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11 changes: 11 additions & 0 deletions doc/home.md
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Expand Up @@ -517,6 +517,17 @@ documentation for Dorieh platform
Documentation utilities to simplify creation of consistent
documentation for Dorieh platform

* [cwl2md](members/cwl2md) Generates [Markdown](https://www.markdownguide.org/basic-syntax/)
documentation for a CWL tool or workflow
* [collector](members/collector) Generates automatic
[reStructuredText](https://docutils.sourceforge.io/rst.html)
templates for all Python modules
* [copy_section](members/copy_section) Copies a specified section from one markdown document
to another. This way we can collect summaries in one file<!-- end of section documentation utilities overview from dorieh.docutils -->

Documentation utilities to simplify creation of consistent
documentation for Dorieh platform

* [cwl2md](members/cwl2md) Generates [Markdown](https://www.markdownguide.org/basic-syntax/)
documentation for a CWL tool or workflow
* [collector](members/collector) Generates automatic
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2 changes: 1 addition & 1 deletion docs/DBT.html
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<li class="toctree-l1"><a class="reference internal" href="guts.html">Data Platform Internals</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Database Testing Framework</a><ul>
<li class="toctree-l2"><a class="reference internal" href="members/create_test.html">Utility to generate test queries</a></li>
<li class="toctree-l2"><a class="reference internal" href="members/dbt_runner.html">Utility to generate test queries</a></li>
<li class="toctree-l2"><a class="reference internal" href="members/dbt_runner.html">Test runner: Utility to run generated tests</a></li>
<li class="toctree-l2"><a class="reference internal" href="members/gen_dbt_cwl.html">The gen_dbt_cwl Module</a></li>
<li class="toctree-l2"><a class="reference internal" href="TestingWorkflows.html">Testing bundled workflows</a></li>
<li class="toctree-l2"><a class="reference internal" href="guts.html">Data Platform Internals</a></li>
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14 changes: 1 addition & 13 deletions docs/Medicaid.html
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<li class="toctree-l4"><a class="reference internal" href="#sample-user-request">Sample user request:</a></li>
</ul>
</li>
<li class="toctree-l3 current"><a class="reference internal" href="Medicare.html">Medicare Files Handling</a><ul class="current">
<li class="toctree-l4"><a class="reference internal" href="members/mcr_sas2yaml.html">The mcr_sas2yaml Module</a></li>
<li class="toctree-l4"><a class="reference internal" href="members/mcr_sas2db.html">The mcr_sas2db Module</a></li>
<li class="toctree-l4"><a class="reference internal" href="members/fts2yaml.html">Parser for FTS files that accompany CMS data from ResDac</a></li>
<li class="toctree-l4"><a class="reference internal" href="members/medicare_yaml.html">Medicare.yaml</a></li>
<li class="toctree-l4"><a class="reference internal" href="MedicareLineage.html">Data dictionary and lineage for Medicare processing</a></li>
<li class="toctree-l4 current"><a class="current reference internal" href="#">Handling Medicaid data</a></li>
<li class="toctree-l4"><a class="reference internal" href="Medicare.html#processing-pipeline">Processing pipeline</a></li>
<li class="toctree-l4"><a class="reference internal" href="Medicare.html#ingesting-raw-files">Ingesting Raw Files</a></li>
<li class="toctree-l4"><a class="reference internal" href="Medicare.html#combining-raw-files-into-a-single-view">Combining raw files into a single view</a></li>
<li class="toctree-l4"><a class="reference internal" href="Medicare.html#creating-qc-tables">Creating QC Tables</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="Medicare.html">Medicare Files Handling</a></li>
<li class="toctree-l3"><a class="reference internal" href="MedicareLineage.html">Data dictionary and lineage for Medicare processing</a></li>
<li class="toctree-l3"><a class="reference internal" href="QueringMedicaid.html">Querying Medicaid Data</a></li>
<li class="toctree-l3"><a class="reference internal" href="cms.html#overview-of-health-data-medicare-and-medicaid">Overview of health data (Medicare and Medicaid)</a></li>
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14 changes: 1 addition & 13 deletions docs/MedicareLineage.html
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<li class="toctree-l1 current"><a class="reference internal" href="domains.html">Data Domains</a><ul class="current">
<li class="toctree-l2 current"><a class="reference internal" href="cms.html">Health</a><ul class="current">
<li class="toctree-l3"><a class="reference internal" href="Medicaid.html">Handling Medicaid data</a></li>
<li class="toctree-l3 current"><a class="reference internal" href="Medicare.html">Medicare Files Handling</a><ul class="current">
<li class="toctree-l4"><a class="reference internal" href="members/mcr_sas2yaml.html">The mcr_sas2yaml Module</a></li>
<li class="toctree-l4"><a class="reference internal" href="members/mcr_sas2db.html">The mcr_sas2db Module</a></li>
<li class="toctree-l4"><a class="reference internal" href="members/fts2yaml.html">Parser for FTS files that accompany CMS data from ResDac</a></li>
<li class="toctree-l4"><a class="reference internal" href="members/medicare_yaml.html">Medicare.yaml</a></li>
<li class="toctree-l4 current"><a class="current reference internal" href="#">Data dictionary and lineage for Medicare processing</a></li>
<li class="toctree-l4"><a class="reference internal" href="Medicaid.html">Handling Medicaid data</a></li>
<li class="toctree-l4"><a class="reference internal" href="Medicare.html#processing-pipeline">Processing pipeline</a></li>
<li class="toctree-l4"><a class="reference internal" href="Medicare.html#ingesting-raw-files">Ingesting Raw Files</a></li>
<li class="toctree-l4"><a class="reference internal" href="Medicare.html#combining-raw-files-into-a-single-view">Combining raw files into a single view</a></li>
<li class="toctree-l4"><a class="reference internal" href="Medicare.html#creating-qc-tables">Creating QC Tables</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="Medicare.html">Medicare Files Handling</a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">Data dictionary and lineage for Medicare processing</a><ul>
<li class="toctree-l4"><a class="reference internal" href="lineage/medicare.dot.html">Table Lineage Diagram</a></li>
<li class="toctree-l4"><a class="reference internal" href="lineage/table-list.html">Alphabetic list of all tables</a></li>
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<!DOCTYPE html>
<html class="writer-html5" lang="en">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>&lt;no title&gt; &mdash; Dorieh Data Platform 0.0.1 documentation</title>
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<link rel="stylesheet" type="text/css" href="_static/css/dorieh.css" />


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Dorieh Data Platform
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<p class="caption" role="heading"><span class="caption-text">Contents</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="home.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="rationale.html">What is Data Platform</a></li>
<li class="toctree-l1"><a class="reference internal" href="domains.html">Data Domains</a></li>
<li class="toctree-l1"><a class="reference internal" href="pipelines.html">Data Processing Pipelines</a></li>
<li class="toctree-l1"><a class="reference internal" href="packages.html">Python Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Datamodels.html">Data Modelling for Dorieh Data Platform</a></li>
<li class="toctree-l1"><a class="reference internal" href="examples.html">Examples</a></li>
<li class="toctree-l1"><a class="reference internal" href="guts.html">Data Platform Internals</a></li>
<li class="toctree-l1"><a class="reference internal" href="DBT.html">Database Testing Framework</a></li>
<li class="toctree-l1"><a class="reference internal" href="adding_data.html">Adding more data</a></li>
<li class="toctree-l1"><a class="reference internal" href="AppPipelineGenerator.html">Executing containerized apps</a></li>
<li class="toctree-l1"><a class="reference internal" href="glossary.html">Terms and Acronyms</a></li>
<li class="toctree-l1"><a class="reference internal" href="docindices.html">Indices</a></li>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">

<ul>
<li><p>Introduction</p></li>
<li><p>What functionality the Data Platform provides?
– Data management
– Data Ingestion
– Data manipulation
– Reporting and Data Export
– Reproducible data manipulation workflows
– Building feature stores for ML, statistical computations and AI
– Testing of data manipulation workflows</p></li>
<li><p>Data Platform Pillars
– Data Ingestion tools and libraries</p>
<blockquote>
<div><p>— Automatic introspection and ingestion
— Explicit data schema definitions in YaML files
— Importing data schema from third party tools (SAS)
— Automatic introspection + manual editing</p>
</div></blockquote>
<p>– Runtime execution environment
– Data architecture tools and wokflow definition language
– Data dictionary and data lineage tools</p>
</li>
<li><p>Data Domains
– Domain specific tooling for the following knowledge domains:</p>
<blockquote>
<div><p>— Health (CMS: Medicare and Medicaid)
— Climate
— Exposure (Air pollution)
— EPA data
— Demographics</p>
</div></blockquote>
</li>
<li><p>Python packages and libraries</p></li>
<li><p>Examples</p></li>
<li><p>Terms and acronyms</p></li>
<li><p>Building and executing containerized apps</p></li>
</ul>
<hr class="docutils" />
<p>Match Files to Sections:</p>
<p>### Introduction</p>
<p>#### Files:
- <cite>home.md</cite>
- <cite>introduction.md</cite>
- <cite>rationale.md</cite></p>
<p>### What functionality the Data Platform provides?</p>
<p>#### Files:
- <cite>functionality/data_management.md</cite>
- <cite>functionality/data_ingestion.md</cite>
- <cite>functionality/data_manipulation.md</cite>
- <cite>functionality/reporting_data_export.md</cite>
- <cite>functionality/reproducible_workflows.md</cite>
- <cite>functionality/feature_stores.md</cite>
- <cite>functionality/workflow_testing.md</cite></p>
<p>### Data Platform Pillars</p>
<p>#### Files:
- <cite>pillars/data_ingestion_tools.md</cite>
- <cite>pillars/runtime_execution.md</cite>
- <cite>pillars/data_architecture.md</cite>
- <cite>pillars/data_dictionary_lineage.md</cite></p>
<p>### Data Ingestion tools and libraries</p>
<p>#### Files:
- <cite>pillars/ingestion/automatic_introspection.md</cite>
- <cite>pillars/ingestion/explicit_schema_definitions.md</cite>
- <cite>pillars/ingestion/importing_schemas.md</cite>
- <cite>pillars/ingestion/introspection_manual_editing.md</cite></p>
<p>### Data Domains</p>
<p>#### Files:
- <cite>domains/cms.md</cite>
- <cite>domains/climate.md</cite>
- <cite>domains/exposure.md</cite>
- <cite>domains/epa_data.md</cite>
- <cite>domains/demographics.md</cite></p>
<p>### CMS (Health) Domain</p>
<p>#### Files:
- <cite>cms.md</cite>
- <cite>Medicaid.md</cite>
- <cite>Medicare.md</cite>
- <cite>MedicareLineage.md</cite>
- <cite>QueringMedicaid.md</cite></p>
<p>### Python Packages and Libraries</p>
<p>#### Files:
- <cite>CoreLibrary.md</cite>
- <cite>CMSLibrary.md</cite>
- <cite>cwl_tools.md</cite>
- <cite>DataLoader.md</cite>
- <cite>docutils.md</cite></p>
<p>### Examples</p>
<p>#### Files:
- <cite>examples.md</cite>
- <cite>Example-climate-workflow.md</cite>
- <cite>example_request_yaml.md</cite></p>
<p>### Terms and Acronyms</p>
<p>#### Files:
- <cite>terms_acronyms.md</cite>
- <cite>glossary.md</cite></p>
<p>### Building and Executing Containerized Apps</p>
<p>#### Files:
- <cite>docker_readme.md</cite>
- <cite>deployment.md</cite>
- <cite>Dockerfile.amd64.md</cite>
- <cite>Dockerfile.arm64.md</cite></p>
<p>### Platform Internals</p>
<p>#### Files:
- <cite>platform.md</cite>
- <cite>MonitoringDB.md</cite>
- <cite>ProjectLoader.md</cite>
- <cite>DBConnections.md</cite>
- <cite>core_prj_struct.md</cite></p>
<p>### Supplementary Documents</p>
<p>#### Files:
- <cite>DBT.md</cite>
- <cite>fts.md</cite>
- <cite>pipelines.md</cite>
- <cite>AppPipelineGenerator.md</cite>
- <cite>TerritorialCodes.md</cite>
- <cite>TestingWorkflows.md</cite></p>
<p>### General Documentation Indices</p>
<p>#### Files:
- <cite>index.md</cite></p>


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2 changes: 1 addition & 1 deletion docs/TestingWorkflows.html
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<li class="toctree-l1"><a class="reference internal" href="guts.html">Data Platform Internals</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="DBT.html">Database Testing Framework</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="members/create_test.html">Utility to generate test queries</a></li>
<li class="toctree-l2"><a class="reference internal" href="members/dbt_runner.html">Utility to generate test queries</a></li>
<li class="toctree-l2"><a class="reference internal" href="members/dbt_runner.html">Test runner: Utility to run generated tests</a></li>
<li class="toctree-l2"><a class="reference internal" href="members/gen_dbt_cwl.html">The gen_dbt_cwl Module</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Testing bundled workflows</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#introduction-to-testing-and-prerequisites">Introduction to testing and prerequisites</a></li>
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---
members/create_test
members/dbt_runner
members/gen_dbt_cwl.rst
members/gen_dbt_cwl
TestingWorkflows.md
guts.md
```
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