malva_client package

Submodules

• malva_client.auth module
• malva_client.cli module
• Client
  • Convenience Functions
• Configuration
  • Config
    • Config.load()
    • Config.save()
    • Config.set_value()
    • Config.get_value()
    • Config.show()
    • Config.validate()
    • Config.reset_to_defaults()
    • Config.delete_config_file()
• Exceptions
  • MalvaAPIError
  • AuthenticationError
  • SearchError
  • QuotaExceededError
  • ValidationError
  • ConfigurationError
  • StorageError
  • NetworkError
  • TimeoutError
• Models
  • SearchResult
    • SearchResult
      • SearchResult.__init__()
      • SearchResult.job_id
      • SearchResult.status
      • SearchResult.results
      • SearchResult.total_cells
      • SearchResult.enrich_with_metadata()
  • MalvaDataFrame
    • MalvaDataFrame
      • MalvaDataFrame.__init__()
      • MalvaDataFrame.df
      • MalvaDataFrame.filter_by()
      • MalvaDataFrame.aggregate_by()
      • MalvaDataFrame.plot_expression_by()
      • MalvaDataFrame.plot_expression_summary()
      • MalvaDataFrame.to_pandas()
      • MalvaDataFrame.available_fields()
      • MalvaDataFrame.available_filter_fields()
      • MalvaDataFrame.field_info()
      • MalvaDataFrame.unique_values()
      • MalvaDataFrame.value_counts()
  • CellExpressionMatrixResult
    • CellExpressionMatrixResult
      • CellExpressionMatrixResult.__init__()
      • CellExpressionMatrixResult.cells
      • CellExpressionMatrixResult.features
      • CellExpressionMatrixResult.normalization_factors
      • CellExpressionMatrixResult.sample_metadata
      • CellExpressionMatrixResult.matrix_entries
      • CellExpressionMatrixResult.get_cell_ids()
      • CellExpressionMatrixResult.positive_cells()
      • CellExpressionMatrixResult.to_dataframe()
      • CellExpressionMatrixResult.for_sample()
      • CellExpressionMatrixResult.to_single_cell_result()
      • CellExpressionMatrixResult.project()
  • SingleCellResult
    • SingleCellResult
      • SingleCellResult.__init__()
      • SingleCellResult.is_completed
      • SingleCellResult.is_pending
      • SingleCellResult.has_results
      • SingleCellResult.cell_count
      • SingleCellResult.sample_count
      • SingleCellResult.query_gene
      • SingleCellResult.to_dataframe()
      • SingleCellResult.get_cell_ids()
      • SingleCellResult.get_expression_values()
      • SingleCellResult.get_sample_ids()
      • SingleCellResult.filter_by_expression()
      • SingleCellResult.filter_by_samples()
      • SingleCellResult.get_top_expressing_cells()
      • SingleCellResult.aggregate_by_sample()
      • SingleCellResult.get_expression_stats()
      • SingleCellResult.enrich_with_metadata()
      • SingleCellResult.save_to_csv()
  • CoverageResult
    • CoverageResult
      • CoverageResult.__init__()
      • CoverageResult.to_dataframe()
      • CoverageResult.get_filter_options()
      • CoverageResult.download_wig()
      • CoverageResult.plot()
  • CoexpressionResult
    • CoexpressionResult
      • CoexpressionResult.__init__()
      • CoexpressionResult.genes_to_dataframe()
      • CoexpressionResult.scores_to_dataframe()
      • CoexpressionResult.umap_to_dataframe()
      • CoexpressionResult.go_to_dataframe()
      • CoexpressionResult.cell_type_enrichment_to_dataframe()
      • CoexpressionResult.tissue_breakdown_to_dataframe()
      • CoexpressionResult.get_top_genes()
      • CoexpressionResult.plot_umap()
      • CoexpressionResult.plot_top_genes()
      • CoexpressionResult.plot_go_enrichment()
  • UMAPCoordinates
    • UMAPCoordinates
      • UMAPCoordinates.__init__()
      • UMAPCoordinates.to_dataframe()
      • UMAPCoordinates.plot()
• malva_client.storage module
• malva_client.tools module

Module contents

Malva Client - Python client for the Malva genomic search platform

exception malva_client.MalvaAPIError(message, response_data=None)

Bases: Exception

Base exception for Malva API errors

exception malva_client.AuthenticationError(message, response_data=None)

Bases: MalvaAPIError

Authentication failed

exception malva_client.SearchError(message, job_id=None, response_data=None)

Bases: MalvaAPIError

Search operation failed

exception malva_client.QuotaExceededError(message, quota_info=None)

Bases: MalvaAPIError

API quota exceeded

exception malva_client.ValidationError(message, response_data=None)

Bases: MalvaAPIError

Input validation failed

exception malva_client.ConfigurationError(message, response_data=None)

Bases: MalvaAPIError

Configuration error

class malva_client.Config(config_path=None)

Bases: object

Configuration management for Malva client

classmethod load(config_path=None)

Load configuration from file or environment

save()

Save configuration to file

set_value(key, value)

Set configuration value

Parameters:

• key (str) – Configuration key

• value (str) – Configuration value

get_value(key)

Get configuration value

Parameters:

key (str) – Configuration key

Return type:

Optional[str]

Returns:

Configuration value or None

show()

Show current configuration

Return type:

Dict[str, Any]

Returns:

Dictionary with current configuration

validate()

Validate current configuration

Return type:

List[str]

Returns:

List of validation errors (empty if valid)

reset_to_defaults()

Reset configuration to defaults

delete_config_file()

Delete configuration file

Return type:

bool

Returns:

True if file was deleted