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: | diff --git a/README.md b/README.md index 3a9c573..d82716f 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. 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 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 + 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. diff --git a/bin/generate_pac_bio_id b/bin/generate_pac_bio_id new file mode 100755 index 0000000..aeef03c --- /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.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" +) + +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() 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 58% rename from npg_id_generation/main.py rename to npg_id_generation/pac_bio.py index 96768f6..13cadc5 100644 --- a/npg_id_generation/main.py +++ b/npg_id_generation/pac_bio.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/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", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"] +dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] +docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] +tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"] +tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"] [[package]] name = "black" -version = "22.6.0" +version = "22.10.0" description = "The uncompromising code formatter." category = "dev" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7" [package.dependencies] click = ">=8.0.0" @@ -54,11 +46,22 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} [[package]] name = "colorama" -version = "0.4.5" +version = "0.4.6" description = "Cross-platform colored terminal text." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" + +[[package]] +name = "exceptiongroup" +version = "1.0.0rc9" +description = "Backport of PEP 654 (exception groups)" +category = "dev" +optional = false +python-versions = ">=3.7" + +[package.extras] +test = ["pytest (>=6)"] [[package]] name = "flake8" @@ -110,11 +113,11 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pathspec" -version = "0.9.0" +version = "0.10.1" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" +python-versions = ">=3.7" [[package]] name = "platformdirs" @@ -125,8 +128,8 @@ optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"] -test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"] +docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx (>=4)", "sphinx-autodoc-typehints (>=1.12)"] +test = ["appdirs (==1.4.4)", "pytest (>=6)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)"] [[package]] name = "pluggy" @@ -137,16 +140,8 @@ optional = false python-versions = ">=3.6" [package.extras] -testing = ["pytest-benchmark", "pytest"] -dev = ["tox", "pre-commit"] - -[[package]] -name = "py" -version = "1.11.0" -description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +dev = ["pre-commit", "tox"] +testing = ["pytest", "pytest-benchmark"] [[package]] name = "pycodestyle" @@ -158,14 +153,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "pydantic" -version = "1.9.1" +version = "1.10.2" description = "Data validation and settings management using python type hints" category = "main" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.7" [package.dependencies] -typing-extensions = ">=3.7.4.3" +typing-extensions = ">=4.1.0" [package.extras] dotenv = ["python-dotenv (>=0.10.4)"] @@ -188,25 +183,24 @@ optional = false python-versions = ">=3.6.8" [package.extras] -diagrams = ["railroad-diagrams", "jinja2"] +diagrams = ["jinja2", "railroad-diagrams"] [[package]] name = "pytest" -version = "7.1.2" +version = "7.2.0" description = "pytest: simple powerful testing with Python" category = "dev" optional = false python-versions = ">=3.7" [package.dependencies] -atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""} attrs = ">=19.2.0" colorama = {version = "*", markers = "sys_platform == \"win32\""} +exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" packaging = "*" pluggy = ">=0.12,<2.0" -py = ">=1.8.2" -tomli = ">=1.0.0" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"] @@ -221,7 +215,7 @@ python-versions = ">=3.7" [[package]] name = "typing-extensions" -version = "4.3.0" +version = "4.4.0" description = "Backported and Experimental Type Hints for Python 3.7+" category = "main" optional = false @@ -233,45 +227,44 @@ python-versions = "^3.10" content-hash = "32ca18c5753172a63ffe306ec75a27324bd3dc27ef4a51ee94148ac5c3efe4ee" [metadata.files] -atomicwrites = [ - {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"}, -] attrs = [ {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"}, {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"}, ] black = [ - {file = "black-22.6.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:f586c26118bc6e714ec58c09df0157fe2d9ee195c764f630eb0d8e7ccce72e69"}, - {file = "black-22.6.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b270a168d69edb8b7ed32c193ef10fd27844e5c60852039599f9184460ce0807"}, - {file = "black-22.6.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6797f58943fceb1c461fb572edbe828d811e719c24e03375fd25170ada53825e"}, - {file = "black-22.6.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c85928b9d5f83b23cee7d0efcb310172412fbf7cb9d9ce963bd67fd141781def"}, - {file = "black-22.6.0-cp310-cp310-win_amd64.whl", hash = "sha256:f6fe02afde060bbeef044af7996f335fbe90b039ccf3f5eb8f16df8b20f77666"}, - {file = "black-22.6.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:cfaf3895a9634e882bf9d2363fed5af8888802d670f58b279b0bece00e9a872d"}, - {file = "black-22.6.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:94783f636bca89f11eb5d50437e8e17fbc6a929a628d82304c80fa9cd945f256"}, - {file = "black-22.6.0-cp36-cp36m-win_amd64.whl", hash = "sha256:2ea29072e954a4d55a2ff58971b83365eba5d3d357352a07a7a4df0d95f51c78"}, - {file = "black-22.6.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:e439798f819d49ba1c0bd9664427a05aab79bfba777a6db94fd4e56fae0cb849"}, - {file = "black-22.6.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:187d96c5e713f441a5829e77120c269b6514418f4513a390b0499b0987f2ff1c"}, - {file = "black-22.6.0-cp37-cp37m-win_amd64.whl", hash = "sha256:074458dc2f6e0d3dab7928d4417bb6957bb834434516f21514138437accdbe90"}, - {file = "black-22.6.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:a218d7e5856f91d20f04e931b6f16d15356db1c846ee55f01bac297a705ca24f"}, - {file = "black-22.6.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:568ac3c465b1c8b34b61cd7a4e349e93f91abf0f9371eda1cf87194663ab684e"}, - {file = "black-22.6.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:6c1734ab264b8f7929cef8ae5f900b85d579e6cbfde09d7387da8f04771b51c6"}, - {file = "black-22.6.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c9a3ac16efe9ec7d7381ddebcc022119794872abce99475345c5a61aa18c45ad"}, - {file = "black-22.6.0-cp38-cp38-win_amd64.whl", hash = "sha256:b9fd45787ba8aa3f5e0a0a98920c1012c884622c6c920dbe98dbd05bc7c70fbf"}, - {file = "black-22.6.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:7ba9be198ecca5031cd78745780d65a3f75a34b2ff9be5837045dce55db83d1c"}, - {file = "black-22.6.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:a3db5b6409b96d9bd543323b23ef32a1a2b06416d525d27e0f67e74f1446c8f2"}, - {file = "black-22.6.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:560558527e52ce8afba936fcce93a7411ab40c7d5fe8c2463e279e843c0328ee"}, - {file = "black-22.6.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b154e6bbde1e79ea3260c4b40c0b7b3109ffcdf7bc4ebf8859169a6af72cd70b"}, - {file = "black-22.6.0-cp39-cp39-win_amd64.whl", hash = "sha256:4af5bc0e1f96be5ae9bd7aaec219c901a94d6caa2484c21983d043371c733fc4"}, - {file = "black-22.6.0-py3-none-any.whl", hash = "sha256:ac609cf8ef5e7115ddd07d85d988d074ed00e10fbc3445aee393e70164a2219c"}, - {file = "black-22.6.0.tar.gz", hash = "sha256:6c6d39e28aed379aec40da1c65434c77d75e65bb59a1e1c283de545fb4e7c6c9"}, + {file = "black-22.10.0-1fixedarch-cp310-cp310-macosx_11_0_x86_64.whl", hash = "sha256:5cc42ca67989e9c3cf859e84c2bf014f6633db63d1cbdf8fdb666dcd9e77e3fa"}, + {file = "black-22.10.0-1fixedarch-cp311-cp311-macosx_11_0_x86_64.whl", hash = "sha256:5d8f74030e67087b219b032aa33a919fae8806d49c867846bfacde57f43972ef"}, + {file = "black-22.10.0-1fixedarch-cp37-cp37m-macosx_10_16_x86_64.whl", hash = "sha256:197df8509263b0b8614e1df1756b1dd41be6738eed2ba9e9769f3880c2b9d7b6"}, + {file = "black-22.10.0-1fixedarch-cp38-cp38-macosx_10_16_x86_64.whl", hash = "sha256:2644b5d63633702bc2c5f3754b1b475378fbbfb481f62319388235d0cd104c2d"}, + {file = "black-22.10.0-1fixedarch-cp39-cp39-macosx_11_0_x86_64.whl", hash = "sha256:e41a86c6c650bcecc6633ee3180d80a025db041a8e2398dcc059b3afa8382cd4"}, + {file = "black-22.10.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2039230db3c6c639bd84efe3292ec7b06e9214a2992cd9beb293d639c6402edb"}, + {file = "black-22.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:14ff67aec0a47c424bc99b71005202045dc09270da44a27848d534600ac64fc7"}, + {file = "black-22.10.0-cp310-cp310-win_amd64.whl", hash = "sha256:819dc789f4498ecc91438a7de64427c73b45035e2e3680c92e18795a839ebb66"}, + {file = "black-22.10.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:5b9b29da4f564ba8787c119f37d174f2b69cdfdf9015b7d8c5c16121ddc054ae"}, + {file = "black-22.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b8b49776299fece66bffaafe357d929ca9451450f5466e997a7285ab0fe28e3b"}, + {file = "black-22.10.0-cp311-cp311-win_amd64.whl", hash = "sha256:21199526696b8f09c3997e2b4db8d0b108d801a348414264d2eb8eb2532e540d"}, + {file = "black-22.10.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1e464456d24e23d11fced2bc8c47ef66d471f845c7b7a42f3bd77bf3d1789650"}, + {file = "black-22.10.0-cp37-cp37m-win_amd64.whl", hash = "sha256:9311e99228ae10023300ecac05be5a296f60d2fd10fff31cf5c1fa4ca4b1988d"}, + {file = "black-22.10.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:fba8a281e570adafb79f7755ac8721b6cf1bbf691186a287e990c7929c7692ff"}, + {file = "black-22.10.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:915ace4ff03fdfff953962fa672d44be269deb2eaf88499a0f8805221bc68c87"}, + {file = "black-22.10.0-cp38-cp38-win_amd64.whl", hash = "sha256:444ebfb4e441254e87bad00c661fe32df9969b2bf224373a448d8aca2132b395"}, + {file = "black-22.10.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:974308c58d057a651d182208a484ce80a26dac0caef2895836a92dd6ebd725e0"}, + {file = "black-22.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:72ef3925f30e12a184889aac03d77d031056860ccae8a1e519f6cbb742736383"}, + {file = "black-22.10.0-cp39-cp39-win_amd64.whl", hash = "sha256:432247333090c8c5366e69627ccb363bc58514ae3e63f7fc75c54b1ea80fa7de"}, + {file = "black-22.10.0-py3-none-any.whl", hash = "sha256:c957b2b4ea88587b46cf49d1dc17681c1e672864fd7af32fc1e9664d572b3458"}, + {file = "black-22.10.0.tar.gz", hash = "sha256:f513588da599943e0cde4e32cc9879e825d58720d6557062d1098c5ad80080e1"}, ] click = [ {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"}, {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"}, ] colorama = [ - {file = "colorama-0.4.5-py2.py3-none-any.whl", hash = "sha256:854bf444933e37f5824ae7bfc1e98d5bce2ebe4160d46b5edf346a89358e99da"}, - {file = "colorama-0.4.5.tar.gz", hash = "sha256:e6c6b4334fc50988a639d9b98aa429a0b57da6e17b9a44f0451f930b6967b7a4"}, + {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, + {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, +] +exceptiongroup = [ + {file = "exceptiongroup-1.0.0rc9-py3-none-any.whl", hash = "sha256:2e3c3fc1538a094aab74fad52d6c33fc94de3dfee3ee01f187c0e0c72aec5337"}, + {file = "exceptiongroup-1.0.0rc9.tar.gz", hash = "sha256:9086a4a21ef9b31c72181c77c040a074ba0889ee56a7b289ff0afb0d97655f96"}, ] flake8 = [ {file = "flake8-4.0.1-py2.py3-none-any.whl", hash = "sha256:479b1304f72536a55948cb40a32dce8bb0ffe3501e26eaf292c7e60eb5e0428d"}, @@ -294,8 +287,8 @@ packaging = [ {file = "packaging-21.3.tar.gz", hash = "sha256:dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb"}, ] pathspec = [ - {file = "pathspec-0.9.0-py2.py3-none-any.whl", hash = "sha256:7d15c4ddb0b5c802d161efc417ec1a2558ea2653c2e8ad9c19098201dc1c993a"}, - {file = "pathspec-0.9.0.tar.gz", hash = "sha256:e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1"}, + {file = "pathspec-0.10.1-py3-none-any.whl", hash = "sha256:46846318467efc4556ccfd27816e004270a9eeeeb4d062ce5e6fc7a87c573f93"}, + {file = "pathspec-0.10.1.tar.gz", hash = "sha256:7ace6161b621d31e7902eb6b5ae148d12cfd23f4a249b9ffb6b9fee12084323d"}, ] platformdirs = [ {file = "platformdirs-2.5.2-py3-none-any.whl", hash = "sha256:027d8e83a2d7de06bbac4e5ef7e023c02b863d7ea5d079477e722bb41ab25788"}, @@ -305,50 +298,47 @@ pluggy = [ {file = "pluggy-1.0.0-py2.py3-none-any.whl", hash = "sha256:74134bbf457f031a36d68416e1509f34bd5ccc019f0bcc952c7b909d06b37bd3"}, {file = "pluggy-1.0.0.tar.gz", hash = "sha256:4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159"}, ] -py = [ - {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"}, - {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"}, -] pycodestyle = [ {file = "pycodestyle-2.8.0-py2.py3-none-any.whl", hash = "sha256:720f8b39dde8b293825e7ff02c475f3077124006db4f440dcbc9a20b76548a20"}, {file = "pycodestyle-2.8.0.tar.gz", hash = "sha256:eddd5847ef438ea1c7870ca7eb78a9d47ce0cdb4851a5523949f2601d0cbbe7f"}, ] pydantic = [ - {file = "pydantic-1.9.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c8098a724c2784bf03e8070993f6d46aa2eeca031f8d8a048dff277703e6e193"}, - {file = "pydantic-1.9.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c320c64dd876e45254bdd350f0179da737463eea41c43bacbee9d8c9d1021f11"}, - {file = "pydantic-1.9.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:18f3e912f9ad1bdec27fb06b8198a2ccc32f201e24174cec1b3424dda605a310"}, - {file = "pydantic-1.9.1-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c11951b404e08b01b151222a1cb1a9f0a860a8153ce8334149ab9199cd198131"}, - {file = "pydantic-1.9.1-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:8bc541a405423ce0e51c19f637050acdbdf8feca34150e0d17f675e72d119580"}, - {file = "pydantic-1.9.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:e565a785233c2d03724c4dc55464559639b1ba9ecf091288dd47ad9c629433bd"}, - {file = "pydantic-1.9.1-cp310-cp310-win_amd64.whl", hash = "sha256:a4a88dcd6ff8fd47c18b3a3709a89adb39a6373f4482e04c1b765045c7e282fd"}, - {file = "pydantic-1.9.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:447d5521575f18e18240906beadc58551e97ec98142266e521c34968c76c8761"}, - {file = "pydantic-1.9.1-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:985ceb5d0a86fcaa61e45781e567a59baa0da292d5ed2e490d612d0de5796918"}, - {file = "pydantic-1.9.1-cp36-cp36m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:059b6c1795170809103a1538255883e1983e5b831faea6558ef873d4955b4a74"}, - {file = "pydantic-1.9.1-cp36-cp36m-musllinux_1_1_i686.whl", hash = "sha256:d12f96b5b64bec3f43c8e82b4aab7599d0157f11c798c9f9c528a72b9e0b339a"}, - {file = "pydantic-1.9.1-cp36-cp36m-musllinux_1_1_x86_64.whl", hash = "sha256:ae72f8098acb368d877b210ebe02ba12585e77bd0db78ac04a1ee9b9f5dd2166"}, - {file = "pydantic-1.9.1-cp36-cp36m-win_amd64.whl", hash = "sha256:79b485767c13788ee314669008d01f9ef3bc05db9ea3298f6a50d3ef596a154b"}, - {file = "pydantic-1.9.1-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:494f7c8537f0c02b740c229af4cb47c0d39840b829ecdcfc93d91dcbb0779892"}, - {file = "pydantic-1.9.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f0f047e11febe5c3198ed346b507e1d010330d56ad615a7e0a89fae604065a0e"}, - {file = "pydantic-1.9.1-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:969dd06110cb780da01336b281f53e2e7eb3a482831df441fb65dd30403f4608"}, - {file = "pydantic-1.9.1-cp37-cp37m-musllinux_1_1_i686.whl", hash = "sha256:177071dfc0df6248fd22b43036f936cfe2508077a72af0933d0c1fa269b18537"}, - {file = "pydantic-1.9.1-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:9bcf8b6e011be08fb729d110f3e22e654a50f8a826b0575c7196616780683380"}, - {file = "pydantic-1.9.1-cp37-cp37m-win_amd64.whl", hash = "sha256:a955260d47f03df08acf45689bd163ed9df82c0e0124beb4251b1290fa7ae728"}, - {file = "pydantic-1.9.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:9ce157d979f742a915b75f792dbd6aa63b8eccaf46a1005ba03aa8a986bde34a"}, - {file = "pydantic-1.9.1-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:0bf07cab5b279859c253d26a9194a8906e6f4a210063b84b433cf90a569de0c1"}, - {file = "pydantic-1.9.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5d93d4e95eacd313d2c765ebe40d49ca9dd2ed90e5b37d0d421c597af830c195"}, - {file = "pydantic-1.9.1-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:1542636a39c4892c4f4fa6270696902acb186a9aaeac6f6cf92ce6ae2e88564b"}, - {file = "pydantic-1.9.1-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:a9af62e9b5b9bc67b2a195ebc2c2662fdf498a822d62f902bf27cccb52dbbf49"}, - {file = "pydantic-1.9.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:fe4670cb32ea98ffbf5a1262f14c3e102cccd92b1869df3bb09538158ba90fe6"}, - {file = "pydantic-1.9.1-cp38-cp38-win_amd64.whl", hash = "sha256:9f659a5ee95c8baa2436d392267988fd0f43eb774e5eb8739252e5a7e9cf07e0"}, - {file = "pydantic-1.9.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:b83ba3825bc91dfa989d4eed76865e71aea3a6ca1388b59fc801ee04c4d8d0d6"}, - {file = "pydantic-1.9.1-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:1dd8fecbad028cd89d04a46688d2fcc14423e8a196d5b0a5c65105664901f810"}, - {file = "pydantic-1.9.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:02eefd7087268b711a3ff4db528e9916ac9aa18616da7bca69c1871d0b7a091f"}, - {file = "pydantic-1.9.1-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:7eb57ba90929bac0b6cc2af2373893d80ac559adda6933e562dcfb375029acee"}, - {file = "pydantic-1.9.1-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:4ce9ae9e91f46c344bec3b03d6ee9612802682c1551aaf627ad24045ce090761"}, - {file = "pydantic-1.9.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:72ccb318bf0c9ab97fc04c10c37683d9eea952ed526707fabf9ac5ae59b701fd"}, - {file = "pydantic-1.9.1-cp39-cp39-win_amd64.whl", hash = "sha256:61b6760b08b7c395975d893e0b814a11cf011ebb24f7d869e7118f5a339a82e1"}, - {file = "pydantic-1.9.1-py3-none-any.whl", hash = "sha256:4988c0f13c42bfa9ddd2fe2f569c9d54646ce84adc5de84228cfe83396f3bd58"}, - {file = "pydantic-1.9.1.tar.gz", hash = "sha256:1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a"}, + {file = "pydantic-1.10.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:bb6ad4489af1bac6955d38ebcb95079a836af31e4c4f74aba1ca05bb9f6027bd"}, + {file = "pydantic-1.10.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:a1f5a63a6dfe19d719b1b6e6106561869d2efaca6167f84f5ab9347887d78b98"}, + {file = "pydantic-1.10.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:352aedb1d71b8b0736c6d56ad2bd34c6982720644b0624462059ab29bd6e5912"}, + {file = "pydantic-1.10.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:19b3b9ccf97af2b7519c42032441a891a5e05c68368f40865a90eb88833c2559"}, + {file = "pydantic-1.10.2-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:e9069e1b01525a96e6ff49e25876d90d5a563bc31c658289a8772ae186552236"}, + {file = "pydantic-1.10.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:355639d9afc76bcb9b0c3000ddcd08472ae75318a6eb67a15866b87e2efa168c"}, + {file = "pydantic-1.10.2-cp310-cp310-win_amd64.whl", hash = "sha256:ae544c47bec47a86bc7d350f965d8b15540e27e5aa4f55170ac6a75e5f73b644"}, + {file = "pydantic-1.10.2-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:a4c805731c33a8db4b6ace45ce440c4ef5336e712508b4d9e1aafa617dc9907f"}, + {file = "pydantic-1.10.2-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:d49f3db871575e0426b12e2f32fdb25e579dea16486a26e5a0474af87cb1ab0a"}, + {file = "pydantic-1.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:37c90345ec7dd2f1bcef82ce49b6235b40f282b94d3eec47e801baf864d15525"}, + {file = "pydantic-1.10.2-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:7b5ba54d026c2bd2cb769d3468885f23f43710f651688e91f5fb1edcf0ee9283"}, + {file = "pydantic-1.10.2-cp311-cp311-musllinux_1_1_i686.whl", hash = "sha256:05e00dbebbe810b33c7a7362f231893183bcc4251f3f2ff991c31d5c08240c42"}, + {file = "pydantic-1.10.2-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:2d0567e60eb01bccda3a4df01df677adf6b437958d35c12a3ac3e0f078b0ee52"}, + {file = "pydantic-1.10.2-cp311-cp311-win_amd64.whl", hash = "sha256:c6f981882aea41e021f72779ce2a4e87267458cc4d39ea990729e21ef18f0f8c"}, + {file = "pydantic-1.10.2-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:c4aac8e7103bf598373208f6299fa9a5cfd1fc571f2d40bf1dd1955a63d6eeb5"}, + {file = "pydantic-1.10.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:81a7b66c3f499108b448f3f004801fcd7d7165fb4200acb03f1c2402da73ce4c"}, + {file = "pydantic-1.10.2-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:bedf309630209e78582ffacda64a21f96f3ed2e51fbf3962d4d488e503420254"}, + {file = "pydantic-1.10.2-cp37-cp37m-musllinux_1_1_i686.whl", hash = "sha256:9300fcbebf85f6339a02c6994b2eb3ff1b9c8c14f502058b5bf349d42447dcf5"}, + {file = "pydantic-1.10.2-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:216f3bcbf19c726b1cc22b099dd409aa371f55c08800bcea4c44c8f74b73478d"}, + {file = "pydantic-1.10.2-cp37-cp37m-win_amd64.whl", hash = "sha256:dd3f9a40c16daf323cf913593083698caee97df2804aa36c4b3175d5ac1b92a2"}, + {file = "pydantic-1.10.2-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:b97890e56a694486f772d36efd2ba31612739bc6f3caeee50e9e7e3ebd2fdd13"}, + {file = "pydantic-1.10.2-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:9cabf4a7f05a776e7793e72793cd92cc865ea0e83a819f9ae4ecccb1b8aa6116"}, + {file = "pydantic-1.10.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:06094d18dd5e6f2bbf93efa54991c3240964bb663b87729ac340eb5014310624"}, + {file = "pydantic-1.10.2-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:cc78cc83110d2f275ec1970e7a831f4e371ee92405332ebfe9860a715f8336e1"}, + {file = "pydantic-1.10.2-cp38-cp38-musllinux_1_1_i686.whl", hash = "sha256:1ee433e274268a4b0c8fde7ad9d58ecba12b069a033ecc4645bb6303c062d2e9"}, + {file = "pydantic-1.10.2-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:7c2abc4393dea97a4ccbb4ec7d8658d4e22c4765b7b9b9445588f16c71ad9965"}, + {file = "pydantic-1.10.2-cp38-cp38-win_amd64.whl", hash = "sha256:0b959f4d8211fc964772b595ebb25f7652da3f22322c007b6fed26846a40685e"}, + {file = "pydantic-1.10.2-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:c33602f93bfb67779f9c507e4d69451664524389546bacfe1bee13cae6dc7488"}, + {file = "pydantic-1.10.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:5760e164b807a48a8f25f8aa1a6d857e6ce62e7ec83ea5d5c5a802eac81bad41"}, + {file = "pydantic-1.10.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6eb843dcc411b6a2237a694f5e1d649fc66c6064d02b204a7e9d194dff81eb4b"}, + {file = "pydantic-1.10.2-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:4b8795290deaae348c4eba0cebb196e1c6b98bdbe7f50b2d0d9a4a99716342fe"}, + {file = "pydantic-1.10.2-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:e0bedafe4bc165ad0a56ac0bd7695df25c50f76961da29c050712596cf092d6d"}, + {file = "pydantic-1.10.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:2e05aed07fa02231dbf03d0adb1be1d79cabb09025dd45aa094aa8b4e7b9dcda"}, + {file = "pydantic-1.10.2-cp39-cp39-win_amd64.whl", hash = "sha256:c1ba1afb396148bbc70e9eaa8c06c1716fdddabaf86e7027c5988bae2a829ab6"}, + {file = "pydantic-1.10.2-py3-none-any.whl", hash = "sha256:1b6ee725bd6e83ec78b1aa32c5b1fa67a3a65badddde3976bca5fe4568f27709"}, + {file = "pydantic-1.10.2.tar.gz", hash = "sha256:91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410"}, ] pyflakes = [ {file = "pyflakes-2.4.0-py2.py3-none-any.whl", hash = "sha256:3bb3a3f256f4b7968c9c788781e4ff07dce46bdf12339dcda61053375426ee2e"}, @@ -359,14 +349,14 @@ pyparsing = [ {file = "pyparsing-3.0.9.tar.gz", hash = "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb"}, ] pytest = [ - {file = "pytest-7.1.2-py3-none-any.whl", hash = "sha256:13d0e3ccfc2b6e26be000cb6568c832ba67ba32e719443bfe725814d3c42433c"}, - {file = "pytest-7.1.2.tar.gz", hash = "sha256:a06a0425453864a270bc45e71f783330a7428defb4230fb5e6a731fde06ecd45"}, + {file = "pytest-7.2.0-py3-none-any.whl", hash = "sha256:892f933d339f068883b6fd5a459f03d85bfcb355e4981e146d2c7616c21fef71"}, + {file = "pytest-7.2.0.tar.gz", hash = "sha256:c4014eb40e10f11f355ad4e3c2fb2c6c6d1919c73f3b5a433de4708202cade59"}, ] tomli = [ {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"}, {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"}, ] typing-extensions = [ - {file = "typing_extensions-4.3.0-py3-none-any.whl", hash = "sha256:25642c956049920a5aa49edcdd6ab1e06d7e5d467fc00e0506c44ac86fbfca02"}, - {file = "typing_extensions-4.3.0.tar.gz", hash = "sha256:e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6"}, + {file = "typing_extensions-4.4.0-py3-none-any.whl", hash = "sha256:16fa4864408f655d35ec496218b85f79b3437c829e93320c7c9215ccfd92489e"}, + {file = "typing_extensions-4.4.0.tar.gz", hash = "sha256:1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa"}, ] diff --git a/pyproject.toml b/pyproject.toml index 92df3c8..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" @@ -14,6 +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" diff --git a/tests/test_hashing.py b/tests/test_hashing.py index 1fded1d..67a61c1 100644 --- a/tests/test_hashing.py +++ b/tests/test_hashing.py @@ -17,9 +17,11 @@ # 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.""" -from npg_id_generation.main import PacBioEntity +import pytest +from pydantic import ValidationError +from npg_id_generation.pac_bio import PacBioEntity def test_different_orderings(): @@ -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."""