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Merged
khoroshevskyi merged 3 commits into from
Feb 26, 2026
Merged

Modernize - phase 6 - docstrings #108

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cff7a16
Modernizing - docstrings
khoroshevskyi Feb 17, 2026
69b4aa4
more docstrings adjustment
khoroshevskyi Feb 17, 2026
c315bf3
Updated incorrect docstrings
khoroshevskyi Feb 26, 2026
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0 .github/workflows/black.yml → .github/workflows/format.yml
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99 changes: 56 additions & 43 deletions bbconf/bbagent.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,8 +52,9 @@ def __init__(
Initialize connection to the pep_db database. You can use the basic connection parameters
or libpq connection string.

:param config: path to the configuration file
:param init_ml: initialize ML models for search (default: True)
Args:
config: Path to the configuration file.
init_ml: Initialize ML models for search (default: True).
"""

self.config = BedBaseConfig(config, init_ml)
Expand Down Expand Up @@ -83,9 +84,10 @@ def __repr__(self) -> str:

def get_stats(self) -> StatsReturn:
"""
Get statistics for a bed file
Get statistics for a bed file.

:return: statistics
Returns:
Statistics.
"""
with Session(self.config.db_engine.engine) as session:
number_of_bed = session.execute(select(func.count(Bed.id))).one()[0]
Expand All @@ -103,10 +105,13 @@ def get_stats(self) -> StatsReturn:

def get_detailed_stats(self, concise: bool = False) -> FileStats:
"""
Get comprehensive statistics for all bed files
Get comprehensive statistics for all bed files.

:param concise: if True, return only top 20 items for each category
:return: FileStats object containing detailed statistics
Args:
concise: If True, return only top 20 items for each category.

Returns:
FileStats object containing detailed statistics.
"""

_LOGGER.info("Getting detailed statistics for all bed files")
Expand Down Expand Up @@ -270,7 +275,8 @@ def get_detailed_usage(self) -> UsageStats:
Get detailed usage statistics for the bedbase platform.
This method will only return top 20 items for each category.

:return: UsageStats object containing detailed usage statistics
Returns:
UsageStats object containing detailed usage statistics.
"""

_LOGGER.info("Getting detailed usage statistics.")
Expand Down Expand Up @@ -339,9 +345,10 @@ def get_detailed_usage(self) -> UsageStats:

def get_list_genomes(self) -> list[str]:
"""
Get list of genomes from the database
Get list of genomes from the database.

:return: list of genomes
Returns:
List of genomes.
"""
statement = (
select(Bed.genome_alias)
Expand All @@ -354,9 +361,10 @@ def get_list_genomes(self) -> list[str]:

def get_list_assays(self) -> list[str]:
"""
Get list of genomes from the database
Get list of assays from the database.

:return: list of genomes
Returns:
List of assays.
"""
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with Session(self.config.db_engine.engine) as session:
Expand All @@ -371,9 +379,10 @@ def get_list_assays(self) -> list[str]:
@cached_property
def list_of_licenses(self) -> list[str]:
"""
Get list of licenses from the database
Get list of licenses from the database.

:return: list of licenses
Returns:
List of licenses.
"""
statement = select(License.id)
with Session(self.config.db_engine.engine) as session:
Expand Down Expand Up @@ -498,9 +507,11 @@ def _stats_comments(self, sa_session: Session) -> dict[str, int]:
"""
Get statistics about comments that are present in bed files.

:param sa_session: SQLAlchemy session
Args:
sa_session: SQLAlchemy session.

:return: Dict[str, int]
Returns:
Dict mapping comment type to count.
"""
_LOGGER.info("Analyzing bed table for comments in bed files...")

Expand Down Expand Up @@ -552,8 +563,11 @@ def _stats_geo_status(self, sa_session: Session) -> dict[str, int]:
"""
Get statistics about status of GEO bed file processing.

:param sa_session: SQLAlchemy session
:return Dict[str, int]
Args:
sa_session: SQLAlchemy session.

Returns:
Dict mapping status type to count.
"""

success_statement = select(
Expand Down Expand Up @@ -601,20 +615,8 @@ def bed_files_info(self) -> AllFilesInfo:
"""
Get information about all bed files in bedbase.

:param sa_session: SQLAlchemy session
:return AllFilesInfo:
{
"total": int,"
"files": [
{ id: str
bed_compliance: str
data_format: str
mean_region_width: float
file_size: int
number_of_regions: int
},
... ]
}
Returns:
AllFilesInfo containing total count and list of file info objects.
"""

all_files_statement = (
Expand Down Expand Up @@ -661,10 +663,13 @@ def bed_files_info(self) -> AllFilesInfo:

def _bin_number_of_regions(self, number_of_regions: list) -> BinValues:
"""
Create bins for number of regions in bed files
Create bins for number of regions in bed files.

:param number_of_regions: list of number of regions in bed files
:return: BinValues object containing bins and values
Args:
number_of_regions: List of number of regions in bed files.

Returns:
BinValues object containing bins and values.
"""

max_value_threshold = 400_000 # set a threshold for maximum value to avoid outliers in the histogram
Expand All @@ -689,10 +694,13 @@ def _bin_number_of_regions(self, number_of_regions: list) -> BinValues:

def _bin_mean_region_width(self, mean_region_widths: list) -> BinValues:
"""
Create bins for number of regions in bed files
Create bins for number of regions in bed files.

Args:
mean_region_widths: List of mean region widths in bed files.

:param mean_region_widths: list of mean region widths in bed files
:return: BinValues object containing bins and values
Returns:
BinValues object containing bins and values.
"""

max_value_threshold = 5_000 # set a threshold for maximum value to avoid outliers in the histogram
Expand All @@ -717,10 +725,13 @@ def _bin_mean_region_width(self, mean_region_widths: list) -> BinValues:

def _bin_file_size(self, list_file_size: list) -> BinValues:
"""
Create bins for number of regions in bed files
Create bins for number of regions in bed files.

Args:
list_file_size: List of bed file sizes in bytes.

:param list_file_size: list of bed file sizes in bytes
:return: BinValues object containing bins and values
Returns:
BinValues object containing bins and values.
"""

max_value_threshold = 10 * 1024 * 1024
Expand Down Expand Up @@ -748,7 +759,8 @@ def _get_geo_stats(self, sa_session: Session) -> GEOStatistics:
"""
Get GEO statistics for the bedbase platform.

:return: GEOStatistics
Returns:
GEOStatistics.
"""

_LOGGER.info("Getting GEO statistics.")
Expand Down Expand Up @@ -802,7 +814,8 @@ def get_reference_genomes(self) -> dict[str, str]:
"""
Get mapping of genome aliases to reference genome names.

:return: dict mapping genome_alias -> reference_genome_name
Returns:
Dict mapping genome_alias to reference_genome_name.
"""

genomes = {}
Expand Down
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