
||||
|
||||
position INTEGER,
|
||||
posonly BOOL,
|
||||
kwonly BOOL,
|
||||
|
||||
description TEXT
|
||||
);
|
||||
CREATE INDEX FK_func_input_func ON func_input (func);
|
||||
CREATE TABLE func_output(
|
||||
uuid BLOB PRIMARY KEY NOT NULL,
|
||||
name TEXT,
|
||||
typename TEXT NOT NULL,
|
||||
func BLOB NOT NULL REFERENCES func ON UPDATE CASCADE,
|
||||
|
||||
position INTEGER NOT NULL,
|
||||
description TEXT
|
||||
);
|
||||
CREATE INDEX FK_func_output_func ON func_output (func);
|
||||
|
||||
|
||||
-- Tasks are usually executed calls to Functions: they correspond to a
|
||||
-- particular set of inputs which are themselves data (see datum table). A task
|
||||
-- is executed in the context of a "program". Within a program, tasks are
|
||||
-- typically evaluated in a serial manner.
|
||||
CREATE TABLE task(
|
||||
uuid BLOB PRIMARY KEY NOT NULL,
|
||||
program BLOB NOT NULL REFERENCES program ON UPDATE CASCADE,
|
||||
|
||||
-- func is NULL for some built-in functionality like "RECORD" programs
|
||||
func BLOB REFERENCES func ON UPDATE CASCADE
|
||||
);
|
||||
CREATE INDEX FK_task_program ON task (program);
|
||||
CREATE INDEX FK_task_func ON task (func);
|
||||
-- A datum is an object that is computed as the output of a task, given as a
|
||||
-- literal value in a config file, or loaded from a file.
|
||||
CREATE TABLE datum(
|
||||
uuid BLOB PRIMARY KEY NOT NULL,
|
||||
-- provider_type describes where the datum came from. Choices are:
|
||||
-- - COMPUTED: output of a decorated Function
|
||||
-- - IMPORTED: imported output from a prior program
|
||||
-- - LITERAL: literal value provided in a config file
|
||||
-- Note that literals are implicitly imported (hash computed) at runtime
|
||||
provider_type TEXT,
|
||||
|
||||
-- task and task_output are only used when provider_type='COMPUTED'
|
||||
task BLOB REFERENCES task ON UPDATE CASCADE,
|
||||
task_output BLOB REFERENCES func_output ON UPDATE CASCADE,
|
||||
|
||||
literal_json TEXT, -- if provider_type='LITERAL', a JSON representation of the value
|
||||
|
||||
typename TEXT NOT NULL -- string representation of the data type
|
||||
);
|
||||
CREATE INDEX FK_datum_task ON datum (task);
|
||||
CREATE INDEX FK_datum_task_output ON datum (task_output);
|
||||
-- A task_input records the version of a Datum that is passed to a function
|
||||
CREATE TABLE task_input(
|
||||
uuid BLOB PRIMARY KEY NOT NULL,
|
||||
task BLOB NOT NULL REFERENCES task ON UPDATE CASCADE,
|
||||
-- if this was a python function, reference which input
|
||||
func_input BLOB REFERENCES func_input ON UPDATE CASCADE,
|
||||
|
||||
datum BLOB NOT NULL REFERENCES datum ON UPDATE CASCADE,
|
||||
-- Data have versions to facilitate tracking non-const operations. If a datum
|
||||
-- is passed to a non-const operation, it must increment its internal
|
||||
-- version
|
||||
datum_version INTEGER NOT NULL
|
||||
);
|
||||
CREATE INDEX FK_task_input_func_input ON task_input (func_input);
|
||||
CREATE INDEX FK_task_input_datum ON task_input (datum);
|
||||
90
src/program.rs
Normal file
90
src/program.rs
Normal file
@ -0,0 +1,90 @@
|
||||
use log;
|
||||
use rusqlite::{Connection,Error as RSQLError};
|
||||
extern crate derive_more;
|
||||
use derive_more::{From};
|
||||
|
||||
use std::time::{Instant, SystemTime};
|
||||
|
||||
use crate::timing;
|
||||
|
||||
pub struct Task {
|
||||
start: Instant,
|
||||
end: Option<Instant>,
|
||||
uuid: String,
|
||||
}
|
||||
|
||||
pub struct TaskInput<T> {
|
||||
task: Task,
|
||||
datum: T,
|
||||
}
|
||||
|
||||
pub struct Program {
|
||||
}
|
||||
impl Program {
|
||||
//fn new(conn: &Connection) -> Self {
|
||||
//Program {
|
||||
//}
|
||||
//}
|
||||
//fn new_task(self: &Program) -> Task {
|
||||
//}
|
||||
}
|
||||
|
||||
#[derive(Debug)]
|
||||
pub enum ProgramError<E> {
|
||||
CreateTransactionFailed(RSQLError),
|
||||
ProgramFailed(E),
|
||||
CommitFailed(RSQLError),
|
||||
}
|
||||
impl<E> From<E> for ProgramError<E> {
|
||||
fn from(e: E) -> ProgramError<E> { ProgramError::ProgramFailed(e) }
|
||||
}
|
||||
|
||||
/// Run a closure as a program, within a database transaction
|
||||
pub fn with_program<E, F : FnOnce(Program) -> Result<(), E>>(
|
||||
conn: &mut Connection,
|
||||
name: &str,
|
||||
message: &str,
|
||||
f: F,
|
||||
) -> Result<(), ProgramError<E>> {
|
||||
// NOTE: for Errors outside of f(prog), we should not rely on ?, so that we can keep the
|
||||
// From instance for ProgramError as general as possible. Instead, we should manually check
|
||||
// errors in the surrounding code in this function and only use ? for f(prog).
|
||||
|
||||
let log_target = &format!("nancy.program ({})", name);
|
||||
|
||||
log::info!(target: log_target, "Running program {} ({})", name, message);
|
||||
|
||||
// start transaction
|
||||
match conn.transaction() {
|
||||
Err(e) => Err(ProgramError::CreateTransactionFailed(e)),
|
||||
Ok(tx) => {
|
||||
// start timer
|
||||
log::debug!(target: log_target, "Starting timers");
|
||||
let start_st = SystemTime::now();
|
||||
let start = Instant::now();
|
||||
let start_stamp = timing::persistent_stamp(
|
||||
Instant::now(),
|
||||
start,
|
||||
start_st);
|
||||
|
||||
// Instantiate Program
|
||||
// (record name and message for new program, get program ID)
|
||||
let prog = Program {};
|
||||
|
||||
// run closure with program argument
|
||||
f(prog)?; // if closure fails, transaction will be rolled back
|
||||
|
||||
// end timer
|
||||
// Commit scope for RECORD program
|
||||
let end = Instant::now();
|
||||
log::debug!(target: log_target, "Start time: {:?} f64 timestamp={:#?}", start_st, start_stamp);
|
||||
log::debug!(target: log_target, "Elapsed: {} seconds", (end - start).as_secs_f64());
|
||||
// record end time
|
||||
// commit transaction
|
||||
match tx.commit() {
|
||||
Err(e) => Err(ProgramError::CommitFailed(e)),
|
||||
Ok(_) => Ok(()),
|
||||
}
|
||||
},
|
||||
}
|
||||
}
|
||||
11
src/timing.rs
Normal file
11
src/timing.rs
Normal file
@ -0,0 +1,11 @@
|
||||
use std::time::{Instant, SystemTime, UNIX_EPOCH};
|
||||
|
||||
/// This converts an Instant to a double-precision float, which as of October 2022 has roughly 300
|
||||
/// ns of resolution.
|
||||
pub fn persistent_stamp(instant: Instant, base_instant: Instant, base_systime: SystemTime) -> f64 {
|
||||
base_systime.checked_add(instant - base_instant)
|
||||
.expect("Bounds error in std::time::SystemTime::checked_add")
|
||||
.duration_since(UNIX_EPOCH)
|
||||
.expect("Clock may have gone backward")
|
||||
.as_secs_f64()
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user