Data integration and metadata annotation

Repository for integrating data in HDF5 from various sources and managing metadata updates in the integrated files.

Includes tools and workflows for comprehensive data integration and automated metadata review processes.

Installation

Follow these steps to install and set up the project:

1. Download our GitLab repository in your GitLab folder, or alternatively open a Git Bash terminal and run the following commands:

cd Path/to/GitLab
git clone https://gitlab.psi.ch/5505/data-integration-and-metadata-annotation.git

2. Open an Anaconda Prompt (Anaconda3) as administrator, and set the current directory to the path of the project's folder.

3. Create the project's environment multiphase_chemistry_env by running the following command:

conda env create -f environment.yml

Working with Jupyter Notebook on the multiphase_chemistry_env

1. Open an Anaconda Prompt as a regular user, ensure that multiphase_chemistry_env is in the list of available enviroments and activate it by running the following commands:

conda env list
conda activate multiphase_chemistry_env

2. Register the associated kernel in Jupyter by running:

python -m ipykernel install --user --name multiphase_chemistry_env --display-name "Python (multiphase_chemistry_env)"  

3. Start a Jupyter Notebook by running the command:

jupyter notebook

and select the multiphase_chemistry_env environment from the kernel options.

Working with Visual Studio Code (VS Code) on the multiphase_chemistry_env

1. Open the project in VS Code, click on the Python interpreter in the status bar and choose the multiphase_chemistry_env environment.

Data integration workflow

Metadata review workflow

- review through branches
- updating files with metadata in Openbis

Metadata

Attribute	CF Equivalent	Definition
campaign_name	-	Denotes a range of possible campaigns, including laboratory and field experiments, beamtime, smog chamber studies, etc., related to atmospheric chemistry research.
project	-	Denotes a valid name of the project under which the data was collected or produced.
contact	contact (specifically E-mail address)	Denotes the name of data producer who conducted the experiment or carried out the project that produced the raw dataset (or an aggragated dataset with multiple owners)
description	title (only info about content), comment (too broad in scope), source	Provides a short description of methods and processing steps used to arrive at the current version of the dataset.
experiment	-	Denotes a valid name of the specific experiment or study that generated the data.
actris_level	-	Indicates the processing level of the data within the ACTRIS (Aerosol, Clouds and Trace Gases Research Infrastructure) framework.
dataset_startdate	-	Denotes the start datetime of the dataset collection.
dataset_enddate	-	Denotes the end datetime of the dataset collection.
processing_filename	-	Denotes the name of the file used to process an initial version (e.g, original version) of the dataset into a processed dataset.
processing_date	-	The date when the data processing was completed.

Specifying a compound attribute in yaml language.

Consider the compound attribute relative_humidity, which has subattributes value, units, range, and definition. The yaml description of such an attribute is as follows:

relative_humidity:
  value: 65
  units: percentage
  range: '[0,100]'
  definition: 'Relative humidity represents the amount of water vapor present in the air relative to the maximum amount of water vapor the air can hold at a given temperature.'  

Deleting or renaming a compound attribute in yaml language.

• Assume the attribute relative_humidity already exists. Then it should be displayed as follows with the subattribute rename_as. This can be set differently to suggest a renaming of the attribute.
• To suggest deletion of an attribute, we are required to add a subattribute delete with value as true. Below for example, the attribute relative_ humidity is suggested to be deleted. Otherwise if delete is set as false, it will have no effect.

relative_humidity:
  delete: true # we added this line in the review process
  rename_as: relative_humidity
  value: 65
  units: percentage
  range: '[0,100]'
  definition: 'Relative humidity represents the amount of water vapor present in the air relative to the maximum amount of water vapor the air can hold at a given temperature.'

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Getting started

To make it easy for you to get started with GitLab, here's a list of recommended next steps.

Already a pro? Just edit this README.md and make it your own. Want to make it easy? Use the template at the bottom!

TODO

• Talk to Thorsten about rga txt files. Example folder contains incosistent rga txt files, there is no unique column separator (, or )

Add your files

• Create or upload files
• Add files using the command line or push an existing Git repository with the following command:

cd existing_repo
git remote add origin https://gitlab.psi.ch/5505/functionspython.git
git branch -M main
git push -uf origin main

cd existing_repo
git remote add origin https://gitlab.psi.ch/5505/functionspython.git
git branch -M main
git push -uf origin main

Integrate with your tools

Integrate with your tools

• Set up project integrations

Collaborate with your team

• Invite team members and collaborators
• Create a new merge request
• Automatically close issues from merge requests
• Enable merge request approvals
• Automatically merge when pipeline succeeds

Test and Deploy

Use the built-in continuous integration in GitLab.

• Get started with GitLab CI/CD
• Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)
• Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy
• Use pull-based deployments for improved Kubernetes management
• Set up protected environments

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Editing this README

When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to makeareadme.com for this template.

Suggestions for a good README

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