From c548691de6fe07aeff7c555699f4478d9e6f1f89 Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 17:42:50 -0700 Subject: [PATCH 01/12] add crates.io badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 95b866c..d18aacb 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ [![rtemis.a3 status badge](https://rtemis-org.r-universe.dev/rtemis.a3/badges/version)](https://rtemis-org.r-universe.dev/rtemis.a3) [![npm version](https://img.shields.io/npm/v/@rtemis/a3.svg)](https://www.npmjs.com/package/@rtemis/a3) +[![Crates.io Version](https://img.shields.io/crates/v/rtemis_a3)](https://crates.io/crates/rtemis_a3) [![r-ci](https://github.com/rtemis-org/a3/actions/workflows/r-ci.yml/badge.svg)](https://github.com/rtemis-org/a3/actions/workflows/r-ci.yml) [![python-ci](https://github.com/rtemis-org/a3/actions/workflows/python-ci.yml/badge.svg)](https://github.com/rtemis-org/a3/actions/workflows/python-ci.yml) From efee1b873283c1a44adce18b7dca13b8bf7ffb13 Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 19:26:27 -0700 Subject: [PATCH 02/12] add MPL 2.0 text --- python/rtemis_a3/LICENSE | 373 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 373 insertions(+) create mode 100644 python/rtemis_a3/LICENSE diff --git a/python/rtemis_a3/LICENSE b/python/rtemis_a3/LICENSE new file mode 100644 index 0000000..14e2f77 --- /dev/null +++ b/python/rtemis_a3/LICENSE @@ -0,0 +1,373 @@ +Mozilla Public License Version 2.0 +================================== + +1. Definitions +-------------- + +1.1. "Contributor" + means each individual or legal entity that creates, contributes to + the creation of, or owns Covered Software. + +1.2. "Contributor Version" + means the combination of the Contributions of others (if any) used + by a Contributor and that particular Contributor's Contribution. + +1.3. "Contribution" + means Covered Software of a particular Contributor. + +1.4. "Covered Software" + means Source Code Form to which the initial Contributor has attached + the notice in Exhibit A, the Executable Form of such Source Code + Form, and Modifications of such Source Code Form, in each case + including portions thereof. + +1.5. "Incompatible With Secondary Licenses" + means + + (a) that the initial Contributor has attached the notice described + in Exhibit B to the Covered Software; or + + (b) that the Covered Software was made available under the terms of + version 1.1 or earlier of the License, but not also under the + terms of a Secondary License. + +1.6. "Executable Form" + means any form of the work other than Source Code Form. + +1.7. "Larger Work" + means a work that combines Covered Software with other material, in + a separate file or files, that is not Covered Software. + +1.8. "License" + means this document. + +1.9. "Licensable" + means having the right to grant, to the maximum extent possible, + whether at the time of the initial grant or subsequently, any and + all of the rights conveyed by this License. + +1.10. "Modifications" + means any of the following: + + (a) any file in Source Code Form that results from an addition to, + deletion from, or modification of the contents of Covered + Software; or + + (b) any new file in Source Code Form that contains any Covered + Software. + +1.11. "Patent Claims" of a Contributor + means any patent claim(s), including without limitation, method, + process, and apparatus claims, in any patent Licensable by such + Contributor that would be infringed, but for the grant of the + License, by the making, using, selling, offering for sale, having + made, import, or transfer of either its Contributions or its + Contributor Version. + +1.12. "Secondary License" + means either the GNU General Public License, Version 2.0, the GNU + Lesser General Public License, Version 2.1, the GNU Affero General + Public License, Version 3.0, or any later versions of those + licenses. + +1.13. "Source Code Form" + means the form of the work preferred for making modifications. + +1.14. "You" (or "Your") + means an individual or a legal entity exercising rights under this + License. For legal entities, "You" includes any entity that + controls, is controlled by, or is under common control with You. For + purposes of this definition, "control" means (a) the power, direct + or indirect, to cause the direction or management of such entity, + whether by contract or otherwise, or (b) ownership of more than + fifty percent (50%) of the outstanding shares or beneficial + ownership of such entity. + +2. License Grants and Conditions +-------------------------------- + +2.1. Grants + +Each Contributor hereby grants You a world-wide, royalty-free, +non-exclusive license: + +(a) under intellectual property rights (other than patent or trademark) + Licensable by such Contributor to use, reproduce, make available, + modify, display, perform, distribute, and otherwise exploit its + Contributions, either on an unmodified basis, with Modifications, or + as part of a Larger Work; and + +(b) under Patent Claims of such Contributor to make, use, sell, offer + for sale, have made, import, and otherwise transfer either its + Contributions or its Contributor Version. + +2.2. Effective Date + +The licenses granted in Section 2.1 with respect to any Contribution +become effective for each Contribution on the date the Contributor first +distributes such Contribution. + +2.3. Limitations on Grant Scope + +The licenses granted in this Section 2 are the only rights granted under +this License. No additional rights or licenses will be implied from the +distribution or licensing of Covered Software under this License. +Notwithstanding Section 2.1(b) above, no patent license is granted by a +Contributor: + +(a) for any code that a Contributor has removed from Covered Software; + or + +(b) for infringements caused by: (i) Your and any other third party's + modifications of Covered Software, or (ii) the combination of its + Contributions with other software (except as part of its Contributor + Version); or + +(c) under Patent Claims infringed by Covered Software in the absence of + its Contributions. + +This License does not grant any rights in the trademarks, service marks, +or logos of any Contributor (except as may be necessary to comply with +the notice requirements in Section 3.4). + +2.4. Subsequent Licenses + +No Contributor makes additional grants as a result of Your choice to +distribute the Covered Software under a subsequent version of this +License (see Section 10.2) or under the terms of a Secondary License (if +permitted under the terms of Section 3.3). + +2.5. Representation + +Each Contributor represents that the Contributor believes its +Contributions are its original creation(s) or it has sufficient rights +to grant the rights to its Contributions conveyed by this License. + +2.6. Fair Use + +This License is not intended to limit any rights You have under +applicable copyright doctrines of fair use, fair dealing, or other +equivalents. + +2.7. Conditions + +Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted +in Section 2.1. + +3. Responsibilities +------------------- + +3.1. Distribution of Source Form + +All distribution of Covered Software in Source Code Form, including any +Modifications that You create or to which You contribute, must be under +the terms of this License. You must inform recipients that the Source +Code Form of the Covered Software is governed by the terms of this +License, and how they can obtain a copy of this License. You may not +attempt to alter or restrict the recipients' rights in the Source Code +Form. + +3.2. Distribution of Executable Form + +If You distribute Covered Software in Executable Form then: + +(a) such Covered Software must also be made available in Source Code + Form, as described in Section 3.1, and You must inform recipients of + the Executable Form how they can obtain a copy of such Source Code + Form by reasonable means in a timely manner, at a charge no more + than the cost of distribution to the recipient; and + +(b) You may distribute such Executable Form under the terms of this + License, or sublicense it under different terms, provided that the + license for the Executable Form does not attempt to limit or alter + the recipients' rights in the Source Code Form under this License. + +3.3. Distribution of a Larger Work + +You may create and distribute a Larger Work under terms of Your choice, +provided that You also comply with the requirements of this License for +the Covered Software. If the Larger Work is a combination of Covered +Software with a work governed by one or more Secondary Licenses, and the +Covered Software is not Incompatible With Secondary Licenses, this +License permits You to additionally distribute such Covered Software +under the terms of such Secondary License(s), so that the recipient of +the Larger Work may, at their option, further distribute the Covered +Software under the terms of either this License or such Secondary +License(s). + +3.4. Notices + +You may not remove or alter the substance of any license notices +(including copyright notices, patent notices, disclaimers of warranty, +or limitations of liability) contained within the Source Code Form of +the Covered Software, except that You may alter any license notices to +the extent required to remedy known factual inaccuracies. + +3.5. Application of Additional Terms + +You may choose to offer, and to charge a fee for, warranty, support, +indemnity or liability obligations to one or more recipients of Covered +Software. However, You may do so only on Your own behalf, and not on +behalf of any Contributor. You must make it absolutely clear that any +such warranty, support, indemnity, or liability obligation is offered by +You alone, and You hereby agree to indemnify every Contributor for any +liability incurred by such Contributor as a result of warranty, support, +indemnity or liability terms You offer. You may include additional +disclaimers of warranty and limitations of liability specific to any +jurisdiction. + +4. Inability to Comply Due to Statute or Regulation +--------------------------------------------------- + +If it is impossible for You to comply with any of the terms of this +License with respect to some or all of the Covered Software due to +statute, judicial order, or regulation then You must: (a) comply with +the terms of this License to the maximum extent possible; and (b) +describe the limitations and the code they affect. Such description must +be placed in a text file included with all distributions of the Covered +Software under this License. Except to the extent prohibited by statute +or regulation, such description must be sufficiently detailed for a +recipient of ordinary skill to be able to understand it. + +5. Termination +-------------- + +5.1. The rights granted under this License will terminate automatically +if You fail to comply with any of its terms. However, if You become +compliant, then the rights granted under this License from a particular +Contributor are reinstated (a) provisionally, unless and until such +Contributor explicitly and finally terminates Your grants, and (b) on an +ongoing basis, if such Contributor fails to notify You of the +non-compliance by some reasonable means prior to 60 days after You have +come back into compliance. Moreover, Your grants from a particular +Contributor are reinstated on an ongoing basis if such Contributor +notifies You of the non-compliance by some reasonable means, this is the +first time You have received notice of non-compliance with this License +from such Contributor, and You become compliant prior to 30 days after +Your receipt of the notice. + +5.2. If You initiate litigation against any entity by asserting a patent +infringement claim (excluding declaratory judgment actions, +counter-claims, and cross-claims) alleging that a Contributor Version +directly or indirectly infringes any patent, then the rights granted to +You by any and all Contributors for the Covered Software under Section +2.1 of this License shall terminate. + +5.3. In the event of termination under Sections 5.1 or 5.2 above, all +end user license agreements (excluding distributors and resellers) which +have been validly granted by You or Your distributors under this License +prior to termination shall survive termination. + +************************************************************************ +* * +* 6. Disclaimer of Warranty * +* ------------------------- * +* * +* Covered Software is provided under this License on an "as is" * +* basis, without warranty of any kind, either expressed, implied, or * +* statutory, including, without limitation, warranties that the * +* Covered Software is free of defects, merchantable, fit for a * +* particular purpose or non-infringing. The entire risk as to the * +* quality and performance of the Covered Software is with You. * +* Should any Covered Software prove defective in any respect, You * +* (not any Contributor) assume the cost of any necessary servicing, * +* repair, or correction. This disclaimer of warranty constitutes an * +* essential part of this License. No use of any Covered Software is * +* authorized under this License except under this disclaimer. * +* * +************************************************************************ + +************************************************************************ +* * +* 7. Limitation of Liability * +* -------------------------- * +* * +* Under no circumstances and under no legal theory, whether tort * +* (including negligence), contract, or otherwise, shall any * +* Contributor, or anyone who distributes Covered Software as * +* permitted above, be liable to You for any direct, indirect, * +* special, incidental, or consequential damages of any character * +* including, without limitation, damages for lost profits, loss of * +* goodwill, work stoppage, computer failure or malfunction, or any * +* and all other commercial damages or losses, even if such party * +* shall have been informed of the possibility of such damages. This * +* limitation of liability shall not apply to liability for death or * +* personal injury resulting from such party's negligence to the * +* extent applicable law prohibits such limitation. Some * +* jurisdictions do not allow the exclusion or limitation of * +* incidental or consequential damages, so this exclusion and * +* limitation may not apply to You. * +* * +************************************************************************ + +8. Litigation +------------- + +Any litigation relating to this License may be brought only in the +courts of a jurisdiction where the defendant maintains its principal +place of business and such litigation shall be governed by laws of that +jurisdiction, without reference to its conflict-of-law provisions. +Nothing in this Section shall prevent a party's ability to bring +cross-claims or counter-claims. + +9. Miscellaneous +---------------- + +This License represents the complete agreement concerning the subject +matter hereof. If any provision of this License is held to be +unenforceable, such provision shall be reformed only to the extent +necessary to make it enforceable. Any law or regulation which provides +that the language of a contract shall be construed against the drafter +shall not be used to construe this License against a Contributor. + +10. Versions of the License +--------------------------- + +10.1. New Versions + +Mozilla Foundation is the license steward. Except as provided in Section +10.3, no one other than the license steward has the right to modify or +publish new versions of this License. Each version will be given a +distinguishing version number. + +10.2. Effect of New Versions + +You may distribute the Covered Software under the terms of the version +of the License under which You originally received the Covered Software, +or under the terms of any subsequent version published by the license +steward. + +10.3. Modified Versions + +If you create software not governed by this License, and you want to +create a new license for such software, you may create and use a +modified version of this License if you rename the license and remove +any references to the name of the license steward (except to note that +such modified license differs from this License). + +10.4. Distributing Source Code Form that is Incompatible With Secondary +Licenses + +If You choose to distribute Source Code Form that is Incompatible With +Secondary Licenses under the terms of this version of the License, the +notice described in Exhibit B of this License must be attached. + +Exhibit A - Source Code Form License Notice +------------------------------------------- + + This Source Code Form is subject to the terms of the Mozilla Public + License, v. 2.0. If a copy of the MPL was not distributed with this + file, You can obtain one at http://mozilla.org/MPL/2.0/. + +If it is not possible or desirable to put the notice in a particular +file, then You may include the notice in a location (such as a LICENSE +file in a relevant directory) where a recipient would be likely to look +for such a notice. + +You may add additional accurate notices of copyright ownership. + +Exhibit B - "Incompatible With Secondary Licenses" Notice +--------------------------------------------------------- + + This Source Code Form is "Incompatible With Secondary Licenses", as + defined by the Mozilla Public License, v. 2.0. From 0f5df3e97c46a1d418591ad7c17fe307dffcd311 Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 19:32:06 -0700 Subject: [PATCH 03/12] prepare for PyPI --- python/rtemis_a3/pyproject.toml | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/python/rtemis_a3/pyproject.toml b/python/rtemis_a3/pyproject.toml index 6529368..e2886c1 100644 --- a/python/rtemis_a3/pyproject.toml +++ b/python/rtemis_a3/pyproject.toml @@ -1,16 +1,31 @@ [project] name = "rtemis-a3" version = "0.1.0" -description = "Add your description here" +description = "Python implementation of the Amino Acid Annotation (A3) format" readme = "README.md" +license = { text = "MPL-2.0" } authors = [ - { name = "Stathis Gennatas", email = "gennatas@gmail.com" } + { name = "E.D. Gennatas", email = "gennatas@gmail.com" } +] +keywords = ["bioinformatics", "proteomics", "amino acid", "annotation", "protein"] +classifiers = [ + "Intended Audience :: Science/Research", + "License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.13", + "Topic :: Scientific/Engineering :: Bio-Informatics", + "Typing :: Typed", ] requires-python = ">=3.13" dependencies = [ "pydantic>=2.12.5", ] +[project.urls] +Homepage = "https://github.com/rtemis-org/a3" +Repository = "https://github.com/rtemis-org/a3" +Issues = "https://github.com/rtemis-org/a3/issues" + [build-system] requires = ["uv_build>=0.11.2,<0.12.0"] build-backend = "uv_build" From cfe9d886c932a52faa3c9a724482dbfd3bc5d31e Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 19:57:41 -0700 Subject: [PATCH 04/12] up --- python/rtemis_a3/pyproject.toml | 2 -- 1 file changed, 2 deletions(-) diff --git a/python/rtemis_a3/pyproject.toml b/python/rtemis_a3/pyproject.toml index e2886c1..510e3d0 100644 --- a/python/rtemis_a3/pyproject.toml +++ b/python/rtemis_a3/pyproject.toml @@ -10,8 +10,6 @@ authors = [ keywords = ["bioinformatics", "proteomics", "amino acid", "annotation", "protein"] classifiers = [ "Intended Audience :: Science/Research", - "License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)", - "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.13", "Topic :: Scientific/Engineering :: Bio-Informatics", "Typing :: Typed", From 00f07761a13c24d31cb7ee41dfe0ba724ca0752e Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 19:57:57 -0700 Subject: [PATCH 05/12] uv lock --upgrade --- python/rtemis_a3/uv.lock | 114 +++++++++++++++++++-------------------- 1 file changed, 57 insertions(+), 57 deletions(-) diff --git a/python/rtemis_a3/uv.lock b/python/rtemis_a3/uv.lock index b985153..030706e 100644 --- a/python/rtemis_a3/uv.lock +++ 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Gennatas Date: Sun, 5 Apr 2026 20:34:24 -0700 Subject: [PATCH 06/12] fix: update license format in pyproject.toml --- python/rtemis_a3/pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/rtemis_a3/pyproject.toml b/python/rtemis_a3/pyproject.toml index 510e3d0..ed366e4 100644 --- a/python/rtemis_a3/pyproject.toml +++ b/python/rtemis_a3/pyproject.toml @@ -3,7 +3,8 @@ name = "rtemis-a3" version = "0.1.0" description = "Python implementation of the Amino Acid Annotation (A3) format" readme = "README.md" -license = { text = "MPL-2.0" } +license = "MPL-2.0" +license-files = ["LICENSE"] authors = [ { name = "E.D. Gennatas", email = "gennatas@gmail.com" } ] From 1d42cf20737cbcd5c6628ff306c7711bee992479 Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 20:34:30 -0700 Subject: [PATCH 07/12] feat: add schema and version information to JSON output --- python/rtemis_a3/README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/python/rtemis_a3/README.md b/python/rtemis_a3/README.md index dca8c65..349163c 100644 --- a/python/rtemis_a3/README.md +++ b/python/rtemis_a3/README.md @@ -77,7 +77,9 @@ json_string = a3_to_json(a3, indent=2) # pretty-printed ```json { - "sequence": "MKTAYIAKQR", + "$schema": "https://schema.rtemis.org/a3/v1/schema.json", + "a3_version": "1.0.0", + "sequence": "MKTAYIAKQR", "annotations": { "site": { "Active site": { "index": [3, 5], "type": "activeSite" } }, "region": { "Repeat 1": { "index": [[1, 4]], "type": "" } }, From 1d339d2251aaeb25b68294fa301c8dbfacd2f1a9 Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 20:34:39 -0700 Subject: [PATCH 08/12] feat: enhance position validation and error handling in Pydantic models --- python/rtemis_a3/src/rtemis/a3/_models.py | 30 ++++++++++++++++++++--- 1 file changed, 26 insertions(+), 4 deletions(-) diff --git a/python/rtemis_a3/src/rtemis/a3/_models.py b/python/rtemis_a3/src/rtemis/a3/_models.py index 76c9e20..ebb8eab 100644 --- a/python/rtemis_a3/src/rtemis/a3/_models.py +++ b/python/rtemis_a3/src/rtemis/a3/_models.py @@ -16,6 +16,7 @@ field_validator, model_validator, ) +from pydantic.functional_validators import BeforeValidator from ._normalize import ( check_no_overlap, @@ -24,11 +25,26 @@ sort_ranges, ) + +class _BoundsErrors(Exception): + """Internal: carries individual bounds-check messages out of the model validator.""" + + def __init__(self, messages: list[str]) -> None: + self.messages = messages + + # --------------------------------------------------------------------------- # Constrained types # --------------------------------------------------------------------------- -Position = Annotated[int, Field(gt=0)] + +def _reject_bool(v: Any) -> Any: + if isinstance(v, bool): + raise ValueError("boolean values are not valid positions") + return v + + +Position = Annotated[int, BeforeValidator(_reject_bool), Field(gt=0)] # --------------------------------------------------------------------------- # Annotation entry models @@ -71,6 +87,8 @@ def _normalize_ranges(cls, v: Any) -> list[tuple[int, int]]: for item in v: if isinstance(item, (list, tuple)) and len(item) == 2: s, e = item + if isinstance(s, bool) or isinstance(e, bool): + raise ValueError("boolean values are not valid positions") if not (isinstance(s, int) and isinstance(e, int)): raise ValueError( f"range elements must be integers, got [{type(s).__name__}, " @@ -108,12 +126,16 @@ def _normalize_flex_index(cls, v: Any) -> list[int] | list[tuple[int, int]]: return [] # Determine geometry from first element first = v[0] + if isinstance(first, bool): + raise ValueError("boolean values are not valid positions") if isinstance(first, (list, tuple)): # Ranges path coerced: list[tuple[int, int]] = [] for item in v: if isinstance(item, (list, tuple)) and len(item) == 2: s, e = item + if isinstance(s, bool) or isinstance(e, bool): + raise ValueError("boolean values are not valid positions") if not (isinstance(s, int) and isinstance(e, int)): raise ValueError( f"range elements must be integers, got " @@ -132,10 +154,10 @@ def _normalize_flex_index(cls, v: Any) -> list[int] | list[tuple[int, int]]: sorted_ranges = sort_ranges(coerced) check_no_overlap(sorted_ranges) return sorted_ranges - elif isinstance(first, int): + elif isinstance(first, int) and not isinstance(first, bool): # Positions path for item in v: - if not isinstance(item, int): + if isinstance(item, bool) or not isinstance(item, int): raise ValueError( "cannot mix integers and non-integers in index" ) @@ -283,7 +305,7 @@ def _bounds_check(self) -> A3: ) if errors: - raise ValueError("\n".join(errors)) + raise _BoundsErrors(errors) return self From 230897f497cad1447eb4914a2b196b1677c1efa8 Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 20:34:45 -0700 Subject: [PATCH 09/12] feat: improve error handling in A3 creation and JSON parsing --- python/rtemis_a3/src/rtemis/a3/api.py | 39 +++++++++++++++------------ 1 file changed, 22 insertions(+), 17 deletions(-) diff --git a/python/rtemis_a3/src/rtemis/a3/api.py b/python/rtemis_a3/src/rtemis/a3/api.py index 43c62fd..8931a73 100644 --- a/python/rtemis_a3/src/rtemis/a3/api.py +++ b/python/rtemis_a3/src/rtemis/a3/api.py @@ -11,7 +11,7 @@ from pydantic import ValidationError -from ._models import A3, VariantRecord +from ._models import A3, VariantRecord, _BoundsErrors from .errors import A3ParseError, A3ValidationError _A3_SCHEMA_URI = "https://schema.rtemis.org/a3/v1/schema.json" @@ -79,6 +79,9 @@ def create_a3( try: return A3.model_validate(data) + except _BoundsErrors as exc: + errors = [{"loc": (), "msg": msg, "type": "value_error"} for msg in exc.messages] + raise A3ValidationError("\n".join(exc.messages), errors) from exc except ValidationError as exc: raise A3ValidationError(str(exc), cast(list[dict[str, Any]], exc.errors())) from exc @@ -109,33 +112,35 @@ def a3_from_json(text: str) -> A3: raise A3ParseError(f"invalid JSON: {exc}") from exc if not isinstance(data, dict): - raise A3ParseError("JSON root must be an object") + raise A3ValidationError( + "JSON root must be an object", + [{"loc": (), "msg": "JSON root must be an object", "type": "value_error", "input": data}], + ) + envelope_errors: list[dict[str, Any]] = [] schema_val = data.get("$schema") if schema_val is None: - raise A3ParseError("missing required field '$schema'") - if schema_val != _A3_SCHEMA_URI: - raise A3ParseError( - f"'$schema' must be '{_A3_SCHEMA_URI}', got '{schema_val}'" - ) + envelope_errors.append({"loc": ("$schema",), "msg": "missing required field '$schema'", "type": "missing", "input": data}) + elif schema_val != _A3_SCHEMA_URI: + envelope_errors.append({"loc": ("$schema",), "msg": f"'$schema' must be '{_A3_SCHEMA_URI}', got '{schema_val}'", "type": "value_error", "input": schema_val}) version_val = data.get("a3_version") if version_val is None: - raise A3ParseError("missing required field 'a3_version'") - if version_val != _A3_VERSION: - raise A3ParseError( - f"'a3_version' must be '{_A3_VERSION}', got '{version_val}'" + envelope_errors.append({"loc": ("a3_version",), "msg": "missing required field 'a3_version'", "type": "missing", "input": data}) + elif version_val != _A3_VERSION: + envelope_errors.append({"loc": ("a3_version",), "msg": f"'a3_version' must be '{_A3_VERSION}', got '{version_val}'", "type": "value_error", "input": version_val}) + if envelope_errors: + raise A3ValidationError( + "; ".join(e["msg"] for e in envelope_errors), + envelope_errors, ) - if "sequence" not in data: - raise A3ParseError("missing required field 'sequence'") - if "annotations" not in data: - raise A3ParseError("missing required field 'annotations'") - if "metadata" not in data: - raise A3ParseError("missing required field 'metadata'") # Strip envelope keys before passing to the data model for key in _ENVELOPE_KEYS: data.pop(key, None) try: return A3.model_validate(data) + except _BoundsErrors as exc: + errors = [{"loc": (), "msg": msg, "type": "value_error"} for msg in exc.messages] + raise A3ValidationError("\n".join(exc.messages), errors) from exc except ValidationError as exc: raise A3ValidationError(str(exc), cast(list[dict[str, Any]], exc.errors())) from exc From a8d9839841a8417c964247c11ad12023d9b79f68 Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 20:34:50 -0700 Subject: [PATCH 10/12] feat: enhance A3ValidationError documentation and add messages property --- python/rtemis_a3/src/rtemis/a3/errors.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/python/rtemis_a3/src/rtemis/a3/errors.py b/python/rtemis_a3/src/rtemis/a3/errors.py index 3f90601..fc4d6a8 100644 --- a/python/rtemis_a3/src/rtemis/a3/errors.py +++ b/python/rtemis_a3/src/rtemis/a3/errors.py @@ -17,13 +17,22 @@ class A3ValidationError(Exception): message : str Human-readable summary. errors : list[dict[str, Any]] - Structured error list (from Pydantic's ``ValidationError.errors()``). + Structured error list. Each entry has at minimum ``loc`` (tuple of + field path components), ``msg`` (human-readable message), and + ``type`` (error kind string). Pydantic structural errors follow + Pydantic's native format; bounds and envelope errors follow the same + shape for consistency. """ def __init__(self, message: str, errors: list[dict[str, Any]] | None = None): super().__init__(message) self.errors: list[dict[str, Any]] = errors or [] + @property + def messages(self) -> list[str]: + """Individual error messages, one per violation.""" + return [e["msg"] for e in self.errors] + class A3ParseError(Exception): """Raised when JSON parsing or file I/O fails.""" From 1e8ad3bd6354ef99d78a3a35542534c25540290e Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 20:34:55 -0700 Subject: [PATCH 11/12] feat: enhance A3 JSON parsing tests with default handling and validation checks --- python/rtemis_a3/tests/test_api.py | 34 +++++++++++++++++++----------- 1 file changed, 22 insertions(+), 12 deletions(-) diff --git a/python/rtemis_a3/tests/test_api.py b/python/rtemis_a3/tests/test_api.py index bea4e27..31f4bf9 100644 --- a/python/rtemis_a3/tests/test_api.py +++ b/python/rtemis_a3/tests/test_api.py @@ -107,26 +107,36 @@ def test_valid_json_invalid_a3(self): '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "M", "annotations": {}, "metadata": {}}' ) # too short - def test_missing_annotations_field(self): - with pytest.raises(A3ParseError, match="annotations"): - a3_from_json( - '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "MAEPRQ", "metadata": {}}' - ) + def test_missing_annotations_field_defaults(self): + # annotations has a model default — omitting it from JSON is valid + a3 = a3_from_json( + '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "MAEPRQ", "metadata": {}}' + ) + assert a3.annotations.site == {} - def test_missing_metadata_field(self): - with pytest.raises(A3ParseError, match="metadata"): - a3_from_json( - '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "MAEPRQ", "annotations": {}}' - ) + def test_missing_metadata_field_defaults(self): + # metadata has a model default — omitting it from JSON is valid + a3 = a3_from_json( + '{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "1.0.0", "sequence": "MAEPRQ", "annotations": {}}' + ) + assert a3.metadata.uniprot_id == "" def test_missing_schema_field(self): - with pytest.raises(A3ParseError, match=r"\$schema"): + with pytest.raises(A3ValidationError, match=r"\$schema"): a3_from_json('{"a3_version": "1.0.0", "sequence": "MAEPRQ"}') def test_missing_version_field(self): - with pytest.raises(A3ParseError, match="a3_version"): + with pytest.raises(A3ValidationError, match="a3_version"): a3_from_json('{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "sequence": "MAEPRQ"}') + def test_wrong_schema_uri(self): + with pytest.raises(A3ValidationError, match=r"\$schema"): + a3_from_json('{"$schema": "https://wrong.example.com/schema.json", "a3_version": "1.0.0", "sequence": "MAEPRQ"}') + + def test_wrong_version(self): + with pytest.raises(A3ValidationError, match="a3_version"): + a3_from_json('{"$schema": "https://schema.rtemis.org/a3/v1/schema.json", "a3_version": "9.9.9", "sequence": "MAEPRQ"}') + class TestA3ToJson: def test_roundtrip_minimal(self): From 1874a6192b5c5d1b62448f804117ece5e76697d8 Mon Sep 17 00:00:00 2001 From: Stathis Gennatas Date: Sun, 5 Apr 2026 20:35:00 -0700 Subject: [PATCH 12/12] feat: add boolean rejection tests and enhance A3 bounds checking with A3ValidationError --- python/rtemis_a3/tests/test_models.py | 87 +++++++++++++-------------- 1 file changed, 43 insertions(+), 44 deletions(-) diff --git a/python/rtemis_a3/tests/test_models.py b/python/rtemis_a3/tests/test_models.py index c7cc453..b03ace7 100644 --- a/python/rtemis_a3/tests/test_models.py +++ b/python/rtemis_a3/tests/test_models.py @@ -12,6 +12,8 @@ SiteEntry, VariantRecord, ) +from rtemis.a3 import create_a3 +from rtemis.a3.errors import A3ValidationError # --------------------------------------------------------------------------- @@ -45,6 +47,10 @@ def test_negative_rejected(self): with pytest.raises(ValidationError): SiteEntry(index=[-1, 2]) + def test_bool_rejected(self): + with pytest.raises(ValidationError, match="boolean"): + SiteEntry(index=[True, 2]) + def test_frozen(self): entry = SiteEntry(index=[1, 2]) with pytest.raises(ValidationError): @@ -90,6 +96,10 @@ def test_non_positive_rejected(self): with pytest.raises(ValidationError): RegionEntry(index=[(0, 5)]) + def test_bool_rejected(self): + with pytest.raises(ValidationError, match="boolean"): + RegionEntry(index=[(True, 5)]) + # --------------------------------------------------------------------------- # FlexEntry @@ -113,6 +123,14 @@ def test_range_overlap_rejected(self): with pytest.raises(ValidationError, match="overlapping"): FlexEntry(index=[(1, 5), (3, 8)]) + def test_bool_position_rejected(self): + with pytest.raises(ValidationError, match="boolean"): + FlexEntry(index=[True, 2]) + + def test_bool_range_rejected(self): + with pytest.raises(ValidationError, match="boolean"): + FlexEntry(index=[(True, 5)]) + # --------------------------------------------------------------------------- # VariantRecord @@ -140,6 +158,10 @@ def test_non_positive_position_rejected(self): with pytest.raises(ValidationError): VariantRecord(position=0) + def test_bool_position_rejected(self): + with pytest.raises(ValidationError, match="boolean"): + VariantRecord(position=True) + def test_non_json_extra_rejected(self): with pytest.raises(ValidationError, match="not JSON-compatible"): VariantRecord(position=1, **{"callback": lambda: None}) @@ -228,59 +250,36 @@ def test_unknown_top_level_key_rejected(self): A3.model_validate({"sequence": "MA", "extra_field": "nope"}) def test_bounds_check_site_out_of_range(self): - with pytest.raises(ValidationError, match="out of bounds"): - A3.model_validate( - { - "sequence": "MAEPRQ", - "annotations": { - "site": {"bad": {"index": [100], "type": ""}}, - }, - } - ) + with pytest.raises(A3ValidationError, match="out of bounds"): + create_a3("MAEPRQ", site={"bad": {"index": [100], "type": ""}}) def test_bounds_check_region_out_of_range(self): - with pytest.raises(ValidationError, match="out of bounds"): - A3.model_validate( - { - "sequence": "MAEPRQ", - "annotations": { - "region": {"bad": {"index": [[1, 100]], "type": ""}}, - }, - } - ) + with pytest.raises(A3ValidationError, match="out of bounds"): + create_a3("MAEPRQ", region={"bad": {"index": [[1, 100]], "type": ""}}) def test_bounds_check_variant_out_of_range(self): - with pytest.raises(ValidationError, match="out of bounds"): - A3.model_validate( - { - "sequence": "MAEPRQ", - "annotations": { - "variant": [{"position": 100}], - }, - } - ) + with pytest.raises(A3ValidationError, match="out of bounds"): + create_a3("MAEPRQ", variant=[{"position": 100}]) def test_bounds_check_ptm_positions(self): - with pytest.raises(ValidationError, match="out of bounds"): - A3.model_validate( - { - "sequence": "MAEPRQ", - "annotations": { - "ptm": {"bad": {"index": [100], "type": ""}}, - }, - } - ) + with pytest.raises(A3ValidationError, match="out of bounds"): + create_a3("MAEPRQ", ptm={"bad": {"index": [100], "type": ""}}) def test_bounds_check_ptm_ranges(self): - with pytest.raises(ValidationError, match="out of bounds"): - A3.model_validate( - { - "sequence": "MAEPRQ", - "annotations": { - "ptm": {"bad": {"index": [[1, 100]], "type": ""}}, - }, - } + with pytest.raises(A3ValidationError, match="out of bounds"): + create_a3("MAEPRQ", ptm={"bad": {"index": [[1, 100]], "type": ""}}) + + def test_bounds_check_multi_error(self): + with pytest.raises(A3ValidationError) as exc_info: + create_a3( + "MAEPRQ", + site={"s1": {"index": [99], "type": ""}, "s2": {"index": [100], "type": ""}}, + variant=[{"position": 88}], ) + err = exc_info.value + assert len(err.errors) == 3 + assert len(err.messages) == 3 + assert all("out of bounds" in m for m in err.messages) def test_full_valid(self): a3 = A3.model_validate(