0.0.4 release

.changes/0.0.1.md

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+## 0.0.1 - 2024-07-31
+### Added
+* Initial commit
+* README, CHANGELOG, LICENSE
+* Initial folder structure
+* Initial library added to `src`
+* Dockerfiles and docker-compose

.changes/0.0.2.md

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+## 0.0.2 - 2024-07-31
+### Added
+* Added resource limits to docker-compose
+### Changed
+* Removed comments in SQL scripts as its causing issues
+* Progressed MIMIC data version to 2.2, updated SQL scripts to match

.changes/0.0.3.md

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+## 0.0.3 - 2024-07-31
+### Added
+* MIMIC-IV Postgres Functions
+### Changed
+* Allowing MIMIC-IV 2.0 backwards compatibility

.changes/0.0.4.md

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+## 0.0.4 - 2024-08-05
+### Added
+* MIMIC-ED Import Option Closes Issue #5
+### Changed
+* README to correctly reflect volume location Closes Issue #16
+* Updated `docker-compose.yaml` to use env var for data folder
+* Changed the library name to `pgmimic` Closes Issue #16

.changes/header.tpl.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html),
+and is generated by [Changie](https://github.com/miniscruff/changie).

.changie.yaml

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+changesDir: .changes
+unreleasedDir: unreleased
+headerPath: header.tpl.md
+changelogPath: CHANGELOG.md
+versionExt: md
+versionFormat: '## {{.Version}} - {{.Time.Format "2006-01-02"}}'
+kindFormat: '### {{.Kind}}'
+changeFormat: '* {{.Body}}'
+kinds:
+    - label: Added
+      auto: minor
+    - label: Changed
+      auto: major
+    - label: Deprecated
+      auto: minor
+    - label: Removed
+      auto: major
+    - label: Fixed
+      auto: patch
+    - label: Security
+      auto: patch
+newlines:
+    afterChangelogHeader: 1
+    beforeChangelogVersion: 1
+    endOfVersion: 1
+envPrefix: CHANGIE_

.env

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+POSTGRES_USER=mimic
+POSTGRES_PASSWORD=mimic123
+POSTGRES_DB=postgres

.gitignore

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+## DATA FOLDER ##
+data/
+!data/README.md
+
+## bin ##
+bin/notes.md
+
+## PYTHON ##
+__pycache__/*
+*/__pycache__/*
+__pycache__
+
+## JetBrains ##
+.idea/*

CHANGELOG.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html),
+and is generated by [Changie](https://github.com/miniscruff/changie).
+
+
+## 0.0.4 - 2024-08-05
+### Added
+* MIMIC-ED Import Option Closes Issue #5
+### Changed
+* README to correctly reflect volume location Closes Issue #16
+* Updated `docker-compose.yaml` to use env var for data folder
+* Changed the library name to `pgmimic` Closes Issue #16
+
+## 0.0.3 - 2024-07-31
+### Added
+* MIMIC-IV Postgres Functions
+### Changed
+* Allowing MIMIC-IV 2.0 backwards compatibility
+
+## 0.0.2 - 2024-07-31
+### Added
+* Added resource limits to docker-compose
+### Changed
+* Removed comments in SQL scripts as its causing issues
+* Progressed MIMIC data version to 2.2, updated SQL scripts to match
+
+## 0.0.1 - 2024-07-31
+### Added
+* Initial commit
+* README, CHANGELOG, LICENSE
+* Initial folder structure
+* Initial library added to `src`
+* Dockerfiles and docker-compose

CONTRIBUTING.md

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+# How to contribute
+
+Thank you for your interest in our little project. I appreciate any support to help improve this project.
+
+## How to Contribute
+
+1. Fork the repository.
+2. Create a new branch for your feature or bug fix.
+3. Make your changes in the new branch.
+4. Submit a [pull request (PR)](https://github.com/rudolfjs/PostgresMimicImporter/pull/new/master) to the main repository.
+
+## Pull Request Guidelines
+
+When [submitting a pull request](https://github.com/rudolfjs/PostgresMimicImporter/pull/new/master) please ensure that:
+
+1. You clearly describe the problem you're solving or the feature you're adding, linking to [issue](https://github.com/rudolfjs/PostgresMimicImporter/issues).
+2. You outline the changes you've made in detail.
+3. Please make sure your code is formatted using [psf/black](https://github.com/psf/black)
+
+## Review Process
+
+Once you've submitted a pull request:
+
+1. The project maintainers will review your changes.
+2. Maintainers may ask for additional changes or clarifications.
+3. Once approved, your contribution will be merged into the project.

LICENSE

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+MIT License
+
+Copyright (c) 2024 Rudolf J
+
+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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+# Postgres MIMIC Importer
+
+<a href="/LICENSE"><img alt="License: MIT" src="https://img.shields.io/badge/MIT-purple?style=for-the-badge&label=LICENSE"></a>
+<a href="https://www.python.org/downloads/"><img alt="Python Version: 3.8plus" src="https://img.shields.io/badge/3.10-green?style=for-the-badge&label=Python&logo=python"></a>
+<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/black-black?style=for-the-badge&label=Code%20Style"></a>
+
+****
+
+MIMIC data importer for PostgreSQL.
+
+This repository **does not** contain **any** `MIMIC` data.
+
+## Data
+
+The location of the `MIMIC` is to be set as an environment variable before running `docker-compose`.
+
+### Data Preparation
+
+As `MIMIC-IV` and `MIMIC-IV-ED` are separate downloads, please ensure that all data is copied into a single target folder.
+
+The target folder must have the following structure:
+
+```bash
+.
+data
+└───mimiciv
+    └───<version>
+        ├───ed
+        ├───hosp
+        └───icu
+```
+
+If you do not require `MIMIC-IV-ED` data to be imported, edit the `config.json` file to remove the import.
+
+### Set the target location
+
+Using the environment variable (default):
+
+#### Windows
+
+PowerShell:
+```PowerShell
+$env:MIMIC_DATA_PATH = "C:/absolute/path/to/mimic/data"
+```
+
+Command Prompt:
+
+```commandline
+set MIMIC_DATA_PATH=C:/absolute/path/to/mimic/data
+```
+
+#### Linux
+
+```Bash
+export MIMIC_DATA_PATH=/absolute/path/to/mimic/data
+```
+
+The `docker-compose.yaml` can be edited to hard code the location:
+
+```yaml
+version: "3"
+services:
+  mimic_import:
+    volumes:
+       - /absolute/path/to/mimic/data/:/usr/src/app/data
+```
+
+### Compatible Data Versions
+
+| MIMIC Dataset | Version Compatibility |
+|:--------------|:----------------------|
+| MIMIC-IV      | 2.0                   |
+| MIMIC-IV-ED   | 2.0                   |
+| MIMIC-IV      | 2.2                   |
+| MIMIC-IV-ED   | 2.2                   |
+
+## Build MIMIC-IV database services
+
+```bash
+docker-compose build
+```
+
+The service can be started and stopped after being built:
+
+1. Start the service: `docker-compose up`
+    * Start the service as a background daemon: `docker-compose up -d`
+2. Stop the service: `docker-compose down`
+3. Stop the service and remove data: `docker-compose down -v`
+
+## License
+```license
+MIT License
+
+Copyright (c) 2024 Rudolf J
+
+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.
+```

config.json

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+{
+    "database": {
+        "type": "postgresql+asyncpg",
+        "host": "pg",
+        "port": 5432,
+        "database": "postgres",
+        "schema": "public"
+    },
+
+    "data": {
+        "location": "./data/mimiciv",
+        "version": "2.2",
+        "schemas": [
+            "mimic_hosp",
+            "mimic_icu",
+            "mimiciv_ed",
+            "mimic_derived"
+        ],
+        "tables": {
+            "mimic_hosp": [
+                "admissions",
+                "d_hcpcs",
+                "diagnoses_icd",
+                "d_icd_diagnoses",
+                "d_icd_procedures",
+                "d_labitems",
+                "emar_detail",
+                "emar",
+                "hcpcsevents",
+                "labevents",
+                "microbiologyevents",
+                "omr",
+                "patients",
+                "pharmacy",
+                "poe_detail",
+                "poe",
+                "prescriptions",
+                "procedures_icd",
+                "transfers"
+            ],
+            "mimic_icu": [
+                "chartevents",
+                "datetimeevents",
+                "d_items",
+                "icustays",
+                "ingredientevents",
+                "inputevents",
+                "outputevents",
+                "procedureevents"
+            ],
+            "mimiciv_ed": [
+                "diagnosis",
+                "edstays",
+                "medrecon",
+                "pyxis",
+                "triage",
+                "vitalsign"
+            ],
+            "mimic_derived": {
+                "demographics": [
+                    "age"
+                ]
+            }
+        }
+    }
+}