Initial commit of the incomplete digital object processor

.editorconfig

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+# Editor configuration, see http://editorconfig.org
+root = true
+
+[*]
+charset = utf-8
+indent_style = space
+indent_size = 2
+insert_final_newline = true
+trim_trailing_whitespace = true
+max_line_length = 120
+
+[*.md]
+max_line_length = off
+trim_trailing_whitespace = false

.gitignore

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.prettierrc

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+{
+  "singleQuote": true
+}

LICENSE

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+MIT License
+
+Copyright (c) 2023 HuBMAP Consortium
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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-# hra-do-processor
-HRA Digital Objects Processor
+# Human Reference Atlas Digital Objects Processor (do-processor)
+
+This repository contains digital object definitions and a data processor to process conforming digital objects. The primary use case for this processor is to generate the Human Reference Atlas Knowledge Graph (hra-kg).
+
+## Local Setup Requirements
+
+- python 3.x
+- node.js (if not using the virtualenv, which has it installed)
+
+## Local Setup
+
+First create a virtual environment by running:
+
+`./scripts/setup-environment.sh`
+
+After finishing, you can enter the virtual environment by running:
+
+`source .venv/bin/activate`
+
+## Running the do-processor
+
+While in the virtual environment (or if installed globally), use the `do-processor` command.
+
+```bash
+$ do-processor --help
+Usage: do-processor [options] [command]
+
+Digital Object Processing Command-Line Interface
+
+Options:
+  -V, --version                    output the version number
+  --do-home <string>               Digital Objects home directory
+  --processor-home <string>        DO Processor home
+  --skip-validation                Skip validation in each command (default: false)
+  -h, --help                       display help for command
+
+Commands:
+  normalize <digital-object-path>  Mechanically normalizes a Digital Object from it's raw form. Minimally, it converts the source DO type + integrates the
+                                   metadata into a single linkml-compatible JSON file.
+  enrich <digital-object-path>     Enriches a Normalized Digital Object, optionally pulling in data from other sources like Uberon, CL, Ubergraph, or other
+                                   external resources. Minimally, it converts the Normalized JSON file into RDF. Optionally enriches data from the original
+                                   form (ie add Metadata to nodes in the SVG or GLB files).
+  package <digital-object-path>    Packages an Enriched Digital Object, such that it can published to a website/DOI'd/etc and used
+  build <digital-object-path>      Given a Digital Object, checks for and runs normalization, enrichment, and packaging in one command.
+  list [glob]                      Lists digital object information in the DO_HOME directory
+  help [command]                   display help for command
+```
+
+## Digital Object Processor Subcommands
+
+Each subcommand typically takes a path to the digital object and processes it according to the command's requirements. The digital object path usually looks like `${DO_TYPE}/${DO_NAME}/${DO_VERSION}`. For example, the ASCT+B Table for Kidney, v1.2 looks like this: `asct-b/kidney/v1.2`.
+
+normalize - Mechanically normalizes a Digital Object from it's raw form. Minimally, it converts the source DO type + integrates the metadata into a single linkml-compatible JSON file.
+
+enrich - Enriches a Normalized Digital Object, optionally pulling in data from other source like Uberon, CL, Ubergraph, or any other external resource. Minimally, it converts the Normalized JSON file into RDF. Optionally enriches data from the original form (ie add Metadata to nodes in the SVG or GLB files).
+
+package - Packages an Enriched Digital Object, such that it can published to a website/DOI'd/etc.
+
+build - Given a Digital Object, checks for and runs normalization, enrichment, and packaging in one command.
+
+list - Lists digital object information in the DO_HOME directory