63 lines
1.9 KiB
Markdown
63 lines
1.9 KiB
Markdown
# mdm2neo4j
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mdm2neo4j imports ODM-XML-files into a Neo4j graph database.
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## Quickstart
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Create a configuration file, storing your details for the database-connection.
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E.g. in your home-directory with the name `mdm.conf`.
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```ini
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[neo4j]
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uri = bolt://localhost:7687
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username = neo4j
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password = myfancypassword
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```
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Start the program by providing the location of your configuration-file and the location of the XML-files.
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```sh
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python3 src/run.py --conf ~/mdm.conf --files ~/Desktop/datasource
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```
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## Requirements
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- make sure, `python3` is installed
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- install the required libraries with `pip install -r requirements.txt`
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- download all ODM-XML-files from the [MDM portal]( https://mdm.mi.uni-heidelberg.de/access/register ) and place all XML-files you want to load in one folder
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- have a running Neo4j DB (Neo4j version 5)
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- create the configuration-file as described in the [Quickstart section](#quickstart)
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## General Structure of Repo
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The two main scripts that do things are `database_connector.py` and `xml_processor.py`.
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`run.py` is the "main" script where everything comes together and that is responsible for running everything.
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## Detailled Infos
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The mapping of the odm-xml files to Neo4j is based on specification for ODM version 1.3.2.
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The specification document is available on the CDISC website http://www.cdisc.org/odm.
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The mapping includes 18 of 39 elements of the "Study" section (section 3.1.1) of the "General Elements" (section 3) of the ODM specification.
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The Neo4j graph has eleven labels:
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- Study
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- StudyEvent
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- Form
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- ItemGroup
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- Item
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- RangeCheck
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- CodeList
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- CodeListItem
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- BasicDefinitions
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- MeasurementUnit
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- Alias
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## Tech Docu
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Find the technical documentation in the [`docs`-folder.](docs/)
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## Licence
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This program is released under [Version 3 of the GPL or any later version](https://www.gnu.org/licenses/gpl-3.0.en.html).
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