app.components.tools package

Submodules

app.components.tools.R_tools module

app.components.tools.R_tools.impute_qrilc(dataframe, random_seed, errorfile)[source]

Impute missing values using QRILC (via imputeLCMD).

Parameters:

  • dataframe (DataFrame) – Input DataFrame with missing values.

  • random_seed (int) – Seed for reproducibility.

  • errorfile (str) – Base path for error log on failure.

Return type:

DataFrame

Returns:

DataFrame with imputed values.

app.components.tools.R_tools.impute_random_forest(dataframe, random_seed, rev_sample_groups, errorfile)[source]

Impute missing values using randomForest::rfImpute grouped by sample groups.

Parameters:

  • dataframe (DataFrame) – Input DataFrame with missing values (rows=ids; cols=samples).

  • random_seed (int) – Seed for reproducibility.

  • rev_sample_groups (dict) – Mapping sample -> group for supervised imputation.

  • errorfile (str) – Base path for error log on failure.

Return type:

DataFrame

Returns:

DataFrame with imputed values.

app.components.tools.R_tools.run_rscript(r_script_contents, r_script_data, replace_name, errorfile, replace_dir=None, input_df_has_index=True)[source]

Execute an R script with a temp data file and return parsed output.

Parameters:

  • r_script_contents (list) – Lines of the R script; occurrences of replace_name are replaced with temp paths.

  • r_script_data (DataFrame) – DataFrame to write to temp file for R to read.

  • replace_name (str) – Placeholder token to be replaced with temp filename.

  • errorfile (str | list) – Base path (e.g. ‘logs/errors.log’) or list of a file path (e.g. [‘logs’,’errors.log’]) for error log on failure.

  • replace_dir (str | None) – Optional directory placeholder to replace with temp dir.

  • input_df_has_index (bool) – Whether to include index when writing CSV/TSV.

Returns:

DataFrame parsed from R output file.

Raises:

Exception – Re-raises Rscript execution errors after logging.

app.components.tools.R_tools.vsn(dataframe, random_seed, errorfile)[source]

Apply VSN normalization via R’s vsn::justvsn.

Parameters:

  • dataframe (DataFrame) – Input DataFrame (rows=ids in index; columns=samples).

  • random_seed (int) – Seed for reproducibility in R.

  • errorfile (str) – Base path to append Rscript stderr on failure.

Return type:

DataFrame

Returns:

DataFrame of VSN-transformed values, aligned to input.

app.components.tools.utils module

app.components.tools.utils.deep_merge(base, override)[source]

Deep-merge override into base.

Rules: - Dicts merge recursively. - Scalars/lists replace the base value.

Parameters:

  • base (MutableMapping[str, Any]) – Destination mapping to mutate.

  • override (Mapping[str, Any]) – Source mapping providing updates.

Return type:

MutableMapping[str, Any]

Returns:

Mutated base mapping.

app.components.tools.utils.dig_dict(in_dict, key_path)[source]

Traverse nested dict by list of keys.

Parameters:

  • in_dict – Input mapping.

  • key_path – Sequence of keys to descend.

Returns:

Value at the nested path.

app.components.tools.utils.expand_path(path, param_dict)[source]

Expand a ‘params:’ reference into a concrete path from a dict.

Parameters:

  • path – String possibly starting with 'params:'.

  • param_dict – Parameter dictionary.

Returns:

Expanded path string or original value.

app.components.tools.utils.expand_paths(in_dict, param_dict)[source]

Recursively expand ‘params:’ paths in a nested dict structure.

Parameters:

  • in_dict – Input dict to mutate.

  • param_dict – Parameter dictionary supplying values.

Returns:

Mutated input dict with paths expanded.

app.components.tools.utils.load_toml(path)[source]

Load a TOML file into a Python dict using tomlkit.

Parameters:

path (Path) – Path to TOML file.

Return type:

dict[str, Any]

Returns:

Parsed dict.

app.components.tools.utils.normalize_key(s)[source]

Normalize a string for consistent matching.

Steps: - Lowercase and strip directory/extension. - Replace non-alphanumerics with underscore; collapse repeats. - Trim leading/trailing underscores.

Parameters:

s (str) – Input string (e.g., filename).

Return type:

str

Returns:

Normalized key string.

app.components.tools.utils.prefix_relative_paths(data, basepath=None, check_exists=True)[source]

Recursively prefix relative paths in a nested dict.

Values can be strings, lists, or dicts.

Parameters:

  • data (Dict[str, Any]) – Input dictionary.

  • basepath (Union[str, PathLike, None]) – Base path to prepend; if None, uses global BASEPATH.

  • check_exists (bool) – If True, only replace when resulting path exists.

Return type:

Dict[str, Any]

Returns:

New dict with adjusted paths.

app.components.tools.utils.read_toml(toml_file, baseify=['Data paths'], check_exists=False, expand_paths_in_full_dict=True)[source]

Read a TOML file and optionally prefix/expand embedded paths.

Parameters:

  • toml_file (Union[str, Path]) – TOML file path.

  • baseify – Top-level keys whose values should get path prefixing.

  • check_exists – If True, only replace with existing paths.

  • expand_paths_in_full_dict – If True, expand params: references.

Returns:

Parsed and transformed dictionary.

app.components.tools.utils.save_toml(data, path)[source]

Write a TOML document to disk using tomlkit.

Parameters:

  • data (dict[str, Any]) – Dict to serialize.

  • path (Path) – Output path.

Return type:

None

Returns:

None

app.components.tools.utils.zipdir(src_dir, tmpfs_base=None)[source]

Zip a directory and return the created archive path.

The zip contains paths prefixed by the source directory’s basename.

Parameters:

  • src_dir (str | Path) – Directory to zip.

  • tmpfs_base (str | Path | None) – Base directory for temporary working folder (unused placeholder).

Return type:

Path

Returns:

Path to the created ZIP file.

Raises:

  • FileNotFoundError – If src_dir doesn’t exist.

  • NotADirectoryError – If src_dir is not a directory.

Module contents

Tools subpackage for helper utilities.