Add-Ons

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Add-Ons

Overview: Add-ons are small Python programs that extend PASTA-ELN's functionality. Researchers can develop or adopt these tools and share them. Add-ons are categorized into Extractors and other add-ons. Access them via "Configuration" > "Project Group" to specify their location.

Extractor add-ons

Extractors generate metadata when scanning projects or dropping files into folders. They provide:

• Thumbnails for curation and annotation.

• User-metadata for post-processing.

• Vendor-metadata detailing instrument settings.

• Links to instruments or procedures.

PASTA-ELN includes extractors for CSV, JPEG, JSON, MD, and PNG files. PNG and JPEG extractors serve as examples for custom development.

Testing and Optimizing Extractors

To test an extractor interactively, include the following code at the end of the extractor file:

if __name__ == '__main__':
  reply = use('datafile.abc', saveFileName='datafile.png')
  print('User meta:', reply['metaUser'])
  print('Vendor meta:', reply['metaVendor'])

Remove these lines before deployment.

Troubleshooting Extractor Issues

Python Errors: Ensure required libraries are installed. Use pip install <library_name> to resolve missing dependencies.

Metadata Errors: Store metadata as key-value dictionaries. Test with json.dumps() to identify issues.

import json

meta_vendor = {"detector": {"calibration_a": 4, "calibration_b": 1}, "settings": "high"}
try:
  json.dumps(meta_vendor)
except Exception e:
  print(e)

Matplotlib Image Conversion: Convert Matplotlib axes to SVG:

from io import StringIO

figfile = StringIO()
plt.savefig(figfile, format="svg")
image = figfile.getvalue()

Pillow Image Conversion: Convert Matplotlib axes to base64-encoded images:

from io import BytesIO
import base64

figfile = BytesIO()
image.save(figfile, format="PNG")
image_data = base64.b64encode(figfile.getvalue()).decode()
image = "data:image/png;base64," + image_data

File Format Information and Extractor Development

Understanding file formats is crucial for developing extractors. Refer to:

• [Wikipedia: List of filename extensions](https://en.wikipedia.org/wiki/List_of_filename_extensions_(alphabetical))

• [Wikipedia: Chemical file formats](https://en.wikipedia.org/wiki/Chemical_file_format)

• [Wikipedia: List of file formats](https://en.wikipedia.org/wiki/List_of_file_formats)

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Other Add-ons

Other add-ons enhance functionality and may include API keys for external services.

Project Add-ons

Generate reports, presentations, and drafts for scientific papers using the project's hierarchical structure. A default example includes a customizable HTML-based report.

Table Add-ons

Process data from tables:

• Extract data directly from tables.

• Use filenames from table items to generate scientific graphs.

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