Merge pull request #46 from PennChopMicrobiomeProgram/45-incorporate-new-seqbackup-logic

Switch to seqBackup logic

Author: Ulthran

.github/workflows/test.yml

@@ -35,16 +35,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.12']
-        os: [ubuntu-latest, macos-latest]
-        include:
-          - python-version: '3.11'
-            os: ubuntu-latest
-          - python-version: '3.10'
-            os: ubuntu-latest
-          - python-version: '3.9'
-            os: ubuntu-latest
-    runs-on: ${{ matrix.os }}
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+    runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v4

app/sample_registry/README.md

@@ -1,144 +1,46 @@
 [project]
-# This is the name of your project. The first time you publish this
-# package, this name will be registered for you. It will determine how
-# users can install this project, e.g.:
-#
-# $ pip install sampleproject
-#
-# And where it will live on PyPI: https://pypi.org/project/sampleproject/
-#
-# There are some restrictions on what makes a valid project name
-# specification here:
-# https://packaging.python.org/specifications/core-metadata/#name
 name = "sample_registry"  # Required
-
-# Versions should comply with PEP 440:
-# https://www.python.org/dev/peps/pep-0440/
-#
-# For a discussion on single-sourcing the version, see
-# https://packaging.python.org/guides/single-sourcing-package-version/
-#version = "3.0.0"  # Required
 dynamic = ["version"]
-
-# This is a one-line description or tagline of what your project does. This
-# corresponds to the "Summary" metadata field:
-# https://packaging.python.org/specifications/core-metadata/#summary
 description = "PennCHOP Microbiome Program Sample Registry"  # Optional
-
-# This is an optional longer description of your project that represents
-# the body of text which users will see when they visit PyPI.
-#
-# Often, this is the same as your README, so you can just read it in from
-# that file directly (as we have already done above)
-#
-# This field corresponds to the "Description" metadata field:
-# https://packaging.python.org/specifications/core-metadata/#description-optional
 readme = "README.md" # Optional
-
-# Specify which Python versions you support. In contrast to the
-# 'Programming Language' classifiers above, 'pip install' will check this
-# and refuse to install the project if the version does not match. See
-# https://packaging.python.org/guides/distributing-packages-using-setuptools/#python-requires
-requires-python = ">=3.7"
-
-# This is either text indicating the license for the distribution, or a file
-# that contains the license
-# https://packaging.python.org/en/latest/specifications/core-metadata/#license
-#license = {file = "LICENSE.txt"}
-
-# This field adds keywords for your project which will appear on the
-# project page. What does your project relate to?
-#
-# Note that this is a list of additional keywords, separated
-# by commas, to be used to assist searching for the distribution in a
-# larger catalog.
-#keywords = ["sample", "setuptools", "development"]  # Optional
-
-# This should be your name or the name of the organization who originally
-# authored the project, and a valid email address corresponding to the name
-# listed.
+requires-python = ">=3.9"
 authors = [
-  {name = "Kyle Bittinger", email = "kylebitinger@gmail.com"},
+  {name = "Kyle Bittinger", email = "kylebittinger@gmail.com"},
   {name = "Charlie Bushman", email = "ctbushman@gmail.com" } # Optional
 ]
 
-# This should be your name or the names of the organization who currently
-# maintains the project, and a valid email address corresponding to the name
-# listed.
 maintainers = [
   {name = "Charlie Bushman", email = "ctbushman@gmail.com" } # Optional
 ]
 
-# Classifiers help users find your project by categorizing it.
-#
-# For a list of valid classifiers, see https://pypi.org/classifiers/
-classifiers = [  # Optional
-  # How mature is this project? Common values are
-  #   3 - Alpha
-  #   4 - Beta
-  #   5 - Production/Stable
+classifiers = [
   "Development Status :: 5 - Production/Stable",
 
-  # Indicate who your project is intended for
-  #"Intended Audience :: Bioinformaticians",
-  #"Topic :: Bioinformatics :: Metagenomics",
-
-  # Pick your license as you wish
   "License :: OSI Approved :: MIT License",
 
-  # Specify the Python versions you support here. In particular, ensure
-  # that you indicate you support Python 3. These classifiers are *not*
-  # checked by "pip install". See instead "python_requires" below.
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.7",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3 :: Only",
 ]
 
-# This field lists other packages that your project depends on to run.
-# Any package you put here will be installed by pip when your project is
-# installed, so they must be valid existing projects.
-#
-# For an analysis of this field vs pip's requirements files see:
-# https://packaging.python.org/discussions/install-requires-vs-requirements/
-dependencies = [ # Optional
+dependencies = [
     "sqlalchemy",
+    "seqbackup @ git+https://github.com/PennChopMicrobiomeProgram/seqBackup.git@master",
 ]
 
-# List additional groups of dependencies here (e.g. development
-# dependencies). Users will be able to install these using the "extras"
-# syntax, for example:
-#
-#   $ pip install sampleproject[dev]
-#
-# Similar to `dependencies` above, these must be valid existing
-# projects.
 [project.optional-dependencies] # Optional
 dev = ["black"]
 test = ["pytest", "pytest-cov"]
 
-# List URLs that are relevant to your project
-#
-# This field corresponds to the "Project-URL" and "Home-Page" metadata fields:
-# https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
-# https://packaging.python.org/specifications/core-metadata/#home-page-optional
-#
-# Examples listed include a pattern for specifying where the package tracks
-# issues, where the source is hosted, where to say thanks to the package
-# maintainers, and where to support the project financially. The key is
-# what's used to render the link text on PyPI.
 [project.urls]  # Optional
 "Homepage" = "https://github.com/PennChopMicrobiomeProgram/SampleRegistry/"
 "Bug Reports" = "https://github.com/PennChopMicrobiomeProgram/SampleRegistry/issues"
-#"Funding" = "https://donate.pypi.org"
-#"Say Thanks!" = "http://saythanks.io/to/example"
 "Source" = "https://github.com/PennChopMicrobiomeProgram/SampleRegistry/"
 
-# The following would provide a command line executable called `sample`
-# which executes the function `main` from this package when invoked.
 [project.scripts]  # Optional
 register_run = "sample_registry.register:register_run"
 modify_run = "sample_registry.register:modify_run"
@@ -154,13 +56,9 @@ export_samples = "sample_registry.export:export_samples"
 create_test_db = "sample_registry.db:create_test_db"
 sample_registry_version = "sample_registry:sample_registry_version"
 
-# This is configuration specific to the `setuptools` build backend.
-# If you are using a different build backend, you will need to change this.
 [tool.setuptools]
 
 [build-system]
-# These are the assumed default build requirements from pip:
-# https://pip.pypa.io/en/stable/reference/pip/#pep-517-and-518-support
 requires = ["setuptools>=61.0.0", "wheel"]
 build-backend = "setuptools.build_meta"
 

app/sample_registry/pyproject.toml

@@ -4,7 +4,7 @@
 from sqlalchemy import create_engine
 from sqlalchemy.orm import sessionmaker
 
-__version__ = "1.1.0"
+__version__ = "1.1.1"
 
 
 # Doesn't include "NA" because that's what we fill in for missing values

app/sample_registry/src/sample_registry/__init__.py

@@ -6,8 +6,8 @@
 from sqlalchemy.orm import Session
 from typing import Generator
 from sample_registry.mapping import SampleTable
-from sample_registry.illumina import IlluminaFastq
 from sample_registry.registrar import SampleRegistry
+from seqBackupLib.illumina import IlluminaFastq
 
 
 SAMPLES_DESC = """\
@@ -145,7 +145,12 @@ def register_illumina_file(argv=None, session: Session = None, out=sys.stdout):
     registry = SampleRegistry(session)
     f = IlluminaFastq(gzip.open(args.file, "rt"))
     acc = registry.register_run(
-        f.date, f.machine_type, "Nextera XT", f.lane, f.filepath, args.comment
+        f.folder_info["date"],
+        f.machine_type,
+        "Nextera XT",
+        f.lane,
+        str(f.filepath),
+        args.comment,
     )
 
     registry.session.commit()

app/sample_registry/src/sample_registry/illumina.py

@@ -1,4 +1,3 @@
 flask
 flask-sqlalchemy
-sqlalchemy
-psycopg2-binary
+sqlalchemy