Llm extraction schema

[sherjeelshabih]

I got most of the suggestions implemented.

@hampusnasstrom antisolvent quenching is something you should give feedback on. Jesper's suggestion:

Gas quenching and antisolvent quenching
Right now, we have qas quenching as a Boolean field.
We do not have a field for antisolvent quenching. Have we decided that we should add that as a separate deposition step?

For now, my suggestion would be to add a Boolean filed for antisolvent quenching, and add an instruction that it should be added as a separate deposition step. In the long run (i.e. not in this project right now) we would probably implement processing steps as separate modules depending on the deposition method, so that antisolvent details only are asked for when the deposition method is spin-coating.

Summary by Sourcery

Introduce a new schema package and application for LLM extraction in the perovskite solar cell database, enhancing data extraction and user interaction capabilities. Update data types and units for existing fields to improve flexibility and accuracy.

New Features:

• Introduce a new schema package for LLM extraction in the perovskite solar cell database, enabling structured data extraction and management.
• Add a new application entry point for exploring LLM extracted solar cells, providing a user interface for searching and filtering extracted data.

Enhancements:

• Change the type of the 'coefficient' field in the PerovskiteIonComponent class from float to string to accommodate more flexible input formats.
• Update the default display unit for the 'concentration' field in the Impurity class to 'cm^-3'.

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR introduces a new schema package for LLM (Large Language Model) extraction of perovskite solar cell data. The changes include modifications to the composition handling, addition of new schema classes for various solar cell components, and integration of a new app for exploring LLM-extracted data.

Class diagram for LLM Extraction Schema

classDiagram
    class LLMSchemaExtractionPackageEntryPoint {
        +load()
    }
    class PerovskiteIonComponent {
        +coefficient: str
    }
    class Impurity {
        +concentration: float
        +a_eln: ELNAnnotation
    }
    class LLMExtractedPerovskiteSolarCell {
        +DOI_number: str
        +perovskite_composition: PerovskiteComposition
        +device_architecture: MEnum
        +pce: float
        +jsc: float
        +voc: float
        +ff: float
        +active_area: float
        +number_devices: int
        +averaged_quantities: bool
        +light_source: LightSource
        +bandgap: float
        +encapsulated: bool
        +stability: Stability
        +layers: Layer
        +layer_order: str
        +normalize(archive, logger)
    }
    class PerovskiteComposition {
        +abbreviation: str
        +coefficient: str
    }
    class LightSource {
        +type: MEnum
        +description: str
        +light_intensity: float
        +lamp: str
    }
    class Stability {
        +time: float
        +light_intensity: float
        +humidity: float
        +temperature: float
        +PCE_T80: float
        +PCE_at_start: float
        +PCE_after_1000_hours: float
        +PCE_at_end: float
        +potential_bias: MEnum
    }
    class Layer {
        +name: str
        +thickness: float
        +functionality: MEnum
        +deposition: ProcessingStep
        +additional_treatment: str
    }
    class ProcessingStep {
        +step_name: str
        +method: str
        +atmosphere: MEnum
        +temperature: float
        +duration: float
        +gas_quenching: bool
        +antisolvent_quenching: bool
        +solution: ReactionSolution
        +additional_parameters: JSON
    }
    class ReactionSolution {
        +solutes: Solute
        +volume: float
        +temperature: float
        +solvents: Solvent
    }
    class Solute {
        +name: str
        +concentration: float
        +concentration_unit: MEnum
    }
    class Solvent {
        +name: str
        +ratio: float
    }
    LLMSchemaExtractionPackageEntryPoint --> PerovskiteIonComponent
    LLMSchemaExtractionPackageEntryPoint --> Impurity
    LLMSchemaExtractionPackageEntryPoint --> LLMExtractedPerovskiteSolarCell
    LLMExtractedPerovskiteSolarCell --> PerovskiteComposition
    LLMExtractedPerovskiteSolarCell --> LightSource
    LLMExtractedPerovskiteSolarCell --> Stability
    LLMExtractedPerovskiteSolarCell --> Layer
    Layer --> ProcessingStep
    ProcessingStep --> ReactionSolution
    ReactionSolution --> Solute
    ReactionSolution --> Solvent

Loading

File-Level Changes

Change	Details	Files
Changed coefficient type in PerovskiteIonComponent from float to string to support more flexible stoichiometric notation	Modified coefficient type from float to string Updated normalization logic to handle string coefficients Added support for expressions like '1-x' in coefficients	src/perovskite_solar_cell_database/composition.py
Created new schema package for LLM extraction of solar cell data	Added base SectionRevision class with review tracking Created classes for various solar cell components (Ion, LightSource, Solute, etc.) Implemented comprehensive schema for perovskite solar cell data extraction Added stability tracking and measurement parameters	src/perovskite_solar_cell_database/llm_extraction_schema.py
Added new app for exploring LLM-extracted solar cell data	Created new app entry point for LLM extracted data Configured custom columns and filters for the app Added dashboard with visualization widgets Set up filter menus for data exploration	src/perovskite_solar_cell_database/apps/__init__.py src/perovskite_solar_cell_database/apps/llm_extracted_solarcells.py
Updated package configuration and entry points	Added new LLMSchemaExtractionPackageEntryPoint Registered llm_extraction_schema in pyproject.toml	src/perovskite_solar_cell_database/__init__.py pyproject.toml

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[sourcery-ai]

Hey @sherjeelshabih - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟡 Complexity: 1 issue found
• 🟢 Documentation: all looks good

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[sourcery-ai]

issue (code-quality): We've found these issues:

• Replace if statement with if expression (assign-if-exp)
• Simplify conditional into switch-like form [×2] (switch)

[sourcery-ai]

issue (code-quality): Remove redundant conditional (remove-redundant-if)