mirror of
https://gitea.psi.ch/APOG/acsm-fairifier.git
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Prepare v1.0.0 release as acsm-fairifier
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CHANGELOG.md
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CHANGELOG.md
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# Changelog
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All notable changes to this project will be documented in this file, which is a **cumulative record**.
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Each version entry follows a consistent structure with the following optional sections:
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- **Added** – New features
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- **Changed** – Modifications to existing functionality
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- **Deprecated** – Features marked for future removal
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- **Removed** – Features removed in this version
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- **Fixed** – Bug fixes
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- **Security** – Vulnerability fixes
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Format based on [Keep a Changelog](https://keepachangelog.com) and [Semantic Versioning](https://semver.org).
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## [v1.0.0] - 2025-07-04
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### Added
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- Initial release of the ACSM FAIRifier
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14
README.md
14
README.md
@ -113,16 +113,16 @@ Open **Git Bash** and run:
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```bash
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cd Gitea
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git clone --recurse-submodules https://gitea.psi.ch/apog/acsmnode.git
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cd acsmnode
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git clone --recurse-submodules https://gitea.psi.ch/apog/acsm-fairifier.git
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cd acsm-fairifier
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```
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## Run the ACSM FAIRifier Toolkit
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This toolkit includes a containerized JupyterLab environment for executing the data processing pipeline, plus an optional dashboard for manual flagging.
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1. Open **PowerShell as Administrator** and navigate to the `acsmnode` repository.
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2. Create a `.env` file in the root of `acsmnode/`.
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1. Open **PowerShell as Administrator** and navigate to the `acsm-fairifier` repository.
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2. Create a `.env` file in the root of `acsm-fairifier/`.
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3. **Securely store your network drive access credentials** in the `.env` file by adding the following lines:
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```plaintext
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CIFS_USER=<your-username>
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@ -175,13 +175,9 @@ We recommend using Miniforge to manage your conda environments. Miniforge ensure
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2. Create the Environment from `environment.yml`
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After installing Miniforge, open **Miniforge Prompt** or a terminal with access to conda and run:
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```bash
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cd path/to/Gitea/acsmnode
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cd path/to/Gitea/acsm-fairifier
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conda env create --file environment.yml
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```
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3. Activate the Environment
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```bash
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conda activate acsmnode_env
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```
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### Working with Jupyter Notebooks
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We now make the previously installed Python environment `acsmnode_env` selectable as a kernel in Jupyter's interface.
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@ -20,9 +20,36 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\dima\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\dima\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\dima\n",
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"c:\\Users\\juanf\\envs\\acsmnode_env\\python311.zip\n",
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"c:\\Users\\juanf\\envs\\acsmnode_env\\DLLs\n",
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"c:\\Users\\juanf\\envs\\acsmnode_env\\Lib\n",
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"c:\\Users\\juanf\\envs\\acsmnode_env\n",
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"\n",
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"c:\\Users\\juanf\\envs\\acsmnode_env\\Lib\\site-packages\n",
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"c:\\Users\\juanf\\envs\\acsmnode_env\\Lib\\site-packages\\win32\n",
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"c:\\Users\\juanf\\envs\\acsmnode_env\\Lib\\site-packages\\win32\\lib\n",
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"c:\\Users\\juanf\\envs\\acsmnode_env\\Lib\\site-packages\\Pythonwin\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\third_party\\acsmProcessingSoftware\\src\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\third_party\\acsmProcessingSoftware\\src\\db\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\third_party\\acsmProcessingSoftware\\src\\iointerface\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\third_party\\acsmProcessingSoftware\n",
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"workflow_acsm_data_JFJ_2024\n"
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]
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}
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],
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"source": [
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"import sys\n",
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"import os\n",
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@ -81,9 +108,58 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Manually loaded .env from: C:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\.env\n",
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"Success : True\n",
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"[Notice] All files already exist at ../data/collection_1_JFJ_2024_2025-07-04/, skipping copy.\n",
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"\n",
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"[Start] Data integration :\n",
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"Source: ..\\data\\collection_1_JFJ_2024_2025-07-04\n",
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"Destination: ..\\data\\collection_1_JFJ_2024_2025-07-04.h5\n",
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"\n",
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"Starting data transfer from instFolder: /ACSM_TOFWARE/2024\n",
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"Completed transfer for //ACSM_TOFWARE/2024/calibration_params.yaml\n",
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"Completed transfer for //ACSM_TOFWARE/2024/limits_of_detection.yaml\n",
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"Completed transfer for //ACSM_TOFWARE/2024/validity_thresholds.yaml\n",
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"[==================================================--------------------------------------------------] 50.0% ...\n",
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"Completed data transfer for instFolder: /ACSM_TOFWARE/2024\n",
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"Completed transfer for //ACSM_TOFWARE/2024/ACSM_JFJ_2024_meta.txt\n",
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"Completed transfer for //ACSM_TOFWARE/2024/ACSM_JFJ_2024_timeseries.txt\n",
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"Startdate 20240101000000\n",
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"\n",
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"Completed transfer for //ACSM_TOFWARE/2024/CH0001G.20240101000000.20250430141458.cpc.particle_number_concentration.aerosol.1y.1mn.CH02L_TSI_3772_JFJ.CH02L_CPC.lev1.nas\n",
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"Completed transfer for //ACSM_TOFWARE/2024/Org_data_valid.csv\n",
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"Completed transfer for //ACSM_TOFWARE/2024/Org_err_valid.csv\n",
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"Completed transfer for //ACSM_TOFWARE/2024/Org_mz_valid.csv\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\dima\\instruments\\readers\\acsm_tofware_reader.py:112: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
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" df = pd.read_csv(tmp_filename,\n",
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"c:\\Users\\juanf\\OneDrive\\Documents\\Gitea\\acsmnode\\dima\\instruments\\readers\\acsm_tofware_reader.py:112: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n",
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" df = pd.read_csv(tmp_filename,\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Completed transfer for //ACSM_TOFWARE/2024/Org_time_valid.csv\n",
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"[====================================================================================================] 100.0% ...\n",
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"Completed data transfer for instFolder: /ACSM_TOFWARE/2024\n",
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"[End] Data integration\n"
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]
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}
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],
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"source": [
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"path_to_config_file = '../campaignDescriptor.yaml'\n",
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"paths_to_hdf5_files = get_campaign_data(path_to_config_file)\n",
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@ -353,7 +429,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "acsmnode_env",
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"language": "python",
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"name": "python3"
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},
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@ -367,7 +443,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.10"
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"version": "3.11.13"
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}
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},
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"nbformat": 4,
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