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…ing, including acceptance criteria.
…is and use cases for data modeling while removing outdated sections.
…or data modeling entities and relationships.
…nks, and definitions. Introduce YAML and JSON schema structures for demographic, medical history, and project data, enhancing the overall schema framework.
…es, and enums for data modeling.
… files for dependency management and project metadata.
… new commons.heartdata.baker.edu.au domain, ensuring consistency across all data models.
…lock with additional packages including appnope, asttokens, cffi, comm, debugpy, stack-data, tornado, traitlets, and wcwidth.
…validation module for meta schema and business rules validation.
…ments, user inputs, and internal properties for data modeling.
… a summary of schema keys, enhancing clarity and usability for data modeling.
…schema key definitions, adding required fields, and including visual examples for better understanding.
…ts, and handy tips sections for improved clarity and usability. Add a new README file outlining core concepts and usage of Gen3SchemaDev as a data modeling tool.
…tions of the Gen3 data model, including definitions for key terms and a visual example. Improve clarity on the required entities and their relationships within the data dictionary.
…creation sections, enhancing navigation and user experience.
…ew of schema fields, including examples and clarifications on user input requirements. This update aims to improve understanding of Gen3 schema structure and usage.
… links in the Gen3 data model. Enhance examples and explanations for link definitions, including required fields and subgroup linking, to improve understanding of entity relationships.
…ifications for schema fields, including links to external definitions and improved formatting. This update aims to improve understanding of property types and their usage within the Gen3 data model.
…en3 data dictionary content. Introduce new sections for descriptors, links, properties, and dictionary configuration, while removing outdated README.md. This update aims to improve clarity and usability for users engaging with the Gen3 data modeling framework.
… the documentation structure. Change headings to use proper markdown hierarchy and refine the organization of content for better navigation and user experience.
… section formatting for better navigation. The introduction now emphasizes the goal of providing documentation, learning materials, and tools for Gen3 data modeling.
… materials" for improved clarity.
…Gen3 data modeling topics. The dictionary overview is now listed first for better clarity and navigation.
- Expanded the content to include detailed explanations of relational and graph models, terminology comparisons, and data types. - Added sections on nodes, properties, links, and examples to provide a comprehensive guide for users creating their first Gen3 data dictionary. - Improved clarity and structure to facilitate better understanding of the data model components.
- Changed references from "entities" to "nodes" to accurately reflect the graph-based data model. - Adjusted definitions in the summary section to align with the updated terminology, enhancing clarity for users navigating the Gen3 data dictionary.
- Updated the introduction to emphasize the graph model used by Gen3, replacing references to relational models. - Clarified terminology related to Gen3 schemas, data dictionaries, and bundled schemas for better user understanding. - Added a new section on the `input_yaml` file, detailing its role in defining data model components. - Improved organization of content to facilitate navigation and comprehension for users creating their first Gen3 data dictionary.
…ple-schema Fix consolidate example schema
- Updated the LICENSE, README, and various Python files to replace references to "entity" with "node" to align with the graph-based data model. - Adjusted function names, class definitions, and documentation to reflect the new terminology. - Ensured consistency in the schema templates and example files to enhance clarity for users working with the Gen3 data model.
- Revised definitions in the LICENSE file to replace "node" with "entity" to align with updated terminology. - Ensured clarity in the legal definitions and roles related to contributions and licensing.
…d codebase - Revised README, Jupyter notebooks, and Python files to replace references to "entities" with "nodes" for consistency with the graph-based data model. - Adjusted error messages, function parameters, and schema definitions to reflect the updated terminology. - Ensured that example YAML and JSON files are aligned with the new terminology, enhancing clarity for users working with the Gen3 data model.
- Revised multiple markdown files to reflect the updated terminology, enhancing clarity in the Gen3 data model documentation. - Adjusted descriptions, examples, and error messages to ensure alignment with the graph-based structure of the data model. - Ensured that all references to "entities" are consistently replaced with "nodes" across the documentation and example files.
- Revised multiple markdown files to replace references to "entity" with "node" for clarity and consistency in the Gen3 data model documentation. - Adjusted descriptions, examples, and error messages to align with the graph-based structure of the data model. - Ensured that all instances of "entity" are replaced with "node" across various documentation files, enhancing user understanding.
- Clarified the interchangeable use of "data model" and "data dictionary" terminology. - Enhanced descriptions of nodes and relationships to better reflect the graph-based data model. - Updated the summary section to specify that the bundled schema contains a combined dictionary of jsonschemas for each node.
…-node Fix change entity to node
…cture - Updated README to replace "Example Usage" with "Quickstart" and improved the link to the first dictionary guide. - Enhanced the first dictionary documentation with a detailed table of contents and structured sections for better navigation. - Added comprehensive explanations for nodes, properties, and links, including examples and YAML snippets to aid user understanding. - Improved overall organization and clarity to facilitate the creation of Gen3 data dictionaries.
- Introduced a new "Introduction" section to provide context on the Gen3 data model. - Updated the table of contents to include the new section for improved navigation. - Enhanced overall structure for better clarity and user understanding.
- Introduced a new entry for the "datetime" type in the properties table, specifying its format as an ISO 8601 date/time string recognized by Gen3SchemaDev. - Enhanced the documentation to provide clearer guidance on data types used in the Gen3 data model.
- Introduced a new property reference '$ref' pointing to '_definitions.yaml#/ubiquitous_properties' in the construct_props function. - Updated related test cases to validate the inclusion of the ubiquitous property reference in the output for both lipidomics_file and sample properties.
- Introduced a new quickstart guide in the documentation to provide users with step-by-step instructions for installing Gen3SchemaDev, creating input templates, generating schemas, validating them, bundling, and visualizing the results. - Enhanced user experience by offering clear commands and links to further resources for advanced configuration and schema modification.
… "visualise" for consistency with British English. Enhanced section title for clarity on the Gen3 Data Dictionary.
- Introduced a new CONTRIBUTING.md file to outline the contribution process and guidelines for the Gen3SchemaDev project. - Updated README.md to include a section for developers, detailing installation, testing, and contribution encouragement. - Added pre-reading documentation in docs/core_concepts/pre_reading.md to familiarize contributors with core data modeling concepts relevant to the project.
- Changed the link text in the pre-reading documentation from "node-relationship diagram" to "entity-relationship diagram" for accuracy and clarity in representing core data modeling concepts.
…umentation - Added a new "Troubleshooting" link in the README to guide users to the relevant documentation. - Revised the troubleshooting document to focus on Pydantic validation errors, providing detailed explanations and examples to assist users in resolving input YAML validation issues. - Improved clarity and structure of the troubleshooting content for better user understanding.
…tation - Included a new "Pre-requisites" section in both the first dictionary and quickstart documents, specifying required versions for Python, Poetry, and optional Docker Compose for visualization. - Enhanced clarity for users regarding the necessary tools for working with Gen3SchemaDev.
- Replaced print statements with logging calls for better error handling and debugging. - Improved the clarity of messages related to Docker container management and schema visualization processes. - Enhanced overall maintainability of the code by standardizing output methods.
- Introduced a new subcommand 'visualise' in the CLI to allow users to visualize schemas using a bundled Gen3 JsonSchema file. - Added input argument for specifying the path to the schema file and an optional debug flag for logging. - Enhanced user interaction by providing clear output when visualizing schemas.
- Added a "Pre-requisites" section in the setup documentation, specifying required versions for Python, Poetry, and optional Docker Compose. - Updated the first dictionary and quickstart documents to include links directing users to detailed setup instructions. - Improved clarity and accessibility of installation steps for developers.
Feature ddvis
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