From d2e67ee1daf9eb608c0ae4516bb8596d968a7b62 Mon Sep 17 00:00:00 2001 From: mksanger Date: Fri, 14 Oct 2022 16:10:57 +0100 Subject: [PATCH 1/8] Add pac bio id generation script --- bin/generate_pac_bio_id | 44 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100755 bin/generate_pac_bio_id diff --git a/bin/generate_pac_bio_id b/bin/generate_pac_bio_id new file mode 100755 index 0000000..a051df3 --- /dev/null +++ b/bin/generate_pac_bio_id @@ -0,0 +1,44 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +# +# Copyright © 2022 Genome Research Ltd. All rights reserved. +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +# @author Michael Kubiak + +import argparse +from npg_id_generation import PacBioEntity + +parser = argparse.ArgumentParser( + description="A script to generate a product id for a pac bio product from a given run and well" +) + +parser.add_argument( + "run_name", type=str, help="The name of the run to which the product belongs" +) + +parser.add_argument("well_label", type=str, help="The well label") + +args = parser.parse_args() + + +def main(): + print( + f"{PacBioEntity(run_name=args.run_name, well_label=args.well_label).hash_product_id()}\n" + ) + + +if __name__ == "__main__": + main() From 15e3e3f3ef4e227b46b45529dae06b6182c54a9c Mon Sep 17 00:00:00 2001 From: mksanger Date: Mon, 17 Oct 2022 16:41:18 +0100 Subject: [PATCH 2/8] Add pac bio id script to build so that it is available when installing the package with pip --- pyproject.toml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 92df3c8..9a7e33e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,6 +14,9 @@ pytest = "^7.1.2" black = "^22.6.0" flake8 = "^4.0.1" +[tool.poetry.scripts] +generate_pac_bio_id = { reference = "bin/generate_pac_bio_id", type = "file", extras = [] } + [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" From 268e2edef818d05ba0c1d7b5cf6578f076158f8f Mon Sep 17 00:00:00 2001 From: mgcam Date: Wed, 19 Oct 2022 19:00:26 +0100 Subject: [PATCH 3/8] Added attrs validation and tests for tags attr --- npg_id_generation/main.py | 27 ++++++++++++++----- tests/test_hashing.py | 55 ++++++++++++++++++++++++++++++++++++++- 2 files changed, 74 insertions(+), 8 deletions(-) diff --git a/npg_id_generation/main.py b/npg_id_generation/main.py index 96768f6..13cadc5 100644 --- a/npg_id_generation/main.py +++ b/npg_id_generation/main.py @@ -18,22 +18,35 @@ # this program. If not, see . from hashlib import sha256 -from pydantic import BaseModel, Field +from pydantic import BaseModel, Extra, Field, validator -class PacBioEntity(BaseModel): - """A PacBio entity class used to create hashes.""" +class PacBioEntity(BaseModel, extra=Extra.forbid): + """A PacBio entity class for ID generation.""" # Order these alphabetically, to allow for interoperability with # a possible Perl API. # Alternatively the sorting could be achieved with json.dumps()'s # sort_keys argument. See https://docs.python.org/3/library/json.html#basic-usage - run_name: str - well_label: str - tags: str = Field(default=None) + run_name: str = Field(title="Pac Bio run name as in LIMS") + well_label: str = Field(title="Pac Bio well label") + tags: str = Field( + default=None, + title="A string representing tag or tags", + description=""" + A string representing a single tag (index) sequence or a comma-separated + list of multiple tags. It is important to order multiple tags consistently. + """, + ) + + @validator("run_name", "well_label", "tags") + def attributes_are_non_empty_strings(cls, v): + if (v is not None) and (v == ""): + raise ValueError("Cannot be an empty string") + return v def hash_product_id(self): - """Generate a sha256sum for the PacBioWell""" + """Generate a sha256sum for the PacBio Entity""" return sha256( self.json(exclude_none=True, separators=(",", ":")).encode() diff --git a/tests/test_hashing.py b/tests/test_hashing.py index 1fded1d..d04713e 100644 --- a/tests/test_hashing.py +++ b/tests/test_hashing.py @@ -17,8 +17,10 @@ # You should have received a copy of the GNU General Public License along with # this program. If not, see . -"""Tests checking the hashing behaviour of input objects.""" +"""Tests checking the hashing behaviour of objects.""" +import pytest +from pydantic import ValidationError from npg_id_generation.main import PacBioEntity @@ -56,6 +58,57 @@ def test_whitespace(): assert len(set(results)) == 1 +def test_different_ways_to_create_object(): + + results = [] + results.append(PacBioEntity(run_name="MARATHON", well_label="A1").hash_product_id()) + results.append(PacBioEntity(well_label="A1", run_name="MARATHON").hash_product_id()) + results.append( + PacBioEntity(run_name="MARATHON", well_label="A1", tags=None).hash_product_id() + ) + results.append( + PacBioEntity.parse_raw( + '{"run_name": "MARATHON", "well_label": "A1"}', content_type="json" + ).hash_product_id() + ) + assert len(set(results)) == 1 + + with pytest.raises(ValidationError) as excinfo: + PacBioEntity(run_name="MARATHON", well_label="A1", some_arg=3) + assert "extra fields not permitted" in str(excinfo.value) + + +def test_tags_make_difference(): + + id_1 = PacBioEntity( + run_name="MARATHON", well_label="A1", tags="acgt" + ).hash_product_id() + id_2 = PacBioEntity( + run_name="MARATHON", well_label="A1", tags="actg" + ).hash_product_id() + id_3 = PacBioEntity(run_name="MARATHON", well_label="A1").hash_product_id() + assert id_1 != id_2 + assert id_3 != id_2 + + +def test_attributes_cannot_be_empty(): + + with pytest.raises(ValidationError) as excinfo: + PacBioEntity(run_name="MARATHON", well_label="A1", tags="") + assert "Cannot be an empty string" in str(excinfo.value) + with pytest.raises(ValidationError) as excinfo: + PacBioEntity(run_name="", well_label="A1") + assert "Cannot be an empty string" in str(excinfo.value) + with pytest.raises(ValidationError) as excinfo: + PacBioEntity(run_name="MARATHON", well_label="") + assert "Cannot be an empty string" in str(excinfo.value) + with pytest.raises(ValidationError) as excinfo: + PacBioEntity.parse_raw( + '{"run_name": "MARATHON", "well_label": ""}', content_type="json" + ) + assert "Cannot be an empty string" in str(excinfo.value) + + def test_expected_hashes(): """Test against expected hashes.""" From ce3ac1b554c2bb1ee669cf086657daa6953f6389 Mon Sep 17 00:00:00 2001 From: mgcam Date: Wed, 19 Oct 2022 19:00:57 +0100 Subject: [PATCH 4/8] Added package documentation --- README.md | 63 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 62 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 3a9c573..da46141 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,65 @@ # npg_id_generation -An API used to generate product IDs, which are hashes of the JSON representation of an object. +An API used to generate product IDs, which are hashes of the JSON representation +of an object. +For different sequencing platforms different sets of identifiers might be used to +fully describe the origin of data. For reasons of efficiency and interobility +between different systems it is sometimes desirable to be able to use a single +identifier, which will be unique not only within data for a single platform, +but also between different platforms. + +In the Sanger Institute run ID, lane number and numerical tag index are used +as identifiers for the Illumina platform. Historically, the first algorithm for +generating unique identifiers was implemented in Perl for the Illumina platform, +see [documentation](https://github.com/wtsi-npg/npg_tracking/blob/master/lib/npg_tracking/glossary/composition.pm +). + +Later a need to have a similar API for other sequencing platforms arose. This +package implements a Python API. The attributes of objects are sequencing +platform specific. The generator for the PacBio platform is implemented by the +`PacBioEntity` class. + +Examles of generating IDs for PacBio data: + +``` +from npg_id_generation.main import PacBioEntity + +# from a JSON string via a class method +test_case = '{"run_name": "MARATHON","well_label": "D1"}' +print(PacBioEntity.parse_raw(test_case, content_type="json").hash_product_id()) + +# by setting object's attributes +print(PacBioEntity(run_name="MARATHON", well_label="D1").hash_product_id() + +# sample-specific indentifier +# for multiple tags a sorted comma-separated list of tagscan be used +print(PacBioEntity(run_name="MARATHON", well_label="D1", tags="AAGTACGT").hash_product_id() +``` + +All generators should conform to a few simple rules: + +1. Uniquness of the ID should be guaranteed. +2. The ID should be a 64 characher string. +3. It should be possible to generate an ID from a JSON string. +4. The value of the ID should **not** depend on the order of attributes given + to the cinstructor or the order of keys used in JSON. +5. The value of the ID should **not** depend on the amount of whitespace in + the input JSON. +6. The value of the ID should **not** depend on whether the undefined values + of attributes are explicitly set. + +The examples below clarity the rules. Objects `o1` - `o6` should generate the same ID. + +``` +o1 = PacBioEntity(run_name="r1", well_label="l1") +o2 = PacBioEntity(run_name="r1", well_label="l1", tags = None) +o3 = PacBioEntity(well_label="l1", run_name="r1", ) +o4 = PacBioEntity.parse_raw('{"run_name": "r1","well_label": "l1"}', content_type="json") +o5 = PacBioEntity.parse_raw('{"well_label": "l1", "run_name": "r1"}', content_type="json") +o6 = PacBioEntity.parse_raw('{"well_label": "l1","run_name": "r1", "tags": null}', content_type="json") +``` + +The algorithm used for generation of identifiers can be replicated in Perl; +on identical input data it gives identical results. However, we cannot guarantee +that this parity will always be maintained in future. From 9c5cbdf2c7a627561bc9c75c9a3de01415507918 Mon Sep 17 00:00:00 2001 From: mgcam Date: Fri, 21 Oct 2022 16:36:05 +0100 Subject: [PATCH 5/8] Fixed typos --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index da46141..d82716f 100644 --- a/README.md +++ b/README.md @@ -39,11 +39,11 @@ print(PacBioEntity(run_name="MARATHON", well_label="D1", tags="AAGTACGT").hash_p All generators should conform to a few simple rules: -1. Uniquness of the ID should be guaranteed. +1. Uniqueness of the ID should be guaranteed. 2. The ID should be a 64 characher string. 3. It should be possible to generate an ID from a JSON string. 4. The value of the ID should **not** depend on the order of attributes given - to the cinstructor or the order of keys used in JSON. + to the constructor or the order of keys used in JSON. 5. The value of the ID should **not** depend on the amount of whitespace in the input JSON. 6. The value of the ID should **not** depend on whether the undefined values From 7dbc49b9525e24a7dbcea6c630c086f5e5d51b34 Mon Sep 17 00:00:00 2001 From: mksanger Date: Tue, 25 Oct 2022 18:04:10 +0100 Subject: [PATCH 6/8] Move main.py code to pac_bio.py --- bin/generate_pac_bio_id | 2 +- npg_id_generation/__init__.py | 1 - npg_id_generation/{main.py => pac_bio.py} | 0 tests/test_hashing.py | 2 +- 4 files changed, 2 insertions(+), 3 deletions(-) rename npg_id_generation/{main.py => pac_bio.py} (100%) diff --git a/bin/generate_pac_bio_id b/bin/generate_pac_bio_id index a051df3..aeef03c 100755 --- a/bin/generate_pac_bio_id +++ b/bin/generate_pac_bio_id @@ -19,7 +19,7 @@ # @author Michael Kubiak import argparse -from npg_id_generation import PacBioEntity +from npg_id_generation.pac_bio import PacBioEntity parser = argparse.ArgumentParser( description="A script to generate a product id for a pac bio product from a given run and well" diff --git a/npg_id_generation/__init__.py b/npg_id_generation/__init__.py index f706caa..e69de29 100644 --- a/npg_id_generation/__init__.py +++ b/npg_id_generation/__init__.py @@ -1 +0,0 @@ -from .main import PacBioEntity diff --git a/npg_id_generation/main.py b/npg_id_generation/pac_bio.py similarity index 100% rename from npg_id_generation/main.py rename to npg_id_generation/pac_bio.py diff --git a/tests/test_hashing.py b/tests/test_hashing.py index d04713e..67a61c1 100644 --- a/tests/test_hashing.py +++ b/tests/test_hashing.py @@ -21,7 +21,7 @@ import pytest from pydantic import ValidationError -from npg_id_generation.main import PacBioEntity +from npg_id_generation.pac_bio import PacBioEntity def test_different_orderings(): From 3a8e8f4f89bc56cf5e19e942656bed5b688cc611 Mon Sep 17 00:00:00 2001 From: mksanger Date: Tue, 25 Oct 2022 18:06:41 +0100 Subject: [PATCH 7/8] Add dynamic versioning, update poetry.lock --- poetry.lock | 214 +++++++++++++++++++++++-------------------------- pyproject.toml | 11 ++- 2 files changed, 110 insertions(+), 115 deletions(-) diff --git a/poetry.lock b/poetry.lock index 70cd93c..5bcf1b5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,11 +1,3 @@ -[[package]] -name = "atomicwrites" -version = "1.4.1" -description = "Atomic file writes." -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - [[package]] name = "attrs" version = "22.1.0" @@ -15,18 +7,18 @@ optional = false python-versions = ">=3.5" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", 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--git a/pyproject.toml b/pyproject.toml index 9a7e33e..3a2c644 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "npg_id_generation" -version = "0.1.0" +version = "0.0.0" description = "Product ID generation." authors = ["Adam Blanchet "] license = "GPL3-or-later" @@ -14,9 +14,14 @@ pytest = "^7.1.2" black = "^22.6.0" flake8 = "^4.0.1" +[tool.poetry-dynamic-versioning] +enable = true +pattern = '^((?P\d+)!)?(?P\d+(\.\d+)*)([-._]?((?P[a-zA-Z]+)[-._]?(?P\d+)?))?(\+(?P.+))?$' +format-jinja = "{% if distance == 0 %}{{ base }}{% else %}{{ base }}+{{ distance }}.{{ commit }}{% endif %}" + [tool.poetry.scripts] generate_pac_bio_id = { reference = "bin/generate_pac_bio_id", type = "file", extras = [] } [build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"] +build-backend = "poetry_dynamic_versioning.backend" From 77e06853a61fd70f29f6b37130c3dae6955ea1e1 Mon Sep 17 00:00:00 2001 From: mksanger Date: Wed, 26 Oct 2022 17:11:26 +0100 Subject: [PATCH 8/8] Remove mysql requirement from ci, add poetry dynamic version plugin to ci --- .github/workflows/test.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a6cffcb..e7643a5 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -26,10 +26,6 @@ jobs: test: runs-on: ubuntu-latest - strategy: - matrix: - mysql-version: ["5.7", "8.0"] - steps: - uses: actions/checkout@v3 @@ -46,6 +42,7 @@ jobs: run: | poetry env use '3.10' poetry install + poetry self add "poetry-dynamic_versioning[plugin]" - name: Run pytest run: |