Start setting up tree_traverser
This commit is contained in:
parent
e07c06b1ee
commit
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README.md
21
README.md
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# Q<sup>3</sup> Quick Querying of Qubes
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This repostitory contains a collection of components designed to deliver user friendly cataloging for ecmwf's data. The STAC Server, Frontend and a periodic job to do tree compression can be deployed together to kubernetes using the [helm chart](./helm_chart). Thise deployment can then be accessed either via the Query Builder Web interface or the python client.
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## 📦 Components Overview
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### 🌲 [Tree Compressor](./tree_compresser)
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> **Python/Rust Package**
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📋 Lists the datasets in an **FDB** and converts the output into a **compressed tree representation** for fast querying.
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---
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### 🚀 [STAC Server](./stac_server)
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### 🚀 [Qubed STAC Server](./stac_server)
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> **FastAPI STAC Server Backend**
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- 🌟 Implements our proposed [Datacube STAC Extension](./structured_stac.md).
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- 🛠️ Allows efficient traversal of ECMWF's datacubes.
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- 🔗 **[Live Example](http://catalogue.lumi.apps.dte.destination-earth.eu/stac?class=d1&dataset=extremes-dt&expver=0001&stream=oper)**.
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- Part of the implementation of this is [🌲 Tree Compressor](./tree_compresser), a **compressed tree representation** optimised for storing trees with many duplicated subtress.
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- 🔗 **[Live Example]()**.
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---
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### 🌐 [Web Query Builder](./web_query_builder)
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### 🌐 [Qubed Web Query Builder](./web_query_builder)
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> **Web Frontend**
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- 👀 Displays data from the **STAC Server** in an intuitive user interface.
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@ -34,7 +23,7 @@ This repostitory contains a collection of components designed to deliver user fr
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---
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### TODO: 🐍 [Python Query Builder](./python_query_builder)
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### TODO: 🐍 [Qubed Python Query Builder](./python_query_builder)
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> **Python Client**
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- 🤖 A Python client for the **STAC Server**.
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tree_compresser/.gitignore
vendored
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tree_compresser/.gitignore
vendored
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/target
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# Byte-compiled / optimized / DLL files
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__pycache__/
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.pytest_cache/
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*.py[cod]
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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.venv/
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env/
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bin/
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build/
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develop-eggs/
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dist/
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eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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include/
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man/
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venv/
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*.egg-info/
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.installed.cfg
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*.egg
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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pip-selfcheck.json
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.cache
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nosetests.xml
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coverage.xml
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# Translations
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*.mo
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# Mr Developer
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.mr.developer.cfg
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.project
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.pydevproject
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# Rope
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.ropeproject
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# Django stuff:
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*.log
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*.pot
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.DS_Store
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# Sphinx documentation
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docs/_build/
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# PyCharm
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.idea/
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# VSCode
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.vscode/
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# Pyenv
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.python-version
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tree_compresser/Cargo.lock
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tree_compresser/Cargo.lock
generated
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# This file is automatically @generated by Cargo.
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|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "b5b9d34b8991d19d98081b46eacdd8eb58c6f2b201139f7c5f643cc155a633af"
|
||||
dependencies = [
|
||||
"proc-macro2",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "regex"
|
||||
version = "1.11.1"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "b544ef1b4eac5dc2db33ea63606ae9ffcfac26c1416a2806ae0bf5f56b201191"
|
||||
dependencies = [
|
||||
"aho-corasick",
|
||||
"memchr",
|
||||
"regex-automata",
|
||||
"regex-syntax",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "regex-automata"
|
||||
version = "0.4.9"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "809e8dc61f6de73b46c85f4c96486310fe304c434cfa43669d7b40f711150908"
|
||||
dependencies = [
|
||||
"aho-corasick",
|
||||
"memchr",
|
||||
"regex-syntax",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "regex-syntax"
|
||||
version = "0.8.5"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "2b15c43186be67a4fd63bee50d0303afffcef381492ebe2c5d87f324e1b8815c"
|
||||
|
||||
[[package]]
|
||||
name = "rsfdb"
|
||||
version = "0.1.0"
|
||||
source = "git+https://github.com/ecmwf/rsfdb?branch=develop#ab8c9590bba15d22167c274db9238cd9b897baf1"
|
||||
dependencies = [
|
||||
"libc",
|
||||
"libloading",
|
||||
"once_cell",
|
||||
"rsfindlibs",
|
||||
"serde",
|
||||
"serde_json",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "rsfindlibs"
|
||||
version = "0.1.1"
|
||||
source = "git+https://github.com/ecmwf-projects/rsfindlibs.git#1358b1049bf3e0b581badfc8005a9828a542cdaa"
|
||||
dependencies = [
|
||||
"cc",
|
||||
"clap",
|
||||
"env_logger",
|
||||
"libloading",
|
||||
"log",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "ryu"
|
||||
version = "1.0.18"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f"
|
||||
|
||||
[[package]]
|
||||
name = "serde"
|
||||
version = "1.0.215"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "6513c1ad0b11a9376da888e3e0baa0077f1aed55c17f50e7b2397136129fb88f"
|
||||
dependencies = [
|
||||
"serde_derive",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "serde_derive"
|
||||
version = "1.0.215"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "ad1e866f866923f252f05c889987993144fb74e722403468a4ebd70c3cd756c0"
|
||||
dependencies = [
|
||||
"proc-macro2",
|
||||
"quote",
|
||||
"syn",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "serde_json"
|
||||
version = "1.0.133"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "c7fceb2473b9166b2294ef05efcb65a3db80803f0b03ef86a5fc88a2b85ee377"
|
||||
dependencies = [
|
||||
"itoa",
|
||||
"memchr",
|
||||
"ryu",
|
||||
"serde",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "shlex"
|
||||
version = "1.3.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
|
||||
|
||||
[[package]]
|
||||
name = "strsim"
|
||||
version = "0.11.1"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
|
||||
|
||||
[[package]]
|
||||
name = "syn"
|
||||
version = "2.0.89"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "44d46482f1c1c87acd84dea20c1bf5ebff4c757009ed6bf19cfd36fb10e92c4e"
|
||||
dependencies = [
|
||||
"proc-macro2",
|
||||
"quote",
|
||||
"unicode-ident",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "target-lexicon"
|
||||
version = "0.12.16"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1"
|
||||
|
||||
[[package]]
|
||||
name = "termcolor"
|
||||
version = "1.4.1"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755"
|
||||
dependencies = [
|
||||
"winapi-util",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "unicode-ident"
|
||||
version = "1.0.14"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "adb9e6ca4f869e1180728b7950e35922a7fc6397f7b641499e8f3ef06e50dc83"
|
||||
|
||||
[[package]]
|
||||
name = "unindent"
|
||||
version = "0.2.3"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce"
|
||||
|
||||
[[package]]
|
||||
name = "utf8parse"
|
||||
version = "0.2.2"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
|
||||
|
||||
[[package]]
|
||||
name = "winapi"
|
||||
version = "0.3.9"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419"
|
||||
dependencies = [
|
||||
"winapi-i686-pc-windows-gnu",
|
||||
"winapi-x86_64-pc-windows-gnu",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "winapi-i686-pc-windows-gnu"
|
||||
version = "0.4.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
|
||||
|
||||
[[package]]
|
||||
name = "winapi-util"
|
||||
version = "0.1.9"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb"
|
||||
dependencies = [
|
||||
"windows-sys 0.59.0",
|
||||
]
|
||||
|
||||
[[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 = "0.52.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
|
||||
dependencies = [
|
||||
"windows-targets",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "windows-sys"
|
||||
version = "0.59.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b"
|
||||
dependencies = [
|
||||
"windows-targets",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "windows-targets"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973"
|
||||
dependencies = [
|
||||
"windows_aarch64_gnullvm",
|
||||
"windows_aarch64_msvc",
|
||||
"windows_i686_gnu",
|
||||
"windows_i686_gnullvm",
|
||||
"windows_i686_msvc",
|
||||
"windows_x86_64_gnu",
|
||||
"windows_x86_64_gnullvm",
|
||||
"windows_x86_64_msvc",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "windows_aarch64_gnullvm"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
|
||||
|
||||
[[package]]
|
||||
name = "windows_aarch64_msvc"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
|
||||
|
||||
[[package]]
|
||||
name = "windows_i686_gnu"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b"
|
||||
|
||||
[[package]]
|
||||
name = "windows_i686_gnullvm"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
|
||||
|
||||
[[package]]
|
||||
name = "windows_i686_msvc"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
|
||||
|
||||
[[package]]
|
||||
name = "windows_x86_64_gnu"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
|
||||
|
||||
[[package]]
|
||||
name = "windows_x86_64_gnullvm"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
|
||||
|
||||
[[package]]
|
||||
name = "windows_x86_64_msvc"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
|
17
tree_compresser/Cargo.toml
Normal file
17
tree_compresser/Cargo.toml
Normal file
@ -0,0 +1,17 @@
|
||||
[package]
|
||||
name = "qubed_tree"
|
||||
version = "0.1.0"
|
||||
edition = "2021"
|
||||
|
||||
[dependencies]
|
||||
rsfdb = {git = "https://github.com/ecmwf/rsfdb", branch = "develop"}
|
||||
serde = { version = "1.0", features = ["derive"] }
|
||||
serde_json = "1.0"
|
||||
pyo3 = "0.23.1"
|
||||
|
||||
|
||||
[lib]
|
||||
name = "tree_traverser"
|
||||
crate-type = ["cdylib"]
|
||||
path = "./rust_src/lib.rs"
|
||||
|
0
tree_compresser/README.md
Normal file
0
tree_compresser/README.md
Normal file
@ -1,13 +1,27 @@
|
||||
[build-system]
|
||||
requires = ["setuptools >= 61.0"]
|
||||
build-backend = "setuptools.build_meta"
|
||||
requires = ["maturin>=1.7,<2.0"]
|
||||
build-backend = "maturin"
|
||||
|
||||
[project]
|
||||
name = "TreeTraverser"
|
||||
name = "tree_traverser"
|
||||
description = "Tools to work with compressed Datacubes and Trees"
|
||||
readme = "README.md"
|
||||
authors = [
|
||||
{name = "Tom Hodson", email = "thomas.hodson@ecmwf.int"},
|
||||
]
|
||||
classifiers = [
|
||||
"Programming Language :: Rust",
|
||||
"Programming Language :: Python :: Implementation :: CPython",
|
||||
"Programming Language :: Python :: Implementation :: PyPy",
|
||||
]
|
||||
requires-python = ">= 3.11"
|
||||
dynamic = ["version"]
|
||||
dependencies = [
|
||||
"fastapi",
|
||||
"pe"
|
||||
]
|
||||
|
||||
[tool.maturin]
|
||||
python-source = "python_src"
|
||||
module-name = "tree_traverser.rust"
|
||||
features = ["pyo3/extension-module"]
|
||||
|
||||
|
1
tree_compresser/python_src/tree_traverser/__init__.py
Normal file
1
tree_compresser/python_src/tree_traverser/__init__.py
Normal file
@ -0,0 +1 @@
|
||||
from . import rust as backend
|
88
tree_compresser/rust_src/lib.rs
Normal file
88
tree_compresser/rust_src/lib.rs
Normal file
@ -0,0 +1,88 @@
|
||||
#![allow(unused_imports)]
|
||||
#![allow(dead_code)]
|
||||
#![allow(unused_variables)]
|
||||
|
||||
use rsfdb::listiterator::KeyValueLevel;
|
||||
use rsfdb::request::Request;
|
||||
use rsfdb::FDB; // Make sure the `fdb` crate is correctly specified in the dependencies
|
||||
|
||||
use serde_json::{json, Value};
|
||||
use std::time::Instant;
|
||||
|
||||
use pyo3::prelude::*;
|
||||
use pyo3::types::{PyDict, PyList, PyString};
|
||||
|
||||
use crate::tree::TreeNode;
|
||||
use std::collections::HashMap;
|
||||
|
||||
/// Formats the sum of two numbers as string.
|
||||
#[pyfunction]
|
||||
#[pyo3(signature = (request, fdb_config = None))]
|
||||
fn traverse_fdb(
|
||||
request: HashMap<String, Vec<String>>,
|
||||
fdb_config: Option<&str>,
|
||||
) -> PyResult<String> {
|
||||
let start_time = Instant::now();
|
||||
let fdb = FDB::new(fdb_config).unwrap();
|
||||
|
||||
let list_request =
|
||||
Request::from_json(json!(request)).expect("Failed to create request from python dict");
|
||||
|
||||
let list = fdb.list(&list_request, true, true).unwrap();
|
||||
|
||||
// for item in list {
|
||||
// for kvl in item.request {
|
||||
// println!("{:?}", kvl);
|
||||
// }
|
||||
// }
|
||||
|
||||
let mut root = TreeNode::new(KeyValueLevel {
|
||||
key: "root".to_string(),
|
||||
value: "root".to_string(),
|
||||
level: 0,
|
||||
});
|
||||
|
||||
for item in list {
|
||||
if let Some(request) = &item.request {
|
||||
root.insert(&request);
|
||||
}
|
||||
}
|
||||
|
||||
// Traverse and print the tree
|
||||
root.traverse(0, &|node, level| {
|
||||
let indent = " ".repeat(level);
|
||||
println!("{}{}={}", indent, node.key.key, node.key.value);
|
||||
});
|
||||
|
||||
// Convert the tree to JSON
|
||||
// let json_output = root.to_json();
|
||||
|
||||
// // Print the JSON output
|
||||
// // println!("{}", serde_json::to_string_pretty(&json_output).unwrap());
|
||||
// std::fs::write(
|
||||
// "output.json",
|
||||
// serde_json::to_string_pretty(&json_output).unwrap(),
|
||||
// )
|
||||
// .expect("Unable to write file");
|
||||
|
||||
// let duration = start_time.elapsed();
|
||||
// println!("Total runtime: {:?}", duration);
|
||||
|
||||
Ok(("test").to_string())
|
||||
}
|
||||
|
||||
use pyo3::prelude::*;
|
||||
|
||||
/// Formats the sum of two numbers as string.
|
||||
#[pyfunction]
|
||||
fn sum_as_string(a: usize, b: usize) -> PyResult<String> {
|
||||
Ok((a + b + 2).to_string())
|
||||
}
|
||||
|
||||
/// A Python module implemented in Rust. The name of this function must match
|
||||
/// the `lib.name` setting in the `Cargo.toml`, else Python will not be able to
|
||||
/// import the module.
|
||||
#[pymodule]
|
||||
fn rust(m: &Bound<'_, PyModule>) -> PyResult<()> {
|
||||
m.add_function(wrap_pyfunction!(traverse_fdb, m)?)
|
||||
}
|
66
tree_compresser/rust_src/tree.rs
Normal file
66
tree_compresser/rust_src/tree.rs
Normal file
@ -0,0 +1,66 @@
|
||||
#[derive(Debug)]
|
||||
pub struct TreeNode {
|
||||
key: KeyValueLevel,
|
||||
children: Vec<TreeNode>,
|
||||
}
|
||||
|
||||
impl TreeNode {
|
||||
pub fn new(key: KeyValueLevel) -> Self {
|
||||
TreeNode {
|
||||
key,
|
||||
children: Vec::new(),
|
||||
}
|
||||
}
|
||||
|
||||
pub fn insert(&mut self, path: &[KeyValueLevel]) {
|
||||
if path.is_empty() {
|
||||
return;
|
||||
}
|
||||
|
||||
let kvl = &path[0];
|
||||
|
||||
// Check if a child with the same key and value exists
|
||||
if let Some(child) = self.children.iter_mut().find(|child| child.key == *kvl) {
|
||||
// Insert the remaining path into the existing child
|
||||
child.insert(&path[1..]);
|
||||
} else {
|
||||
// Create a new child node
|
||||
let mut new_child = TreeNode::new(kvl.clone());
|
||||
new_child.insert(&path[1..]);
|
||||
self.children.push(new_child);
|
||||
}
|
||||
}
|
||||
|
||||
pub fn traverse<F>(&self, level: usize, callback: &F)
|
||||
where
|
||||
F: Fn(&TreeNode, usize),
|
||||
{
|
||||
callback(self, level);
|
||||
for child in &self.children {
|
||||
child.traverse(level + 1, callback);
|
||||
}
|
||||
}
|
||||
|
||||
pub fn to_json(&self) -> Value {
|
||||
let formatted_key = format!("{}={}", self.key.key, self.key.value);
|
||||
|
||||
let children_json: Value = if self.children.is_empty() {
|
||||
Value::Object(serde_json::Map::new())
|
||||
} else {
|
||||
Value::Object(
|
||||
self.children
|
||||
.iter()
|
||||
.map(|child| {
|
||||
(
|
||||
format!("{}={}", child.key.key, child.key.value),
|
||||
child.to_json(),
|
||||
)
|
||||
})
|
||||
.collect(),
|
||||
)
|
||||
};
|
||||
|
||||
// Combine the formatted key with children
|
||||
serde_json::json!({ formatted_key: children_json })
|
||||
}
|
||||
}
|
26
tree_compresser/tests/test.py
Normal file
26
tree_compresser/tests/test.py
Normal file
@ -0,0 +1,26 @@
|
||||
from tree_traverser import backend
|
||||
|
||||
|
||||
|
||||
config = """
|
||||
---
|
||||
type: remote
|
||||
host: databridge-prod-catalogue1-ope.ewctest.link
|
||||
port: 10000
|
||||
engine: remote
|
||||
store: remote
|
||||
"""
|
||||
|
||||
def massage_request(r):
|
||||
return {k : v if isinstance(v, list) else [v]
|
||||
for k, v in r.items()}
|
||||
|
||||
request = {
|
||||
"class": "d1",
|
||||
"dataset": "extremes-dt",
|
||||
"expver": "0001",
|
||||
"stream": "oper",
|
||||
"date": ["20241117", "20241116"],
|
||||
}
|
||||
|
||||
backend.traverse_fdb(massage_request(request), fdb_config = config)
|
Loading…
x
Reference in New Issue
Block a user