fhir-moldef 0.7.0__tar.gz

fhir_moldef-0.7.0/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
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fhir_moldef-0.7.0/PKG-INFO

@@ -0,0 +1,395 @@
+Metadata-Version: 2.4
+Name: fhir-moldef
+Version: 0.7.0
+Summary: A Python implementation of the HL7 FHIR MolecularDefinition resource that supports associated profiles and enables bidirectional translation between MolecularDefinition profiles and genomic representations, including VRS, HGVS, and SPDI.
+Author: Salem Bajjali, Robert R. Freimuth
+License:                                  Apache License
+                                   Version 2.0, January 2004
+                                http://www.apache.org/licenses/
+        
+           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+        
+           1. Definitions.
+        
+              "License" shall mean the terms and conditions for use, reproduction,
+              and distribution as defined by Sections 1 through 9 of this document.
+        
+              "Licensor" shall mean the copyright owner or entity authorized by
+              the copyright owner that is granting the License.
+        
+              "Legal Entity" shall mean the union of the acting entity and all
+              other entities that control, are controlled by, or are under common
+              control with that entity. For the purposes of this definition,
+              "control" means (i) the power, direct or indirect, to cause the
+              direction or management of such entity, whether by contract or
+              otherwise, or (ii) ownership of fifty percent (50%) or more of the
+              outstanding shares, or (iii) beneficial ownership of such entity.
+        
+              "You" (or "Your") shall mean an individual or Legal Entity
+              exercising permissions granted by this License.
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+              "Source" form shall mean the preferred form for making modifications,
+              including but not limited to software source code, documentation
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+              not limited to compiled object code, generated documentation,
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+              Object form, made available under the License, as indicated by a
+              copyright notice that is included in or attached to the work
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+        
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+              form, that is based on (or derived from) the Work and for which the
+              editorial revisions, annotations, elaborations, or other modifications
+              represent, as a whole, an original work of authorship. For the purposes
+              of this License, Derivative Works shall not include works that remain
+              separable from, or merely link (or bind by name) to the interfaces of,
+              the Work and Derivative Works thereof.
+        
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+              or by an individual or Legal Entity authorized to submit on behalf of
+              the copyright owner. For the purposes of this definition, "submitted"
+              means any form of electronic, verbal, or written communication sent
+              to the Licensor or its representatives, including but not limited to
+              communication on electronic mailing lists, source code control systems,
+              and issue tracking systems that are managed by, or on behalf of, the
+              Licensor for the purpose of discussing and improving the Work, but
+              excluding communication that is conspicuously marked or otherwise
+              designated in writing by the copyright owner as "Not a Contribution."
+        
+              "Contributor" shall mean Licensor and any individual or Legal Entity
+              on behalf of whom a Contribution has been received by Licensor and
+              subsequently incorporated within the Work.
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+           2. Grant of Copyright License. Subject to the terms and conditions of
+              this License, each Contributor hereby grants to You a perpetual,
+              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+              copyright license to reproduce, prepare Derivative Works of,
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+              Work and such Derivative Works in Source or Object form.
+        
+           3. Grant of Patent License. Subject to the terms and conditions of
+              this License, each Contributor hereby grants to You a perpetual,
+              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+              (except as stated in this section) patent license to make, have made,
+              use, offer to sell, sell, import, and otherwise transfer the Work,
+              where such license applies only to those patent claims licensable
+              by such Contributor that are necessarily infringed by their
+              Contribution(s) alone or by combination of their Contribution(s)
+              with the Work to which such Contribution(s) was submitted. If You
+              institute patent litigation against any entity (including a
+              cross-claim or counterclaim in a lawsuit) alleging that the Work
+              or a Contribution incorporated within the Work constitutes direct
+              or contributory patent infringement, then any patent licenses
+              granted to You under this License for that Work shall terminate
+              as of the date such litigation is filed.
+        
+           4. Redistribution. You may reproduce and distribute copies of the
+              Work or Derivative Works thereof in any medium, with or without
+              modifications, and in Source or Object form, provided that You
+              meet the following conditions:
+        
+              (a) You must give any other recipients of the Work or
+                  Derivative Works a copy of this License; and
+        
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+        
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+        
+              You may add Your own copyright statement to Your modifications and
+              may provide additional or different license terms and conditions
+              for use, reproduction, or distribution of Your modifications, or
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+              reproduction, and distribution of the Work otherwise complies with
+              the conditions stated in this License.
+        
+           5. Submission of Contributions. Unless You explicitly state otherwise,
+              any Contribution intentionally submitted for inclusion in the Work
+              by You to the Licensor shall be under the terms and conditions of
+              this License, without any additional terms or conditions.
+              Notwithstanding the above, nothing herein shall supersede or modify
+              the terms of any separate license agreement you may have executed
+              with Licensor regarding such Contributions.
+        
+           6. Trademarks. This License does not grant permission to use the trade
+              names, trademarks, service marks, or product names of the Licensor,
+              except as required for reasonable and customary use in describing the
+              origin of the Work and reproducing the content of the NOTICE file.
+        
+           7. Disclaimer of Warranty. Unless required by applicable law or
+              agreed to in writing, Licensor provides the Work (and each
+              Contributor provides its Contributions) on an "AS IS" BASIS,
+              WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
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+              PARTICULAR PURPOSE. You are solely responsible for determining the
+              appropriateness of using or redistributing the Work and assume any
+              risks associated with Your exercise of permissions under this License.
+        
+           8. Limitation of Liability. In no event and under no legal theory,
+              whether in tort (including negligence), contract, or otherwise,
+              unless required by applicable law (such as deliberate and grossly
+              negligent acts) or agreed to in writing, shall any Contributor be
+              liable to You for damages, including any direct, indirect, special,
+              incidental, or consequential damages of any character arising as a
+              result of this License or out of the use or inability to use the
+              Work (including but not limited to damages for loss of goodwill,
+              work stoppage, computer failure or malfunction, or any and all
+              other commercial damages or losses), even if such Contributor
+              has been advised of the possibility of such damages.
+        
+           9. Accepting Warranty or Additional Liability. While redistributing
+              the Work or Derivative Works thereof, You may choose to offer,
+              and charge a fee for, acceptance of support, warranty, indemnity,
+              or other liability obligations and/or rights consistent with this
+              License. However, in accepting such obligations, You may act only
+              on Your own behalf and on Your sole responsibility, not on behalf
+              of any other Contributor, and only if You agree to indemnify,
+              defend, and hold each Contributor harmless for any liability
+              incurred by, or claims asserted against, such Contributor by reason
+              of your accepting any such warranty or additional liability.
+        
+           END OF TERMS AND CONDITIONS
+        
+           APPENDIX: How to apply the Apache License to your work.
+        
+              To apply the Apache License to your work, attach the following
+              boilerplate notice, with the fields enclosed by brackets "[]"
+              replaced with your own identifying information. (Don't include
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+              comment syntax for the file format. We also recommend that a
+              file or class name and description of purpose be included on the
+              same "printed page" as the copyright notice for easier
+              identification within third-party archives.
+        
+           Copyright [yyyy] [name of copyright owner]
+        
+           Licensed under the Apache License, Version 2.0 (the "License");
+           you may not use this file except in compliance with the License.
+           You may obtain a copy of the License at
+        
+               http://www.apache.org/licenses/LICENSE-2.0
+        
+           Unless required by applicable law or agreed to in writing, software
+           distributed under the License is distributed on an "AS IS" BASIS,
+           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+           See the License for the specific language governing permissions and
+           limitations under the License.
+        
+Project-URL: Repository, https://github.com/InformaticsGenomicMedicine/fhir-moldef
+Project-URL: Issues, https://github.com/InformaticsGenomicMedicine/fhir-moldef/issues
+Keywords: FHIR,MolecularDefinition,FHIR-python
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pydantic==2.8.2
+Requires-Dist: fhir-core==1.1.4
+Requires-Dist: fhir-resources==8.0.0
+Provides-Extra: translators
+Requires-Dist: ga4gh.vrs[extras]==2.3.1; extra == "translators"
+Requires-Dist: orjson==3.11.6; extra == "translators"
+Provides-Extra: notebooks
+Requires-Dist: ipykernel==6.28.0; extra == "notebooks"
+Provides-Extra: dev
+Requires-Dist: ga4gh.vrs[extras]==2.3.1; extra == "dev"
+Requires-Dist: pytest==9.0.3; extra == "dev"
+Requires-Dist: deepdiff==8.6.1; extra == "dev"
+Requires-Dist: ruff==0.8.3; extra == "dev"
+Dynamic: license-file
+
+<h1 align="center">fhir-moldef</h1>
+
+## Overview
+
+Welcome to the **fhir-moldef** repository. This project provides a Python implementation of the HL7 (Health Level Seven) Fast Healthcare Interoperability Resources (FHIR) Molecular Definition standard. It enables users to create instances of the MolecularDefinition resource and currently supports three profiles: Sequence, Allele, and Variant.
+
+<!--In FHIR, a profile is a structured extension of a resource that defines specific constraints and usage guidelines for particular use cases. -->
+
+Additionally, this repository supports seamless, bidirectional translation between Global Alliance for Genomics and Health (GA4GH) Variant Representation Specification (VRS) Alleles (v2.0) and the FHIR Allele Profile, enabling interoperability between the two standards.
+
+<!-- To help you get started, we provide Jupyter notebooks that serve as an educational guide. These notebooks introduce the MolecularDefinition resource, explain its profiles, and showcase the translation process between VRS Alleles (v2.0) and FHIR Allele with practical examples. -->
+
+
+## Disclaimer
+
+This project uses the `MolecularDefinition` schema from the latest in-progress development version: [Work in Progress Schema](https://build.fhir.org/branches/cg-im-moldef_work_in_progress_2/moleculardefinition.html). This page may occasionally be unavailable due to active development.
+
+It does **not** match the schema in the HL7 FHIR 6.0.0 Ballot 2 release: [FHIR Ballot 2 Schema](https://hl7.org/fhir/6.0.0-ballot2/moleculardefinition.html).
+
+<!-- * **Note**: The [Work in Progress Schema](https://build.fhir.org/branches/cg-im-moldef_work_in_progress_2/moleculardefinition.html) page may occasionally be unavailable due to active development. This downtime is beyond our group's control. If the page is temporarily inaccessible, we recommend trying again later. -->
+
+## Core Functionality
+
+| Category | Currently Supported |
+|----------|---------------------|
+| **Resource** | Generation of HL7 FHIR MolecularDefinition resources |
+| **Profiles** | Sequence, Allele, and Variant profiles |
+| **Translation** | Bidirectional translation between VRS 2.0 and FHIR (full + minimal) |
+| **Notebooks** | Interactive Jupyter notebooks with examples (**see the Notebooks README for details**) |
+| **Pipeline** | Extraction of VRS Allele objects from ClinVar variation files and translation into the FHIR Allele Profile |
+
+<!-- ## Features
+
+### Resource
+* **Generation of Molecular Definition Resources**: Effortlessly create fully compliant Molecular Definition resources based on the HL7 FHIR standard.
+
+### Profile
+* **Sequence**: Sequence is a specialized subclass of the MolecularDefinition resource, enabling you to create sequence-specific representations.
+
+* **Allele**: Allele is a specialized subclass of the MolecularDefinition resource, allowing you to create and manage allele-specific representations.
+
+### Translation
+* **Bidirectional Translation**: Perform seamless, bidirectional translations between FHIR Allele and VRS Alleles (version 2.0), ensuring interoperability and data consistency across diverse platforms.
+
+### Notebooks
+* **Educational Jupyter Notebooks**: Access interactive Jupyter notebooks for a hands-on learning experience, complete with practical examples and educational insights into the implementation’s functionality. -->
+
+## Installation Status
+
+This package is not currently published on PyPI but will be available soon.  
+In the meantime, clone the repository and follow the instructions below to work with the code locally.
+
+## Prerequisites
+
+- **Python 3.11–3.13**
+- **Virtual environment (uv recommended)**: used to manage project dependencies
+
+## Dependencies & Infrastructure
+
+The following infrastructure is required **only for the VRS ↔ FHIR translation functionality**:
+
+- **PostgreSQL 14**
+- **SeqRepo (`biocommons.seqrepo`)**
+
+These dependencies are **not required** if you only plan to instantiate MolecularDefinition profiles.
+
+For instructions on installing and configuring SeqRepo, see the [VRS-Python SeqRepo installation guide](https://github.com/ga4gh/vrs-python).
+
+Containerized setup instructions using **Podman** are planned, including configuration for running SeqRepo (and future UTA support).
+
+<!-- Additional documentation for installing SeqRepo locally is in development. A **docker-compose.yml** configuration will also be provided to run SeqRepo (and future UTA support) in a containerized environment.-->
+
+<!-- ## Local Setup
+
+Follow these steps to set up the project for local development.
+
+### 1. Clone the Repository
+Make sure you’re logged into GitHub, then clone the repository and navigate into it:
+
+```bash
+git clone https://github.com/YourUsername/fhir-moldef.git
+cd fhir-moldef
+```
+
+### 2. Create and Activate a Virtual Environment
+We recommend using Python’s built-in `venv` module.
+
+   ```bash
+   python -m venv venv
+   ```
+
+Activate the virtual environment
+
+- **macOS/Linux**
+   ```bash
+   source venv/bin/activate
+   ```
+- **Windows** 
+   ```bash
+   venv\Scripts\activate
+   ```
+
+### 3. Install the Package
+- **Installation (until the package is published)**
+   ```bash
+   pip install . 
+   ```
+
+- **Local Development**
+   ```bash
+   pip install -e .[dev]
+   ```
+
+### 4. Verify Installation
+Confirm the package was installed successfully
+   ```bash
+   pip show fhir-moldef
+   ``` -->
+
+## Local Setup
+
+Clone the repository and install the package in editable mode based on the parts of the project you want to work with.
+
+```bash
+git clone https://github.com/InformaticsGenomicMedicine/fhir-moldef.git
+cd fhir-moldef
+
+uv venv
+source .venv/bin/activate
+
+# Optional extras: dev, notebooks, translators
+# Install all extras with: uv sync --all-extras
+# Install multiple extras with: uv sync --extra dev --extra notebooks
+uv sync --extra dev
+```
+
+## Contributing
+
+Contributions are welcome! Please feel free to fork the repository and submit a pull request.  
+You can also report bugs or suggest improvements by opening an issue.
+
+## Acknowledgments
+
+This project builds upon the following community standards and open-source implementations.
+
+### Standards
+
+- [GA4GH Variation Representation Specification (VRS)](https://vrs.ga4gh.org/)
+- [HL7 FHIR MolecularDefinition](https://hl7.org/fhir/6.0.0-ballot2/moleculardefinition.html)
+
+### Software
+
+- [vrs-python](https://github.com/ga4gh/vrs-python)
+- [biocommons.seqrepo](https://github.com/biocommons/biocommons.seqrepo)
+- [fhir.resources](https://github.com/nazrulworld/fhir.resources)
+- [fhir-core](https://github.com/nazrulworld/fhir-core)
+
+We gratefully acknowledge the communities and contributors who develop and maintain these standards and software projects.