jamofetch 3.7.6__tar.gz → 3.7.8__tar.gz

jamofetch-3.7.8/.gitignore

@@ -0,0 +1,151 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+**__pycache__
+
+# PyCharm
+.idea/
+
+# RStudio project files
+**.Rproj.user/
+**.Rproj.user*
+**.Rproj
+**.Rhistory
+
+# MacOS
+.DS_Store
+
+# IntelliJ
+*.iml
+
+# Ignore local data directory
+/data/
+/test-data/
+/test-output/
+

jamofetch-3.7.8/.gitlab-ci.yml

@@ -0,0 +1,32 @@
+stages:
+  - install
+  - build
+
+image: python:3.9.18
+
+install:
+  stage: install
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^v[0-9]+(\.[0-9]+)*$/
+      when: always
+  tags:
+    - docker-build  # jgi-docker-runner (#74), confirmed docker executor
+  script:
+    - chmod 544 prepare-gitlab-publish.sh
+    - ./prepare-gitlab-publish.sh
+
+publish:
+  stage: build
+  rules:
+    - if: $CI_COMMIT_TAG =~ /^v[0-9]+(\.[0-9]+)*$/
+      when: always
+  tags:
+    - docker-build  # jgi-docker-runner (#74), confirmed docker executor
+  script:
+    - pip install --upgrade pip
+    # flit_core must stay <4: 4.x emits Metadata-Version 2.5, which twine<7 can't
+    # parse, and twine>=7 requires Python >=3.10 (incompatible with this image).
+    - pip install "flit>=3.9,<4" "flit_core>=3.9,<4" "twine>=6.0,<7"
+    - flit build
+    - twine upload --repository-url "https://code.jgi.doe.gov/api/v4/projects/$CI_PROJECT_ID/packages/pypi" -u gitlab-ci-token -p "$CI_JOB_TOKEN" dist/*
+    - twine upload -u __token__ -p "$PYPI_TOKEN" dist/*

jamofetch-3.7.8/.readthedocs.yml

@@ -0,0 +1,14 @@
+# Required
+version: 2
+
+# Image to use
+build:
+  image: testing
+
+# Configuration
+python:
+  version: 3.9
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

jamofetch-3.7.8/CHANGELOG.md

@@ -0,0 +1,7 @@
+# Changelog
+
+<!--next-version-placeholder-->
+
+## v0.1.0 (07/07/2023)
+
+- First release of `jamofetch`!

jamofetch-3.7.8/CONDUCT.md

@@ -0,0 +1,43 @@
+# Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant homepage](http://contributor-covenant.org/version/1/4), version 1.4.

jamofetch-3.7.8/CONTRIBUTING.md

@@ -0,0 +1,76 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+## Types of Contributions
+
+### Report Bugs
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+### Write Documentation
+
+You can never have enough documentation! Please feel free to contribute to any
+part of the documentation, such as the official docs, docstrings, or even
+on the web in blog posts, articles, and such.
+
+### Submit Feedback
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+## Get Started!
+
+Ready to contribute? Here's how to set up `jamofetch` for local development.
+
+1. Download a copy of `jamofetch` locally.
+2. Install Python 3.9.18 with `pyenv` and install `jamofetch` for local development using `flit`:
+
+    ```console
+    $ pyenv install 3.9.18
+    $ pyenv local 3.9.18
+    $ pip install flit
+    $ flit install --symlink
+    ```
+
+3. Use `git` (or similar) to create a branch for local development and make your changes:
+
+    ```console
+    $ git checkout -b name-of-your-bugfix-or-feature
+    ```
+
+4. When you're done making changes, check that your changes conform to any code formatting requirements and pass any tests.
+
+5. Commit your changes and open a pull request.
+
+## Pull Request Guidelines
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include additional tests if appropriate.
+2. If the pull request adds functionality, the docs should be updated.
+3. The pull request should work for all currently supported operating systems and versions of Python.
+
+## Code of Conduct
+
+Please note that the `jamofetch` project is released with a
+Code of Conduct. By contributing to this project you agree to abide by its terms.

{jamofetch-3.7.6 → jamofetch-3.7.8}/PKG-INFO

@@ -1,17 +1,13 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: jamofetch
-Version: 3.7.6
+Version: 3.7.8
 Summary: A thin wrapper to retrieve sequence from JAMO at NERSC and on Dori.
-License: None
 Author: Duncan Scott
-Requires-Python: >=3.8
-Classifier: License :: Other/Proprietary License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
+Requires-Dist: sphinx-autoapi>=2.1.1,<3 ; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.2.2,<2 ; extra == "docs"
+Provides-Extra: docs
 
 # jamofetch
 thin wrapper on JAMO to allow sequence retrieval on Dori and at NERSC
@@ -93,15 +89,15 @@ options:
 (venv) [dnscott@ln005 jamofetch]$ jamofetch -d data -l NPUNN -l NOOHG -l HOGH -w --max -1
 fetching sequence:
 
-apptainer --silent run docker://doejgi/jamo-dori jamo link -s dori library NPUNN
+apptainer --silent exec docker://doejgi/jamo-dori jamo link -s dori custom '{"metadata.library_name":"NPUNN","metadata.fastq_type":"sdm_normal","group":"sdm"}'
 NPUNN /global/dna/dm_archive/sdm/pacbio/00/27/47/pbio-2747.27352.bc1001_BAK8A_OA--bc1001_BAK8A_OA.ccs.fastq.gz BACKUP_COMPLETE 6391936239a7711d789a9380
 NPUNN /clusterfs/jgi/groups/dsi/homes/dnscott/git/jamofetch/data/NPUNN.pbio-2747.27352.bc1001_BAK8A_OA--bc1001_BAK8A_OA.ccs.fastq.gz
 
-apptainer --silent run docker://doejgi/jamo-dori jamo link -s dori library NOOHG
+apptainer --silent exec docker://doejgi/jamo-dori jamo link -s dori custom '{"metadata.library_name":"NOOHG","metadata.fastq_type":"sdm_normal","group":"sdm"}'
 NOOHG /global/dna/dm_archive/sdm/pacbio/00/26/91/pbio-2691.26653.bc1001_BAK8A_OA--bc1001_BAK8A_OA.ccs.fastq.gz RESTORED 6347dbb35bc59487d7e768d6
 NOOHG /clusterfs/jgi/groups/dsi/homes/dnscott/git/jamofetch/data/NOOHG.pbio-2691.26653.bc1001_BAK8A_OA--bc1001_BAK8A_OA.ccs.fastq.gz
 
-apptainer --silent run docker://doejgi/jamo-dori jamo link -s dori library HOGH
+apptainer --silent exec docker://doejgi/jamo-dori jamo link -s dori custom '{"metadata.library_name":"HOGH","metadata.fastq_type":"sdm_normal","group":"sdm"}'
 HOGH /global/dna/dm_archive/sdm/illumina/00/63/97/6397.2.44053.GGCTAC.fastq.gz RESTORED 51d52a82067c014cd6ef4f6f
 HOGH /clusterfs/jgi/groups/dsi/homes/dnscott/git/jamofetch/data/HOGH.6397.2.44053.GGCTAC.fastq.gz
 

{jamofetch-3.7.6 → jamofetch-3.7.8}/README.md

@@ -78,15 +78,15 @@ options:
 (venv) [dnscott@ln005 jamofetch]$ jamofetch -d data -l NPUNN -l NOOHG -l HOGH -w --max -1
 fetching sequence:
 
-apptainer --silent run docker://doejgi/jamo-dori jamo link -s dori library NPUNN
+apptainer --silent exec docker://doejgi/jamo-dori jamo link -s dori custom '{"metadata.library_name":"NPUNN","metadata.fastq_type":"sdm_normal","group":"sdm"}'
 NPUNN /global/dna/dm_archive/sdm/pacbio/00/27/47/pbio-2747.27352.bc1001_BAK8A_OA--bc1001_BAK8A_OA.ccs.fastq.gz BACKUP_COMPLETE 6391936239a7711d789a9380
 NPUNN /clusterfs/jgi/groups/dsi/homes/dnscott/git/jamofetch/data/NPUNN.pbio-2747.27352.bc1001_BAK8A_OA--bc1001_BAK8A_OA.ccs.fastq.gz
 
-apptainer --silent run docker://doejgi/jamo-dori jamo link -s dori library NOOHG
+apptainer --silent exec docker://doejgi/jamo-dori jamo link -s dori custom '{"metadata.library_name":"NOOHG","metadata.fastq_type":"sdm_normal","group":"sdm"}'
 NOOHG /global/dna/dm_archive/sdm/pacbio/00/26/91/pbio-2691.26653.bc1001_BAK8A_OA--bc1001_BAK8A_OA.ccs.fastq.gz RESTORED 6347dbb35bc59487d7e768d6
 NOOHG /clusterfs/jgi/groups/dsi/homes/dnscott/git/jamofetch/data/NOOHG.pbio-2691.26653.bc1001_BAK8A_OA--bc1001_BAK8A_OA.ccs.fastq.gz
 
-apptainer --silent run docker://doejgi/jamo-dori jamo link -s dori library HOGH
+apptainer --silent exec docker://doejgi/jamo-dori jamo link -s dori custom '{"metadata.library_name":"HOGH","metadata.fastq_type":"sdm_normal","group":"sdm"}'
 HOGH /global/dna/dm_archive/sdm/illumina/00/63/97/6397.2.44053.GGCTAC.fastq.gz RESTORED 51d52a82067c014cd6ef4f6f
 HOGH /clusterfs/jgi/groups/dsi/homes/dnscott/git/jamofetch/data/HOGH.6397.2.44053.GGCTAC.fastq.gz
 

jamofetch-3.7.8/docs/Makefile

@@ -0,0 +1,19 @@
+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = jamofetch
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

jamofetch-3.7.8/docs/changelog.md

@@ -0,0 +1,2 @@
+```{include} ../CHANGELOG.md
+```

jamofetch-3.7.8/docs/conduct.md

@@ -0,0 +1,2 @@
+```{include} ../CONDUCT.md
+```

jamofetch-3.7.8/docs/conf.py

@@ -0,0 +1,35 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+
+project = u"jamofetch"
+copyright = u"2023, Duncan Scott"
+author = u"Duncan Scott"
+
+# -- General configuration ---------------------------------------------------
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "autoapi.extension",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "myst_parser"
+]
+autoapi_dirs = ["../src"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"

jamofetch-3.7.8/docs/contributing.md

@@ -0,0 +1,2 @@
+```{include} ../CONTRIBUTING.md
+```

jamofetch-3.7.8/docs/demo_script.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+
+
+import os.path
+import shutil
+from pathlib import Path
+
+from jamofetch.jamofetch import JamoFetcher, LibSeq
+
+WAIT_INTERVAL = 10  # check if JAMO has provisioned sequence every 10 seconds
+WAIT_MAX = 7200  # max wait is 7200 seconds or 2 hours
+
+LIBRARY_1 = 'NPUNN'
+LIBRARY_2 = 'NOOHG'
+
+
+def get_project_root() -> Path:
+    return Path(__file__).parent.parent
+
+
+# Print the path to the sequence symlink created by JAMO
+# and the real path of the sequence file.  If param wait is True,
+# wait for Jamo to provision sequence before outputting real path.
+def print_lib_seq(lib_seq: LibSeq, wait=False):
+    print(f"{lib_seq.get_lib_name()} sequence symlink: {lib_seq.get_seq_path()}")
+    real_path = lib_seq.get_real_path() if not wait else lib_seq.get_real_path_wait()
+    print(f"{lib_seq.get_lib_name()} sequence real path: {real_path}")
+
+
+# Delete directory "test-output" in project root if it exists.
+# Directory "test-output" will be created by JamoFetcher and
+# be used by JAMO to create symlinks to requested sequence files.
+link_dir = os.path.join(get_project_root(), 'test-output')
+shutil.rmtree(link_dir, ignore_errors=True)
+print(f"\nlink directory: {link_dir}")
+
+# create a fetcher
+fetcher: JamoFetcher = JamoFetcher(link_dir=link_dir, wait_interval_secs=WAIT_INTERVAL, wait_max_secs=WAIT_MAX)
+
+# Call JAMO to link sequence in the background.  Symlinks to the sequence
+# files are created by JAMO in directory <link_directory>.
+lib_seq_1: LibSeq = fetcher.fetch_lib_seq(LIBRARY_1)
+lib_seq_2: LibSeq = fetcher.fetch_lib_seq(LIBRARY_2)
+
+# If JAMO already fetched sequence for the first library,
+# print the real path to the sequence file via call
+# print_lib_seq(lib_seq_1),
+# otherwise just print the symlink created by JAMO.
+print()
+print_lib_seq(lib_seq_1)
+if lib_seq_1.seq_exists():
+    print(f"{lib_seq_1.get_lib_name()} sequence ready")
+else:
+    print(f"{lib_seq_1.get_lib_name()} sequence not yet ready")
+
+# Print real path to sequence file for second library when it
+# has been provisioned by JAMO.
+print(f"\n{lib_seq_2.get_lib_name()} waiting on JAMO to provision sequence")
+print_lib_seq(lib_seq_2, wait=True)
+print()

jamofetch-3.7.8/docs/index.md

@@ -0,0 +1,17 @@
+```{include} ../README.md
+```
+## Demo Script
+docs/demo_script.py
+```{literalinclude} ./demo_script.py
+:language: python
+```
+
+```{toctree}
+:maxdepth: 1
+:hidden:
+
+changelog.md
+contributing.md
+conduct.md
+autoapi/index
+```

jamofetch-3.7.8/docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=jamofetch
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+	echo.then set the SPHINXBUILD environment variable to point to the full
+	echo.path of the 'sphinx-build' executable. Alternatively you may add the
+	echo.Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

jamofetch-3.7.8/docs/requirements.txt

@@ -0,0 +1,3 @@
+myst-nb
+sphinx-autoapi
+sphinx-rtd-theme

jamofetch-3.7.8/prepare-gitlab-publish.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+set -e
+
+VERSION=$(grep version pyproject.toml | awk '{print $3}' | tr -d '"')
+TAGS=$(git tag --points-at HEAD)
+TAG_TO_MATCH="v${VERSION}"
+
+echo project version: $VERSION
+echo tags: $TAGS
+echo tag to match: $TAG_TO_MATCH
+
+if echo $TAGS | grep -qw "$TAG_TO_MATCH"
+then
+  echo version tag matched
+else
+  echo no matching version tag
+  echo exiting
+  exit 1
+fi
+
+python -V
+pip install --upgrade pip
+
+PUBLISHED_VERSIONS=$(pip index versions $CI_PROJECT_NAME \
+  --index-url https://oauth2:$CI_JOB_TOKEN@code.jgi.doe.gov/api/v4/projects/479/packages/pypi/simple \
+  | grep 'Available versions:' \
+  | awk -F: '{print $2}')
+
+echo published versions: $PUBLISHED_VERSIONS
+
+if echo $PUBLISHED_VERSIONS | grep -qw "$VERSION"
+then
+  echo "already published"
+  echo "exiting"
+  exit 1
+fi
+
+# smoke test: confirm the package actually builds before the publish stage runs
+pip install "flit>=3.9,<4" "flit_core>=3.9,<4"
+flit build

jamofetch-3.7.8/push-version-tag.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+set -e
+
+SCRIPT_PATH=$(realpath "${BASH_SOURCE[0]}")
+SCRIPT_DIR=$(dirname "$SCRIPT_PATH")
+
+cd "$SCRIPT_DIR"
+
+VERSION=$(grep version pyproject.toml | awk '{print $3}' | tr -d '"')
+TAG_VERSION="v${VERSION}"
+
+git tag -a "$TAG_VERSION" -m "$TAG_VERSION"
+git push origin --tags
+

jamofetch-3.7.8/pyproject.toml

@@ -0,0 +1,20 @@
+[build-system]
+requires = ["flit_core>=3.9,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "jamofetch"
+version = "3.7.8"
+description = "A thin wrapper to retrieve sequence from JAMO at NERSC and on Dori."
+authors = [{ name = "Duncan Scott" }]
+readme = "README.md"
+requires-python = ">=3.9"
+
+[project.scripts]
+jamofetch = "jamofetch.jamofetch:cli"
+
+[project.optional-dependencies]
+docs = [
+    "sphinx-autoapi>=2.1.1,<3",
+    "sphinx-rtd-theme>=1.2.2,<2",
+]

{jamofetch-3.7.6 → jamofetch-3.7.8}/src/jamofetch/jamofetch.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 
+import json
 import logging
 import os
 import pathlib
@@ -10,17 +11,43 @@ import time
 from argparse import ArgumentParser
 from stat import ST_CTIME
 
-JAMO_CMD_NERSC = 'module load jamo; jamo link library'
-JAMO_CMD_DORI = 'apptainer --silent run docker://doejgi/jamo-dori jamo link -s dori library'
+# Base commands; get_cmd() appends the query.
+#
+# Dori uses `apptainer exec`, not `run`: the jamo-dori image's runscript strips the
+# double quotes out of the JSON query, and jamo then fails with a JSONDecodeError.
+JAMO_CMD_NERSC = 'module load jamo; jamo link'
+JAMO_CMD_DORI = 'apptainer --silent exec docker://doejgi/jamo-dori jamo link -s dori'
 
 TWO_HOURS = 7200  # seconds
 ONE_MINUTE = 60  # seconds
 
 
-def _get_cmd(clean_lib_name) -> str:
-    if os.getenv('SLURM_PARTITION') == 'dori':
-        return f"{JAMO_CMD_DORI} {clean_lib_name}"
-    return f"{JAMO_CMD_NERSC} {clean_lib_name}"
+def get_cmd(clean_lib_name) -> str:
+    """
+    Build the site-appropriate `jamo link` command for a library's SDM fastq.
+
+    Uses a custom query rather than `jamo link library <name>`. That form applies
+    jamo's default `raw_normal` filter, {'metadata.fastq_type': 'sdm_normal',
+    'user': 'sdm'}, and files from SDM's newer pipeline are owned by user
+    'sdm_pipeline' (group still 'sdm'), so it matched nothing for them. Filtering
+    on group instead of user matches both.
+
+    Key order matters: jamo names each symlink '<first string-valued query key's
+    value>.<file_name>', so metadata.library_name must stay first or
+    _find_fastq_path() will not find the link.
+
+    A library sequenced on more than one run matches one fastq per run; nothing
+    here chooses between them.
+    """
+    # Validated because the name is interpolated into a shell command.
+    lib_name = _clean_library_name(clean_lib_name)
+    query = json.dumps({
+        "metadata.library_name": lib_name,
+        "metadata.fastq_type": "sdm_normal",
+        "group": "sdm",
+    }, separators=(',', ':'))
+    base = JAMO_CMD_DORI if os.getenv('SLURM_PARTITION') == 'dori' else JAMO_CMD_NERSC
+    return f"{base} custom '{query}'"
 
 
 def _clean_library_name(library_name):
@@ -172,7 +199,7 @@ class JamoFetcher():
         os.chdir(self._link_dir)
         clean_lib_name = _clean_library_name(lib_name)
 
-        cmd = _get_cmd(clean_lib_name)
+        cmd = get_cmd(clean_lib_name)
         print(f"\n{cmd}", file=out_file)
         output = subprocess.check_output(cmd, shell=True)
         for line in output.splitlines():

jamofetch-3.7.8/tests/test_jamofetch.py

@@ -0,0 +1,47 @@
+import json
+import shlex
+
+import pytest
+
+from jamofetch import jamofetch
+
+
+def _query(cmd):
+    # The query is the single-quoted final argument; shlex undoes the shell quoting.
+    return json.loads(shlex.split(cmd)[-1])
+
+
+def test_nersc_cmd(monkeypatch):
+    monkeypatch.delenv('SLURM_PARTITION', raising=False)
+    cmd = jamofetch.get_cmd('LBBDHFZ')
+    assert cmd.startswith('module load jamo; jamo link custom ')
+    assert _query(cmd) == {
+        "metadata.library_name": "LBBDHFZ",
+        "metadata.fastq_type": "sdm_normal",
+        "group": "sdm",
+    }
+
+
+def test_dori_cmd_uses_exec(monkeypatch):
+    monkeypatch.setenv('SLURM_PARTITION', 'dori')
+    cmd = jamofetch.get_cmd('LBBDHFZ')
+    assert cmd.startswith('apptainer --silent exec docker://doejgi/jamo-dori jamo link -s dori custom ')
+    assert _query(cmd)["metadata.library_name"] == "LBBDHFZ"
+
+
+def test_library_name_is_first_query_key(monkeypatch):
+    # jamo names the symlink after the first string-valued key; _find_fastq_path
+    # relies on that being the library name.
+    monkeypatch.delenv('SLURM_PARTITION', raising=False)
+    assert next(iter(_query(jamofetch.get_cmd('LBBDHFZ')))) == "metadata.library_name"
+
+
+def test_query_does_not_filter_on_user(monkeypatch):
+    monkeypatch.delenv('SLURM_PARTITION', raising=False)
+    assert "user" not in _query(jamofetch.get_cmd('LBBDHFZ'))
+
+
+@pytest.mark.parametrize('bad', ["LBB'DHFZ", 'lbbdhfz', 'LBB DHFZ', 'LBB;rm'])
+def test_invalid_library_name_rejected(bad):
+    with pytest.raises(ValueError):
+        jamofetch.get_cmd(bad)

jamofetch-3.7.6/pyproject.toml

@@ -1,23 +0,0 @@
-[tool.poetry]
-name = "jamofetch"
-version = "3.7.6"
-description = "A thin wrapper to retrieve sequence from JAMO at NERSC and on Dori."
-authors = ["Duncan Scott"]
-license = "None"
-readme = "README.md"
-
-[tool.poetry.dependencies]
-python = ">=3.8"
-
-[tool.poetry.dev-dependencies]
-
-[tool.poetry.group.dev.dependencies]
-sphinx-autoapi = "^2.1.1"
-sphinx-rtd-theme = "^1.2.2"
-
-[tool.poetry.scripts]
-jamofetch = 'jamofetch.jamofetch:cli'
-
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"