Hands-On: Running the Gulf of Riga Workflow

[!NOTE] 📹 Video Reference YouTube video .

This chapter provides step-by-step instructions for running the DGA workflow in Aqua Galaxy. Follow along with the video for visual guidance.

Prerequisites

Before starting, ensure the user have:

  1. ✅ Registered for an Aqua Galaxy account
  2. ✅ Signed into the AquaINFRA Interaction Platform

Step 1: Import Input Data

The workflow requires two datasets to run.

1.1 Import Secchi Depth Point Data

📹 Video: 12:49 - 15:19

  1. Navigate to the Data-to-Knowledge Package page on the AIP
  2. Click on “Latvian Secchi depth and water color”
  3. You’ll see three options:
    • Direct download link
    • Zenodo repository page
    • AquaINFRA dataset page ← Select this one
  4. On the dataset page, click “Import to Galaxy”
  5. The OGC API Features subsetting window opens:
    • Bounding Box: Leave default (or customise for specific area)
    • Number of Points: Set to 5871 (total available points)
    • Query Parameters: Leave empty (we need all data)
  6. Click “Regenerate” to update the link
  7. Click “Import”
  8. You’ll be redirected to Aqua Galaxy
⏳ Import Status
In the History panel (right side):
• Gray = Queued
• Orange = Processing
• Green = Complete
• Red = Error
  1. Rename the dataset for clarity:
    • Click the pencil icon (Edit)
    • Rename to: points
    • Add annotation: “Latvian Secchi depth measurements”

1.2 Import HELCOM Assessment Unit Regions

📹 Video: 15:19 - 19:51

  1. Return to the Data-to-Knowledge Package page
  2. Click on “HELCOM subbasins”
  3. Click “AquaINFRA” to view the dataset page
  4. Click “Visit” to explore original metadata
  5. You’ll find two links:
    • Direct data access link
    • HELCOM interactive map
⚠️ Important: Data Usage Disclaimer
HELCOM data requires accepting a usage disclaimer before import.
  1. Accept the disclaimer:
    • Open the direct download link in a new tab
    • Accept the data usage disclaimer
    • Wait for the download link to activate (don’t download the file)
    • Copy the activated download URL
  2. Import to Galaxy:
    • Return to the AIP dataset page
    • Paste the URL into the import field
    • Click “Import”
  3. Wait for the green status indicator
  4. Rename the dataset:
    • Click the pencil icon
    • Rename to: regions
    • Add annotation: “HELCOM assessment unit polygons”

Step 2: Import the Workflow

📹 Video: 19:51 - 21:29

Method 1: Direct Import from AIP

  1. In the Data-to-Knowledge Package, click “Galaxy” under the workflow section
  2. You’ll be redirected to the workflow preview page in Aqua Galaxy
  3. Click “Import”
  4. Click “Start using this workflow”

Method 2: Manual Import

  1. Navigate to Workflows in Aqua Galaxy (top menu)
  2. Click “Import”
  3. Upload the workflow file (.ga format) from Zenodo

Step 3: Run the Workflow

📹 Video: 21:29 - 25:07

  1. In the Workflows section, find “Gulf of Riga DGA Workflow”
  2. Click the dropdown arrow → Select “Run”
  3. On the workflow run page:
    • Input 1 (Point Data): Select points
    • Input 2 (Region Data): Select regions
  4. (Optional) Click “Expand to full workflow” to customise parameters:
    • Threshold for missing values
    • Minimum number of data points
    • Interpolation settings
  5. Click “Run Workflow”

Step 4: Monitor Progress

📹 Video: 21:35 - 25:07

You’ll be taken to a progress page showing:

Interactive Workflow Graph

  • Visual representation of each step
  • Color-coded status (gray → orange → green)
  • Click on any step to see details

History Panel

  • Lists all outputs chronologically
  • Shows job metrics (runtime, memory usage)
  • Provides download links for results

Step 5: Review Outputs

📹 Video: 25:18 - 29:08

Key Outputs to Check:

1. Spatial Aggregation Output

  • File: Points with assessment unit IDs
  • What to look for: Each point now has a unit_id attribute

2. Temporal Aggregation Output

  • File: Points with season assignments
  • What to look for: New season column (Spring, Summer, Autumn, Winter)

3. Interpolated Time Series

  • File: CSV with continuous data
  • What to look for: Gaps filled, units with <10 points excluded

4. Mann-Kendall Results

  • File: Statistical test results
  • What to look for: Kendall’s Tau values (negative = darkening trend)

5. Interactive Map

  • File: map_shape_file_points.html
  • Action: Click the eye icon → Open in new tab
  • What to see: Assessment units color-coded by trend

6. Bar Chart

  • File: Kendall’s Tau visualization
  • What to see: Negative bars indicate decreasing transparency

Step 6: Interpret Results

📹 Video: 28:11 - 29:08

Example Results from Video:

The workflow identified significant negative trends in:

  • LAT-003 (Summer) - Negative Tau
  • LAT-004 (Summer) - Negative Tau
  • LAT-005 (Autumn) - Negative Tau

Location: All three units are along the Latvian coastline. LAT-005 includes the Daugava River catchment near Riga.

Interpretation: Water transparency is decreasing (darkening) in these coastal regions, confirming the scuba divers’ observations.

Troubleshooting

Issue: Import Fails (Red Status)

  • Solution: Check the internet connection, try re-importing

Issue: Workflow Stuck (Orange for >10 minutes)

  • Solution: Refresh the page, check server status

Issue: No Results Generated

  • Solution: Verify both input datasets were correctly imported and renamed

Next Steps

After successfully running the workflow:

  1. ✅ Download the results for the records
  2. ✅ Experiment with different parameters
  3. ✅ Try applying the workflow to the own data
  4. ✅ Explore other AquaINFRA workflows
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