Compare commits
8 Commits
Author | SHA1 | Date | |
---|---|---|---|
06dbb56c28 | |||
79fcce8b84 | |||
f4064f087e | |||
276665f5fd | |||
fd536862e2 | |||
576dc303f4 | |||
2822a483e3 | |||
b8cebb8ba4 |
11
.devcontainer/Dockerfile
Normal file
11
.devcontainer/Dockerfile
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
FROM mcr.microsoft.com/devcontainers/anaconda:1-3
|
||||||
|
|
||||||
|
# Copy environment.yml (if found) to a temp location so we update the environment. Also
|
||||||
|
# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
|
||||||
|
COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
|
||||||
|
RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/conda env update -n base -f /tmp/conda-tmp/environment.yml; fi \
|
||||||
|
&& rm -rf /tmp/conda-tmp
|
||||||
|
|
||||||
|
# [Optional] Uncomment this section to install additional OS packages.
|
||||||
|
# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
|
||||||
|
# && apt-get -y install --no-install-recommends <your-package-list-here>
|
@ -1,9 +1,11 @@
|
|||||||
// For format details, see https://aka.ms/devcontainer.json. For config options, see the
|
// For format details, see https://aka.ms/devcontainer.json. For config options, see the
|
||||||
// README at: https://github.com/devcontainers/templates/tree/main/src/python
|
// README at: https://github.com/devcontainers/templates/tree/main/src/anaconda
|
||||||
{
|
{
|
||||||
"name": "Python 3",
|
"name": "Anaconda (Python 3)",
|
||||||
// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
|
"build": {
|
||||||
"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
|
"context": "..",
|
||||||
|
"dockerfile": "Dockerfile"
|
||||||
|
}
|
||||||
|
|
||||||
// Features to add to the dev container. More info: https://containers.dev/features.
|
// Features to add to the dev container. More info: https://containers.dev/features.
|
||||||
// "features": {},
|
// "features": {},
|
||||||
@ -12,14 +14,7 @@
|
|||||||
// "forwardPorts": [],
|
// "forwardPorts": [],
|
||||||
|
|
||||||
// Use 'postCreateCommand' to run commands after the container is created.
|
// Use 'postCreateCommand' to run commands after the container is created.
|
||||||
"postCreateCommand": "pip3 install --user -r requirements.txt",
|
// "postCreateCommand": "python --version",
|
||||||
"customizations": {
|
|
||||||
"vscode": {
|
|
||||||
"extensions": [
|
|
||||||
"mechatroner.rainbow-csv"
|
|
||||||
]
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// Configure tool-specific properties.
|
// Configure tool-specific properties.
|
||||||
// "customizations": {},
|
// "customizations": {},
|
||||||
|
3
.devcontainer/noop.txt
Normal file
3
.devcontainer/noop.txt
Normal file
@ -0,0 +1,3 @@
|
|||||||
|
This file copied into the container along with environment.yml* from the parent
|
||||||
|
folder. This file is included to prevents the Dockerfile COPY instruction from
|
||||||
|
failing if no environment.yml is found.
|
159
.gitignore
vendored
159
.gitignore
vendored
@ -1,6 +1,6 @@
|
|||||||
# File created using '.gitignore Generator' for Visual Studio Code: https://bit.ly/vscode-gig
|
# File created using '.gitignore Generator' for Visual Studio Code: https://bit.ly/vscode-gig
|
||||||
# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode,svelte,python,linux,node
|
# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode,linux,python
|
||||||
# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,svelte,python,linux,node
|
# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,linux,python
|
||||||
|
|
||||||
### Linux ###
|
### Linux ###
|
||||||
*~
|
*~
|
||||||
@ -17,146 +17,6 @@
|
|||||||
# .nfs files are created when an open file is removed but is still being accessed
|
# .nfs files are created when an open file is removed but is still being accessed
|
||||||
.nfs*
|
.nfs*
|
||||||
|
|
||||||
### Node ###
|
|
||||||
# Logs
|
|
||||||
logs
|
|
||||||
*.log
|
|
||||||
npm-debug.log*
|
|
||||||
yarn-debug.log*
|
|
||||||
yarn-error.log*
|
|
||||||
lerna-debug.log*
|
|
||||||
.pnpm-debug.log*
|
|
||||||
|
|
||||||
# Diagnostic reports (https://nodejs.org/api/report.html)
|
|
||||||
report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
|
|
||||||
|
|
||||||
# Runtime data
|
|
||||||
pids
|
|
||||||
*.pid
|
|
||||||
*.seed
|
|
||||||
*.pid.lock
|
|
||||||
|
|
||||||
# Directory for instrumented libs generated by jscoverage/JSCover
|
|
||||||
lib-cov
|
|
||||||
|
|
||||||
# Coverage directory used by tools like istanbul
|
|
||||||
coverage
|
|
||||||
*.lcov
|
|
||||||
|
|
||||||
# nyc test coverage
|
|
||||||
.nyc_output
|
|
||||||
|
|
||||||
# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
|
|
||||||
.grunt
|
|
||||||
|
|
||||||
# Bower dependency directory (https://bower.io/)
|
|
||||||
bower_components
|
|
||||||
|
|
||||||
# node-waf configuration
|
|
||||||
.lock-wscript
|
|
||||||
|
|
||||||
# Compiled binary addons (https://nodejs.org/api/addons.html)
|
|
||||||
build/Release
|
|
||||||
|
|
||||||
# Dependency directories
|
|
||||||
node_modules/
|
|
||||||
jspm_packages/
|
|
||||||
|
|
||||||
# Snowpack dependency directory (https://snowpack.dev/)
|
|
||||||
web_modules/
|
|
||||||
|
|
||||||
# TypeScript cache
|
|
||||||
*.tsbuildinfo
|
|
||||||
|
|
||||||
# Optional npm cache directory
|
|
||||||
.npm
|
|
||||||
|
|
||||||
# Optional eslint cache
|
|
||||||
.eslintcache
|
|
||||||
|
|
||||||
# Optional stylelint cache
|
|
||||||
.stylelintcache
|
|
||||||
|
|
||||||
# Microbundle cache
|
|
||||||
.rpt2_cache/
|
|
||||||
.rts2_cache_cjs/
|
|
||||||
.rts2_cache_es/
|
|
||||||
.rts2_cache_umd/
|
|
||||||
|
|
||||||
# Optional REPL history
|
|
||||||
.node_repl_history
|
|
||||||
|
|
||||||
# Output of 'npm pack'
|
|
||||||
*.tgz
|
|
||||||
|
|
||||||
# Yarn Integrity file
|
|
||||||
.yarn-integrity
|
|
||||||
|
|
||||||
# dotenv environment variable files
|
|
||||||
.env
|
|
||||||
.env.development.local
|
|
||||||
.env.test.local
|
|
||||||
.env.production.local
|
|
||||||
.env.local
|
|
||||||
|
|
||||||
# parcel-bundler cache (https://parceljs.org/)
|
|
||||||
.cache
|
|
||||||
.parcel-cache
|
|
||||||
|
|
||||||
# Next.js build output
|
|
||||||
.next
|
|
||||||
out
|
|
||||||
|
|
||||||
# Nuxt.js build / generate output
|
|
||||||
.nuxt
|
|
||||||
dist
|
|
||||||
|
|
||||||
# Gatsby files
|
|
||||||
.cache/
|
|
||||||
# Comment in the public line in if your project uses Gatsby and not Next.js
|
|
||||||
# https://nextjs.org/blog/next-9-1#public-directory-support
|
|
||||||
# public
|
|
||||||
|
|
||||||
# vuepress build output
|
|
||||||
.vuepress/dist
|
|
||||||
|
|
||||||
# vuepress v2.x temp and cache directory
|
|
||||||
.temp
|
|
||||||
|
|
||||||
# Docusaurus cache and generated files
|
|
||||||
.docusaurus
|
|
||||||
|
|
||||||
# Serverless directories
|
|
||||||
.serverless/
|
|
||||||
|
|
||||||
# FuseBox cache
|
|
||||||
.fusebox/
|
|
||||||
|
|
||||||
# DynamoDB Local files
|
|
||||||
.dynamodb/
|
|
||||||
|
|
||||||
# TernJS port file
|
|
||||||
.tern-port
|
|
||||||
|
|
||||||
# Stores VSCode versions used for testing VSCode extensions
|
|
||||||
.vscode-test
|
|
||||||
|
|
||||||
# yarn v2
|
|
||||||
.yarn/cache
|
|
||||||
.yarn/unplugged
|
|
||||||
.yarn/build-state.yml
|
|
||||||
.yarn/install-state.gz
|
|
||||||
.pnp.*
|
|
||||||
|
|
||||||
### Node Patch ###
|
|
||||||
# Serverless Webpack directories
|
|
||||||
.webpack/
|
|
||||||
|
|
||||||
# Optional stylelint cache
|
|
||||||
|
|
||||||
# SvelteKit build / generate output
|
|
||||||
.svelte-kit
|
|
||||||
|
|
||||||
### Python ###
|
### Python ###
|
||||||
# Byte-compiled / optimized / DLL files
|
# Byte-compiled / optimized / DLL files
|
||||||
__pycache__/
|
__pycache__/
|
||||||
@ -202,6 +62,7 @@ htmlcov/
|
|||||||
.nox/
|
.nox/
|
||||||
.coverage
|
.coverage
|
||||||
.coverage.*
|
.coverage.*
|
||||||
|
.cache
|
||||||
nosetests.xml
|
nosetests.xml
|
||||||
coverage.xml
|
coverage.xml
|
||||||
*.cover
|
*.cover
|
||||||
@ -215,6 +76,7 @@ cover/
|
|||||||
*.pot
|
*.pot
|
||||||
|
|
||||||
# Django stuff:
|
# Django stuff:
|
||||||
|
*.log
|
||||||
local_settings.py
|
local_settings.py
|
||||||
db.sqlite3
|
db.sqlite3
|
||||||
db.sqlite3-journal
|
db.sqlite3-journal
|
||||||
@ -278,6 +140,7 @@ celerybeat.pid
|
|||||||
*.sage.py
|
*.sage.py
|
||||||
|
|
||||||
# Environments
|
# Environments
|
||||||
|
.env
|
||||||
.venv
|
.venv
|
||||||
env/
|
env/
|
||||||
venv/
|
venv/
|
||||||
@ -326,13 +189,6 @@ poetry.toml
|
|||||||
# LSP config files
|
# LSP config files
|
||||||
pyrightconfig.json
|
pyrightconfig.json
|
||||||
|
|
||||||
### Svelte ###
|
|
||||||
# gitignore template for the SvelteKit, frontend web component framework
|
|
||||||
# website: https://kit.svelte.dev/
|
|
||||||
|
|
||||||
.svelte-kit/
|
|
||||||
package
|
|
||||||
|
|
||||||
### VisualStudioCode ###
|
### VisualStudioCode ###
|
||||||
.vscode/*
|
.vscode/*
|
||||||
!.vscode/settings.json
|
!.vscode/settings.json
|
||||||
@ -352,9 +208,8 @@ package
|
|||||||
.history
|
.history
|
||||||
.ionide
|
.ionide
|
||||||
|
|
||||||
# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,svelte,python,linux,node
|
# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,linux,python
|
||||||
|
|
||||||
# Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
|
# Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
|
||||||
|
|
||||||
output
|
conda-bld
|
||||||
*.private.*
|
|
5
.vscode/extensions.json
vendored
Normal file
5
.vscode/extensions.json
vendored
Normal file
@ -0,0 +1,5 @@
|
|||||||
|
{
|
||||||
|
"recommendations": [
|
||||||
|
"piotrpalarz.vscode-gitignore-generator"
|
||||||
|
]
|
||||||
|
}
|
14
Jenkinsfile
vendored
14
Jenkinsfile
vendored
@ -2,14 +2,14 @@ pipeline {
|
|||||||
agent {
|
agent {
|
||||||
kubernetes {
|
kubernetes {
|
||||||
cloud 'rsys-devel'
|
cloud 'rsys-devel'
|
||||||
defaultContainer 'pip'
|
defaultContainer 'miniforge3'
|
||||||
inheritFrom 'pip'
|
inheritFrom 'miniforge'
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
stages {
|
stages {
|
||||||
stage("install") {
|
stage("install") {
|
||||||
steps {
|
steps {
|
||||||
sh 'python -m pip install -r requirements.txt'
|
sh 'conda env update -n base -f environment.yml'
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
stage("unit tests") {
|
stage("unit tests") {
|
||||||
@ -22,11 +22,14 @@ pipeline {
|
|||||||
stage("build") {
|
stage("build") {
|
||||||
steps {
|
steps {
|
||||||
sh "python -m build"
|
sh "python -m build"
|
||||||
|
sh "grayskull pypi dist/*.tar.gz --maintainers 'Harrison Deng'"
|
||||||
|
sh "python scripts/patch_recipe.py"
|
||||||
|
sh 'conda build autobigs-engine -c bioconda --output-folder conda-bld --verify'
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
stage("archive") {
|
stage("archive") {
|
||||||
steps {
|
steps {
|
||||||
archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
|
archiveArtifacts artifacts: 'dist/*.tar.gz, dist/*.whl, conda-bld/**/*.conda', fingerprint: true, followSymlinks: false, onlyIfSuccessful: true
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
stage("publish") {
|
stage("publish") {
|
||||||
@ -36,7 +39,8 @@ pipeline {
|
|||||||
CREDS = credentials('username-password-rs-git')
|
CREDS = credentials('username-password-rs-git')
|
||||||
}
|
}
|
||||||
steps {
|
steps {
|
||||||
sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
|
sh 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
|
||||||
|
sh 'curl --user ${CREDS_USR}:${CREDS_PSW} --upload-file conda-bld/**/*.conda https://git.reslate.systems/api/packages/${CREDS_USR}/conda/$(basename conda-bld/**/*.conda)'
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
stage ("pypi.org") {
|
stage ("pypi.org") {
|
||||||
|
44
autobigs-engine/meta.yaml
Normal file
44
autobigs-engine/meta.yaml
Normal file
@ -0,0 +1,44 @@
|
|||||||
|
{% set name = "autoBIGS.engine" %}
|
||||||
|
{% set version = "0.12.1.dev1+gb8cebb8.d20250221" %}
|
||||||
|
|
||||||
|
package:
|
||||||
|
name: {{ name|lower|replace(".", "-") }}
|
||||||
|
version: {{ version }}
|
||||||
|
|
||||||
|
source:
|
||||||
|
url: file:///workspaces/autoBIGS.engine/dist/autobigs_engine-0.12.1.dev1%2Bgb8cebb8.d20250221.tar.gz
|
||||||
|
sha256: c86441b94f935cfa414ff28ca4c026a070e0fb15988ea3bb7d1a942859a09b16
|
||||||
|
|
||||||
|
build:
|
||||||
|
noarch: python
|
||||||
|
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
|
||||||
|
number: 0
|
||||||
|
run_exports:
|
||||||
|
- {{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}
|
||||||
|
requirements:
|
||||||
|
host:
|
||||||
|
- python >=3.12
|
||||||
|
- setuptools >=64
|
||||||
|
- setuptools-scm >=8
|
||||||
|
- pip
|
||||||
|
run:
|
||||||
|
- python >=3.12
|
||||||
|
- biopython ==1.85
|
||||||
|
- aiohttp ==3.11.*
|
||||||
|
|
||||||
|
test:
|
||||||
|
imports:
|
||||||
|
- autobigs
|
||||||
|
commands:
|
||||||
|
- pip check
|
||||||
|
requires:
|
||||||
|
- pip
|
||||||
|
|
||||||
|
about:
|
||||||
|
summary: A library to rapidly fetch fetch MLST profiles given sequences for various diseases.
|
||||||
|
license: GPL-3.0-or-later
|
||||||
|
license_file: LICENSE
|
||||||
|
home: https://github.com/Syph-and-VPD-Lab/autoBIGS.engine
|
||||||
|
extra:
|
||||||
|
recipe-maintainers:
|
||||||
|
- Harrison Deng
|
16
environment.yml
Normal file
16
environment.yml
Normal file
@ -0,0 +1,16 @@
|
|||||||
|
name: ci
|
||||||
|
channels:
|
||||||
|
- bioconda
|
||||||
|
- conda-forge
|
||||||
|
dependencies:
|
||||||
|
- aiohttp==3.11.*
|
||||||
|
- biopython==1.85
|
||||||
|
- pytest
|
||||||
|
- pytest-asyncio
|
||||||
|
- python-build
|
||||||
|
- conda-build
|
||||||
|
- twine==6.0.1
|
||||||
|
- setuptools_scm
|
||||||
|
- pytest-cov
|
||||||
|
- grayskull
|
||||||
|
- curl
|
@ -1,8 +0,0 @@
|
|||||||
aiohttp[speedups]==3.11.*
|
|
||||||
biopython==1.85
|
|
||||||
pytest
|
|
||||||
pytest-asyncio
|
|
||||||
build
|
|
||||||
twine
|
|
||||||
setuptools_scm
|
|
||||||
pytest-cov
|
|
103
scripts/patch_recipe.py
Normal file
103
scripts/patch_recipe.py
Normal file
@ -0,0 +1,103 @@
|
|||||||
|
#!/usr/bin/env python3
|
||||||
|
|
||||||
|
import argparse
|
||||||
|
from os import fdopen, path
|
||||||
|
import os
|
||||||
|
import re
|
||||||
|
import shutil
|
||||||
|
from sys import argv
|
||||||
|
import tempfile
|
||||||
|
|
||||||
|
INDENTATION = " "
|
||||||
|
GRAYSKULL_OUTPUT_PATH = "autoBIGS.engine"
|
||||||
|
RUN_EXPORTED_VALUE = r'{{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}'
|
||||||
|
LICENSE_SUFFIX = "-or-later"
|
||||||
|
HOME_PAGE = "https://github.com/Syph-and-VPD-Lab/autoBIGS.engine"
|
||||||
|
|
||||||
|
def _calc_indentation(line: str):
|
||||||
|
return len(re.findall(INDENTATION, line.split(line.strip())[0])) if line != "\n" else 0
|
||||||
|
|
||||||
|
def read_grayskull_output():
|
||||||
|
original_recipe = path.abspath(GRAYSKULL_OUTPUT_PATH)
|
||||||
|
original_meta = path.join(original_recipe, "meta.yaml")
|
||||||
|
meta_file = open(original_meta)
|
||||||
|
lines = meta_file.readlines()
|
||||||
|
meta_file.close()
|
||||||
|
return lines
|
||||||
|
|
||||||
|
def update_naming_scheme(lines):
|
||||||
|
modified_lines = []
|
||||||
|
for line in lines:
|
||||||
|
matches = re.finditer(r"\{\{\s*name\|lower()\s+\}\}", line)
|
||||||
|
modified_line = line
|
||||||
|
for match in matches:
|
||||||
|
modified_line = modified_line[:match.start(1)] + r'|replace(".", "-")' + modified_line[match.end(1):]
|
||||||
|
modified_lines.append(modified_line)
|
||||||
|
return modified_lines
|
||||||
|
|
||||||
|
def inject_run_exports(lines: list[str]):
|
||||||
|
package_indent = False
|
||||||
|
modified_lines = []
|
||||||
|
for line in lines:
|
||||||
|
indentation_count = _calc_indentation(line)
|
||||||
|
if line == "build:\n" and indentation_count == 0:
|
||||||
|
package_indent = True
|
||||||
|
modified_lines.append(line)
|
||||||
|
elif package_indent and indentation_count == 0:
|
||||||
|
modified_lines.append(INDENTATION*1 + "run_exports:\n")
|
||||||
|
modified_lines.append(INDENTATION*2 + "- " + RUN_EXPORTED_VALUE + "\n")
|
||||||
|
package_indent = False
|
||||||
|
else:
|
||||||
|
modified_lines.append(line)
|
||||||
|
return modified_lines
|
||||||
|
|
||||||
|
def suffix_license(lines: list[str]):
|
||||||
|
about_indent = False
|
||||||
|
modified_lines = []
|
||||||
|
for line in lines:
|
||||||
|
indentation_count = _calc_indentation(line)
|
||||||
|
if line == "about:\n" and indentation_count == 0:
|
||||||
|
about_indent = True
|
||||||
|
modified_lines.append(line)
|
||||||
|
elif about_indent and indentation_count == 1 and line.lstrip().startswith("license:"):
|
||||||
|
modified_lines.append(line.rstrip() + LICENSE_SUFFIX + "\n")
|
||||||
|
about_indent = False
|
||||||
|
else:
|
||||||
|
modified_lines.append(line)
|
||||||
|
return modified_lines
|
||||||
|
|
||||||
|
def inject_home_page(lines: list[str]):
|
||||||
|
about_indent = False
|
||||||
|
modified_lines = []
|
||||||
|
for line in lines:
|
||||||
|
indentation_count = _calc_indentation(line)
|
||||||
|
if line == "about:\n" and indentation_count == 0:
|
||||||
|
about_indent = True
|
||||||
|
modified_lines.append(line)
|
||||||
|
elif about_indent and indentation_count == 0:
|
||||||
|
modified_lines.append(INDENTATION + "home: " + HOME_PAGE + "\n")
|
||||||
|
about_indent = False
|
||||||
|
else:
|
||||||
|
modified_lines.append(line)
|
||||||
|
return modified_lines
|
||||||
|
|
||||||
|
def write_to_original(lines: list[str]):
|
||||||
|
original_recipe = path.abspath(GRAYSKULL_OUTPUT_PATH)
|
||||||
|
original_meta = path.join(original_recipe, "meta.yaml")
|
||||||
|
with open(original_meta, "w") as file:
|
||||||
|
file.writelines(lines)
|
||||||
|
|
||||||
|
def rename_recipe_dir():
|
||||||
|
new_recipe_name = path.abspath(path.join(GRAYSKULL_OUTPUT_PATH.replace(".", "-").lower()))
|
||||||
|
shutil.rmtree(new_recipe_name, ignore_errors=True)
|
||||||
|
os.replace(path.abspath(GRAYSKULL_OUTPUT_PATH), new_recipe_name)
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
original_grayskull_out = read_grayskull_output()
|
||||||
|
modified_recipe_meta = None
|
||||||
|
modified_recipe_meta = update_naming_scheme(original_grayskull_out)
|
||||||
|
modified_recipe_meta = inject_run_exports(modified_recipe_meta)
|
||||||
|
modified_recipe_meta = suffix_license(modified_recipe_meta)
|
||||||
|
modified_recipe_meta = inject_home_page(modified_recipe_meta)
|
||||||
|
write_to_original(modified_recipe_meta)
|
||||||
|
rename_recipe_dir()
|
@ -22,15 +22,15 @@ from Bio.Align import PairwiseAligner
|
|||||||
class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
|
class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
|
||||||
|
|
||||||
@abstractmethod
|
@abstractmethod
|
||||||
def determine_mlst_allele_variants(self, query_sequence_strings: Iterable[str]) -> AsyncGenerator[Allele, Any]:
|
def determine_mlst_allele_variants(self, query_sequence_strings: Union[Iterable[Union[NamedString, str]], Union[NamedString, str]]) -> AsyncGenerator[Union[Allele, tuple[str, Allele]], Any]:
|
||||||
pass
|
pass
|
||||||
|
|
||||||
@abstractmethod
|
@abstractmethod
|
||||||
async def determine_mlst_st(self, alleles: Union[AsyncIterable[Allele], Iterable[Allele]]) -> MLSTProfile:
|
async def determine_mlst_st(self, alleles: Union[AsyncIterable[Union[Allele, tuple[str, Allele]]], Iterable[Union[Allele, tuple[str, Allele]]]]) -> Union[MLSTProfile, NamedMLSTProfile]:
|
||||||
pass
|
pass
|
||||||
|
|
||||||
@abstractmethod
|
@abstractmethod
|
||||||
async def profile_string(self, query_sequence_strings: Iterable[str]) -> MLSTProfile:
|
async def profile_string(self, query_sequence_strings: Iterable[Union[NamedString, str]]) -> Union[NamedMLSTProfile, MLSTProfile]:
|
||||||
pass
|
pass
|
||||||
|
|
||||||
@abstractmethod
|
@abstractmethod
|
||||||
@ -52,14 +52,14 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
|
|||||||
async def __aenter__(self):
|
async def __aenter__(self):
|
||||||
return self
|
return self
|
||||||
|
|
||||||
async def determine_mlst_allele_variants(self, query_sequence_strings: Union[Iterable[str], str]) -> AsyncGenerator[Allele, Any]:
|
async def determine_mlst_allele_variants(self, query_sequence_strings: Union[Iterable[Union[NamedString, str]], Union[NamedString, str]]) -> AsyncGenerator[Union[Allele, tuple[str, Allele]], Any]:
|
||||||
# See https://bigsdb.pasteur.fr/api/db/pubmlst_bordetella_seqdef/schemes
|
# See https://bigsdb.pasteur.fr/api/db/pubmlst_bordetella_seqdef/schemes
|
||||||
uri_path = "sequence"
|
uri_path = "sequence"
|
||||||
if isinstance(query_sequence_strings, str):
|
if isinstance(query_sequence_strings, str) or isinstance(query_sequence_strings, NamedString):
|
||||||
query_sequence_strings = [query_sequence_strings]
|
query_sequence_strings = [query_sequence_strings]
|
||||||
for sequence_string in query_sequence_strings:
|
for sequence_string in query_sequence_strings:
|
||||||
async with self._http_client.post(uri_path, json={
|
async with self._http_client.post(uri_path, json={
|
||||||
"sequence": sequence_string,
|
"sequence": sequence_string if isinstance(sequence_string, str) else sequence_string.sequence,
|
||||||
"partial_matches": True
|
"partial_matches": True
|
||||||
}) as response:
|
}) as response:
|
||||||
sequence_response: dict = await response.json()
|
sequence_response: dict = await response.json()
|
||||||
@ -70,7 +70,8 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
|
|||||||
for allele_loci, alleles in exact_matches.items():
|
for allele_loci, alleles in exact_matches.items():
|
||||||
for allele in alleles:
|
for allele in alleles:
|
||||||
alelle_id = allele["allele_id"]
|
alelle_id = allele["allele_id"]
|
||||||
yield Allele(allele_locus=allele_loci, allele_variant=alelle_id, partial_match_profile=None)
|
result_allele = Allele(allele_locus=allele_loci, allele_variant=alelle_id, partial_match_profile=None)
|
||||||
|
yield result_allele if isinstance(sequence_string, str) else (sequence_string.name, result_allele)
|
||||||
elif "partial_matches" in sequence_response:
|
elif "partial_matches" in sequence_response:
|
||||||
partial_matches: dict[str, dict[str, Union[str, float, int]]] = sequence_response["partial_matches"]
|
partial_matches: dict[str, dict[str, Union[str, float, int]]] = sequence_response["partial_matches"]
|
||||||
for allele_loci, partial_match in partial_matches.items():
|
for allele_loci, partial_match in partial_matches.items():
|
||||||
@ -82,23 +83,33 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
|
|||||||
gaps=int(partial_match["gaps"]),
|
gaps=int(partial_match["gaps"]),
|
||||||
match_metric=int(partial_match["bitscore"])
|
match_metric=int(partial_match["bitscore"])
|
||||||
)
|
)
|
||||||
yield Allele(
|
result_allele = Allele(
|
||||||
allele_locus=allele_loci,
|
allele_locus=allele_loci,
|
||||||
allele_variant=str(partial_match["allele"]),
|
allele_variant=str(partial_match["allele"]),
|
||||||
partial_match_profile=partial_match_profile
|
partial_match_profile=partial_match_profile
|
||||||
)
|
)
|
||||||
|
yield result_allele if isinstance(sequence_string, str) else (sequence_string.name, result_allele)
|
||||||
else:
|
else:
|
||||||
raise NoBIGSdbMatchesException(self._database_name, self._schema_id)
|
raise NoBIGSdbMatchesException(self._database_name, self._schema_id, sequence_string.name if isinstance(sequence_string, NamedString) else None)
|
||||||
|
|
||||||
async def determine_mlst_st(self, alleles: Union[AsyncIterable[Allele], Iterable[Allele]]) -> MLSTProfile:
|
async def determine_mlst_st(self, alleles: Union[AsyncIterable[Union[Allele, tuple[str, Allele]]], Iterable[Union[Allele, tuple[str, Allele]]]]) -> Union[MLSTProfile, NamedMLSTProfile]:
|
||||||
uri_path = "designations"
|
uri_path = "designations"
|
||||||
allele_request_dict: dict[str, list[dict[str, str]]] = defaultdict(list)
|
allele_request_dict: dict[str, list[dict[str, str]]] = defaultdict(list)
|
||||||
|
names_list = []
|
||||||
|
def insert_allele_to_request_dict(allele: Union[Allele, tuple[str, Allele]]):
|
||||||
|
if isinstance(allele, Allele):
|
||||||
|
allele_val = allele
|
||||||
|
else:
|
||||||
|
allele_val = allele[1]
|
||||||
|
names_list.append(allele[0])
|
||||||
|
allele_request_dict[allele_val.allele_locus].append({"allele": str(allele_val.allele_variant)})
|
||||||
|
|
||||||
if isinstance(alleles, AsyncIterable):
|
if isinstance(alleles, AsyncIterable):
|
||||||
async for allele in alleles:
|
async for allele in alleles:
|
||||||
allele_request_dict[allele.allele_locus].append({"allele": str(allele.allele_variant)})
|
insert_allele_to_request_dict(allele)
|
||||||
else:
|
else:
|
||||||
for allele in alleles:
|
for allele in alleles:
|
||||||
allele_request_dict[allele.allele_locus].append({"allele": str(allele.allele_variant)})
|
insert_allele_to_request_dict(allele)
|
||||||
request_json = {
|
request_json = {
|
||||||
"designations": allele_request_dict
|
"designations": allele_request_dict
|
||||||
}
|
}
|
||||||
@ -111,30 +122,33 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
|
|||||||
schema_fields_returned.setdefault("clonal_complex", "unknown")
|
schema_fields_returned.setdefault("clonal_complex", "unknown")
|
||||||
schema_exact_matches: dict = response_json["exact_matches"]
|
schema_exact_matches: dict = response_json["exact_matches"]
|
||||||
for exact_match_locus, exact_match_alleles in schema_exact_matches.items():
|
for exact_match_locus, exact_match_alleles in schema_exact_matches.items():
|
||||||
if len(exact_match_alleles) > 1:
|
|
||||||
raise ValueError(f"Unexpected number of alleles returned for exact match (Expected 1, retrieved {len(exact_match_alleles)})")
|
|
||||||
allele_set.add(Allele(exact_match_locus, exact_match_alleles[0]["allele_id"], None))
|
allele_set.add(Allele(exact_match_locus, exact_match_alleles[0]["allele_id"], None))
|
||||||
if len(allele_set) == 0:
|
if len(allele_set) == 0:
|
||||||
raise ValueError("Passed in no alleles.")
|
raise ValueError("Passed in no alleles.")
|
||||||
return MLSTProfile(allele_set, schema_fields_returned["ST"], schema_fields_returned["clonal_complex"])
|
result_mlst_profile = MLSTProfile(allele_set, schema_fields_returned["ST"], schema_fields_returned["clonal_complex"])
|
||||||
|
if len(names_list) > 0:
|
||||||
|
result_mlst_profile = NamedMLSTProfile(str(tuple(names_list)), result_mlst_profile)
|
||||||
|
return result_mlst_profile
|
||||||
|
|
||||||
async def profile_string(self, query_sequence_strings: Iterable[str]) -> MLSTProfile:
|
async def profile_string(self, query_sequence_strings: Iterable[Union[NamedString, str]]) -> Union[NamedMLSTProfile, MLSTProfile]:
|
||||||
alleles = self.determine_mlst_allele_variants(query_sequence_strings)
|
alleles = self.determine_mlst_allele_variants(query_sequence_strings)
|
||||||
return await self.determine_mlst_st(alleles)
|
return await self.determine_mlst_st(alleles)
|
||||||
|
|
||||||
async def profile_multiple_strings(self, query_named_string_groups: AsyncIterable[Iterable[NamedString]], stop_on_fail: bool = False) -> AsyncGenerator[NamedMLSTProfile, Any]:
|
async def profile_multiple_strings(self, query_named_string_groups: AsyncIterable[Iterable[NamedString]], stop_on_fail: bool = False) -> AsyncGenerator[NamedMLSTProfile, Any]:
|
||||||
|
tasks = []
|
||||||
async for named_strings in query_named_string_groups:
|
async for named_strings in query_named_string_groups:
|
||||||
names: list[str] = list()
|
tasks.append(self.profile_string(named_strings))
|
||||||
sequences: list[str] = list()
|
for task in asyncio.as_completed(tasks):
|
||||||
for named_string in named_strings:
|
try:
|
||||||
names.append(named_string.name)
|
yield await task
|
||||||
sequences.append(named_string.sequence)
|
except NoBIGSdbMatchesException as e:
|
||||||
try:
|
if stop_on_fail:
|
||||||
yield NamedMLSTProfile("-".join(names), (await self.profile_string(sequences)))
|
raise e
|
||||||
except NoBIGSdbMatchesException as e:
|
causal_name = e.get_causal_query_name()
|
||||||
if stop_on_fail:
|
if causal_name is None:
|
||||||
raise e
|
raise ValueError("Missing query name despite requiring names.")
|
||||||
yield NamedMLSTProfile("-".join(names), None)
|
else:
|
||||||
|
yield NamedMLSTProfile(causal_name, None)
|
||||||
|
|
||||||
async def close(self):
|
async def close(self):
|
||||||
await self._http_client.close()
|
await self._http_client.close()
|
||||||
|
@ -5,9 +5,13 @@ class BIGSDbDatabaseAPIException(Exception):
|
|||||||
|
|
||||||
|
|
||||||
class NoBIGSdbMatchesException(BIGSDbDatabaseAPIException):
|
class NoBIGSdbMatchesException(BIGSDbDatabaseAPIException):
|
||||||
def __init__(self, database_name: str, database_schema_id: int, *args):
|
def __init__(self, database_name: str, database_schema_id: int, query_name: Union[None, str], *args):
|
||||||
|
self._query_name = query_name
|
||||||
super().__init__(f"No matches found with schema with ID {database_schema_id} in the database \"{database_name}\".", *args)
|
super().__init__(f"No matches found with schema with ID {database_schema_id} in the database \"{database_name}\".", *args)
|
||||||
|
|
||||||
|
def get_causal_query_name(self) -> Union[str, None]:
|
||||||
|
return self._query_name
|
||||||
|
|
||||||
class NoBIGSdbExactMatchesException(NoBIGSdbMatchesException):
|
class NoBIGSdbExactMatchesException(NoBIGSdbMatchesException):
|
||||||
def __init__(self, database_name: str, database_schema_id: int, *args):
|
def __init__(self, database_name: str, database_schema_id: int, *args):
|
||||||
super().__init__(f"No exact match found with schema with ID {database_schema_id} in the database \"{database_name}\".", *args)
|
super().__init__(f"No exact match found with schema with ID {database_schema_id} in the database \"{database_name}\".", *args)
|
||||||
|
@ -13,5 +13,8 @@ async def read_fasta(handle: Union[str, TextIOWrapper]) -> Iterable[NamedString]
|
|||||||
return results
|
return results
|
||||||
|
|
||||||
async def read_multiple_fastas(handles: Iterable[Union[str, TextIOWrapper]]) -> AsyncGenerator[Iterable[NamedString], Any]:
|
async def read_multiple_fastas(handles: Iterable[Union[str, TextIOWrapper]]) -> AsyncGenerator[Iterable[NamedString], Any]:
|
||||||
|
tasks = []
|
||||||
for handle in handles:
|
for handle in handles:
|
||||||
yield await read_fasta(handle)
|
tasks.append(read_fasta(handle))
|
||||||
|
for task in asyncio.as_completed(tasks):
|
||||||
|
yield await task
|
Loading…
x
Reference in New Issue
Block a user