# bbconf API

`BedBaseAgent` is the entry point. Its `bed`, `bedset`, `objects`, `snapshot`, and `analysis_files` properties return the agents documented below.

<a id="bbconf.BedBaseAgent"></a>

## `BedBaseAgent`

```python
class BedBaseAgent(config: Path | str, init_ml: bool = True)
```

Initialize connection to the pep_db database. You can use the basic connection parameters
or libpq connection string.

**Parameters:**

- `config` (*Path | str*): Path to the configuration file.
- `init_ml` (*bool*): Initialize ML models for search (default: True). (default: `True`)

### Attributes

- <a id="bbconf.BedBaseAgent.config"></a>**`config`**

### Properties

<a id="bbconf.BedBaseAgent.bed"></a>

#### `bed`

```python
@property
def bed -> BedAgentBedFile
```

<a id="bbconf.BedBaseAgent.bedset"></a>

#### `bedset`

```python
@property
def bedset -> BedAgentBedSet
```

<a id="bbconf.BedBaseAgent.objects"></a>

#### `objects`

```python
@property
def objects -> BBObjects
```

<a id="bbconf.BedBaseAgent.snapshot"></a>

#### `snapshot`

```python
@property
def snapshot -> BedAgentSnapshot
```

<a id="bbconf.BedBaseAgent.analysis_files"></a>

#### `analysis_files`

```python
@property
def analysis_files -> BedAgentAnalysisFile
```

<a id="bbconf.BedBaseAgent.list_of_licenses"></a>

#### `list_of_licenses`

```python
@property
def list_of_licenses -> list[str]
```

Get list of licenses from the database.

**Returns:**

- *list[str]*: List of licenses.

### Methods

<a id="bbconf.BedBaseAgent.get_stats"></a>

#### `get_stats`

```python
def get_stats() -> StatsReturn
```

Get statistics for a bed file.

The result is cached with a TTL because this runs three COUNT queries
against the large bed table and is called on hot API paths.

**Returns:**

- *StatsReturn*: Statistics.

<a id="bbconf.BedBaseAgent.get_detailed_stats"></a>

#### `get_detailed_stats`

```python
def get_detailed_stats(concise: bool = False) -> FileStats
```

Get comprehensive statistics for all bed files.

**Parameters:**

- `concise` (*bool*): If True, return only top 20 items for each category. (default: `False`)

**Returns:**

- *FileStats*: FileStats object containing detailed statistics.

<a id="bbconf.BedBaseAgent.get_detailed_usage"></a>

#### `get_detailed_usage`

```python
def get_detailed_usage() -> UsageStats
```

Get detailed usage statistics for the bedbase platform.
This method will only return top 20 items for each category.

**Returns:**

- *UsageStats*: UsageStats object containing detailed usage statistics.

<a id="bbconf.BedBaseAgent.get_list_genomes"></a>

#### `get_list_genomes`

```python
def get_list_genomes() -> list[str]
```

Get list of genomes from the database.

**Returns:**

- *list[str]*: List of genomes.

<a id="bbconf.BedBaseAgent.get_list_assays"></a>

#### `get_list_assays`

```python
def get_list_assays() -> list[str]
```

Get list of assays from the database.

**Returns:**

- *list[str]*: List of assays.

<a id="bbconf.BedBaseAgent.add_usage"></a>

#### `add_usage`

```python
def add_usage(stats: UsageModel) -> None
```

<a id="bbconf.BedBaseAgent.bed_files_info"></a>

#### `bed_files_info`

```python
def bed_files_info() -> AllFilesInfo
```

Get information about all bed files in bedbase.

**Returns:**

- *AllFilesInfo*: AllFilesInfo containing total count and list of file info objects.

<a id="bbconf.BedBaseAgent.get_reference_genomes"></a>

#### `get_reference_genomes`

```python
def get_reference_genomes() -> dict[str, str]
```

Get mapping of genome aliases to reference genome names.

**Returns:**

- *dict[str, str]*: Dict mapping genome_alias to reference_genome_name.

<a id="bbconf.modules.bedfiles.BedAgentBedFile"></a>

## `BedAgentBedFile`

```python
class BedAgentBedFile(config: BedBaseConfig, bbagent_obj=None)
```

Class that represents a BED file in the Database.

Provides methods to add, delete, get BED files and metadata from the database.

Initialize BedAgentBedFile.

**Parameters:**

- `config` (*BedBaseConfig*): Config object with database and qdrant engine and credentials.
- `bbagent_obj`: BedBaseAgent object (Parent object). (default: `None`)

### Attributes

- <a id="bbconf.modules.bedfiles.BedAgentBedFile.config"></a>**`config`**
- <a id="bbconf.modules.bedfiles.BedAgentBedFile.bb_agent"></a>**`bb_agent`**

### Methods

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get"></a>

#### `get`

```python
def get(identifier: str, full: bool = False) -> BedMetadataAll
```

Get file metadata by identifier.

**Parameters:**

- `identifier` (*str*): Bed file identifier.
- `full` (*bool*): If True, return full metadata, including statistics and files. (default: `False`)

**Returns:**

- *BedMetadataAll*: BED file metadata.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_stats"></a>

#### `get_stats`

```python
def get_stats(identifier: str) -> BedStatsModel
```

Get file statistics by identifier.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *BedStatsModel*: Project statistics as BedStats object.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_plots"></a>

#### `get_plots`

```python
def get_plots(identifier: str) -> BedPlots
```

Get file plots by identifier.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *BedPlots*: Project plots.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_neighbours"></a>

#### `get_neighbours`

```python
def get_neighbours(identifier: str, limit: int = 10, offset: int = 0) -> BedListSearchResult
```

Get nearest neighbours of bed file from qdrant.

**Parameters:**

- `identifier` (*str*): Bed file identifier.
- `limit` (*int*): Number of results to return. (default: `10`)
- `offset` (*int*): Offset to start from. (default: `0`)

**Returns:**

- *BedListSearchResult*: List of nearest neighbours.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_files"></a>

#### `get_files`

```python
def get_files(identifier: str) -> BedFiles
```

Get file files by identifier.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *BedFiles*: Project files.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_classification"></a>

#### `get_classification`

```python
def get_classification(identifier: str) -> BedClassification
```

Get file classification by identifier.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *BedClassification*: Project classification.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_objects"></a>

#### `get_objects`

```python
def get_objects(identifier: str) -> dict[str, FileModel]
```

Get all object related to bedfile.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *dict[str, FileModel]*: Project objects dict.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_embedding"></a>

#### `get_embedding`

```python
def get_embedding(identifier: str) -> BedEmbeddingResult
```

Get bed file embedding of bed file from qdrant.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *BedEmbeddingResult*: Bed file embedding.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_ids_list"></a>

#### `get_ids_list`

```python
def get_ids_list(limit: int = 100, offset: int = 0, genome: str = None, bed_compliance: str = None) -> BedListResult
```

Get list of bed file identifiers.

**Parameters:**

- `limit` (*int*): Number of results to return. (default: `100`)
- `offset` (*int*): Offset to start from. (default: `0`)
- `genome` (*str*): Filter by genome. (default: `None`)
- `bed_compliance` (*str*): Filter by bed type. e.g. 'bed6+4'. (default: `None`)

**Returns:**

- *BedListResult*: List of bed file identifiers.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_reference_validation"></a>

#### `get_reference_validation`

```python
def get_reference_validation(identifier: str) -> RefGenValidReturnModel
```

Get results of reference genome validation for the bed file.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *RefGenValidReturnModel*: Reference genome validation results.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.add"></a>

#### `add`

```python
def add(identifier: str, stats: dict, metadata: dict = None, plots: dict = None, files: dict = None, classification: dict = None, ref_validation: dict[str, BaseModel] | None = None, license_id: str = DEFAULT_LICENSE, upload_qdrant: bool = False, upload_s3: bool = False, local_path: str = None, overwrite: bool = False, nofail: bool = False, processed: bool = True) -> None
```

Add bed file to the database.

**Parameters:**

- `identifier` (*str*): Bed file identifier.
- `stats` (*dict*): Bed file results {statistics, plots, files, metadata}.
- `metadata` (*dict*): Bed file metadata. (default: `None`)
- `plots` (*dict*): Bed file plots. (default: `None`)
- `files` (*dict*): Bed file files. (default: `None`)
- `classification` (*dict*): Bed file classification. (default: `None`)
- `ref_validation` (*dict[str, BaseModel] | None*): Reference validation data. RefGenValidModel. (default: `None`)
- `license_id` (*str*): Bed file license id (default: 'DUO:0000042'). Full list of licenses:
  https://raw.githubusercontent.com/EBISPOT/DUO/master/duo.csv (default: `DEFAULT_LICENSE`)
- `upload_qdrant` (*bool*): Add bed file to qdrant indexes. (default: `False`)
- `upload_s3` (*bool*): Upload files to s3. (default: `False`)
- `local_path` (*str*): Local path to the output files. (default: `None`)
- `overwrite` (*bool*): Overwrite bed file if it already exists. (default: `False`)
- `nofail` (*bool*): Do not raise an error for error in s3/qdrant or record exists and not overwrite. (default: `False`)
- `processed` (*bool*): True if bedfile was processed and statistics and plots were calculated. (default: `True`)

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.update"></a>

#### `update`

```python
def update(identifier: str, stats: dict | None = None, metadata: dict | None = None, plots: dict | None = None, files: dict | None = None, classification: dict | None = None, ref_validation: dict[str, BaseModel] | None = None, license_id: str = DEFAULT_LICENSE, upload_qdrant: bool = False, upload_s3: bool = True, local_path: str = None, overwrite: bool = False, nofail: bool = False, processed: bool = False) -> None
```

Update bed file to the database.

**Parameters:**

- `identifier` (*str*): Bed file identifier.
- `stats` (*dict | None*): Bed file results {statistics, plots, files, metadata}. (default: `None`)
- `metadata` (*dict | None*): Bed file metadata. (default: `None`)
- `plots` (*dict | None*): Bed file plots. (default: `None`)
- `files` (*dict | None*): Bed file files. (default: `None`)
- `classification` (*dict | None*): Bed file classification. (default: `None`)
- `ref_validation` (*dict[str, BaseModel] | None*): Reference validation data. RefGenValidModel. (default: `None`)
- `license_id` (*str*): Bed file license id (default: 'DUO:0000042'). (default: `DEFAULT_LICENSE`)
- `upload_qdrant` (*bool*): Add bed file to qdrant indexes. (default: `False`)
- `upload_s3` (*bool*): Upload files to s3. (default: `True`)
- `local_path` (*str*): Local path to the output files. (default: `None`)
- `overwrite` (*bool*): Overwrite bed file if it already exists. (default: `False`)
- `nofail` (*bool*): Do not raise an error for error in s3/qdrant or record exists and not overwrite. (default: `False`)
- `processed` (*bool*): True if bedfile was processed and statistics and plots were calculated. (default: `False`)

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.delete"></a>

#### `delete`

```python
def delete(identifier: str) -> None
```

Delete bed file from the database.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.upload_file_qdrant"></a>

#### `upload_file_qdrant`

```python
def upload_file_qdrant(bed_id: str, bed_file: str | GRegionSet, payload: dict = None) -> None
```

Convert bed file to vector and add it to qdrant database.

Warning: only hg38 genome can be added to qdrant!

**Parameters:**

- `bed_id` (*str*): Bed file id.
- `bed_file` (*str | GRegionSet*): Path to the bed file, or RegionSet object.
- `payload` (*dict*): Additional metadata to store alongside vectors. (default: `None`)

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.text_to_bed_search"></a>

#### `text_to_bed_search`

```python
def text_to_bed_search(query: str, limit: int = 10, offset: int = 0, with_metadata: bool = True) -> BedListSearchResult
```

Search for bed files by text query in qdrant database.
This is bivec_search.

**Parameters:**

- `query` (*str*): Text query.
- `limit` (*int*): Number of results to return. (default: `10`)
- `offset` (*int*): Offset to start from. (default: `0`)
- `with_metadata` (*bool*): If True, will return metadata for each result. (default: `True`)

**Returns:**

- *BedListSearchResult*: List of bed file metadata.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.bed_to_bed_search"></a>

#### `bed_to_bed_search`

```python
def bed_to_bed_search(region_set: GRegionSet, limit: int = 10, offset: int = 0) -> BedListSearchResult
```

Search for bed files by using region set in qdrant database.

**Parameters:**

- `region_set` (*GRegionSet*): RegionSet object to search for (bed file).
- `limit` (*int*): Number of results to return. (default: `10`)
- `offset` (*int*): Offset to start from. (default: `0`)

**Returns:**

- *BedListSearchResult*: BedListSetResults.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.sql_search"></a>

#### `sql_search`

```python
def sql_search(query: str, genome: str = None, assay: str = None, limit: int = 10, offset: int = 0) -> BedListSearchResult
```

Search for bed files by using sql exact search.
This search will search files by id, name, and description.

**Parameters:**

- `query` (*str*): Text query.
- `genome` (*str*): Genome alias to filter results. (default: `None`)
- `assay` (*str*): Filter by assay type. (default: `None`)
- `limit` (*int*): Number of results to return. (default: `10`)
- `offset` (*int*): Offset to start from. (default: `0`)

**Returns:**

- *BedListSearchResult*: List of bed file metadata.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.reindex_qdrant"></a>

#### `reindex_qdrant`

```python
def reindex_qdrant(batch: int = 100, purge: bool = False) -> None
```

Re-upload all files to qdrant.
Warning: only hg38 genome can be added to qdrant!

If you want to fully reindex/reupload to qdrant, first delete collection and create new one.
Upload all files to qdrant.

**Parameters:**

- `batch` (*int*): Number of files to upload in one batch. (default: `100`)

<a id="bbconf.modules.bedfiles.BedAgentBedFile.delete_qdrant_point"></a>

#### `delete_qdrant_point`

```python
def delete_qdrant_point(identifier: str) -> None
```

Delete bed file from qdrant.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.exists"></a>

#### `exists`

```python
def exists(identifier: str) -> bool
```

Check if bed file exists in the database.

**Parameters:**

- `identifier` (*str*): Bed file identifier.

**Returns:**

- *bool*: True if bed file exists, False otherwise.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.exists_universe"></a>

#### `exists_universe`

```python
def exists_universe(identifier: str) -> bool
```

Check if universe exists in the database.

**Parameters:**

- `identifier` (*str*): Universe identifier.

**Returns:**

- *bool*: True if universe exists, False otherwise.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.add_universe"></a>

#### `add_universe`

```python
def add_universe(bedfile_id: str, bedset_id: str = None, construct_method: str = None) -> str
```

Add universe to the database.

**Parameters:**

- `bedfile_id` (*str*): Bed file identifier.
- `bedset_id` (*str*): Bedset identifier. (default: `None`)
- `construct_method` (*str*): Method used to construct the universe. (default: `None`)

**Returns:**

- *str*: Universe identifier.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.delete_universe"></a>

#### `delete_universe`

```python
def delete_universe(identifier: str) -> None
```

Delete universe from the database.

**Parameters:**

- `identifier` (*str*): Universe identifier.

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.add_tokenized"></a>

#### `add_tokenized`

```python
def add_tokenized(bed_id: str, universe_id: str, token_vector: list, overwrite: bool = False) -> str
```

Add tokenized bed file to the database.

**Parameters:**

- `bed_id` (*str*): Bed file identifier.
- `universe_id` (*str*): Universe identifier.
- `token_vector` (*list*): List of tokens.
- `overwrite` (*bool*): Overwrite tokenized file if it already exists. (default: `False`)

**Returns:**

- *str*: Token path.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_tokenized"></a>

#### `get_tokenized`

```python
def get_tokenized(bed_id: str, universe_id: str) -> TokenizedBedResponse
```

Get zarr file from the database.

**Parameters:**

- `bed_id` (*str*): Bed file identifier.
- `universe_id` (*str*): Universe identifier.

**Returns:**

- *TokenizedBedResponse*: Zarr path.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.delete_tokenized"></a>

#### `delete_tokenized`

```python
def delete_tokenized(bed_id: str, universe_id: str) -> None
```

Delete tokenized bed file from the database.

**Parameters:**

- `bed_id` (*str*): Bed file identifier.
- `universe_id` (*str*): Universe identifier.

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.exist_tokenized"></a>

#### `exist_tokenized`

```python
def exist_tokenized(bed_id: str, universe_id: str) -> bool
```

Check if tokenized bed file exists in the database.

**Parameters:**

- `bed_id` (*str*): Bed file identifier.
- `universe_id` (*str*): Universe identifier.

**Returns:**

- *bool*: True if tokenized bed file exists, False otherwise.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_tokenized_link"></a>

#### `get_tokenized_link`

```python
def get_tokenized_link(bed_id: str, universe_id: str) -> TokenizedPathResponse
```

Get tokenized link to tokenized file.

**Parameters:**

- `bed_id` (*str*): Bed file identifier.
- `universe_id` (*str*): Universe identifier.

**Returns:**

- *TokenizedPathResponse*: Token link.

**Raises:**

- *TokenizeFileNotExistError*: If the tokenized file does not exist.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_missing_plots"></a>

#### `get_missing_plots`

```python
def get_missing_plots(plot_name: str, limit: int = 1000, offset: int = 0) -> list[str]
```

Get list of bed files that are missing plot.

**Parameters:**

- `plot_name` (*str*): Plot name.
- `limit` (*int*): Number of results to return. (default: `1000`)
- `offset` (*int*): Offset to start from. (default: `0`)

**Returns:**

- *list[str]*: List of bed file identifiers.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_missing_stats"></a>

#### `get_missing_stats`

```python
def get_missing_stats(limit: int = 1000, offset: int = 0) -> list[str]
```

Get list of bed files that are missing statistics.

**Parameters:**

- `limit` (*int*): Number of results to return. (default: `1000`)
- `offset` (*int*): Offset to start from. (default: `0`)

**Returns:**

- *list[str]*: List of bed file identifiers.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_missing_files"></a>

#### `get_missing_files`

```python
def get_missing_files(limit: int = 1000, offset: int = 0) -> list[str]
```

Get list of bed files that are missing files (bigBed files).

**Parameters:**

- `limit` (*int*): Number of results to return. (default: `1000`)
- `offset` (*int*): Offset to start from. (default: `0`)

**Returns:**

- *list[str]*: List of bed file identifiers.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.get_unprocessed"></a>

#### `get_unprocessed`

```python
def get_unprocessed(limit: int = 1000, offset: int = 0, genome: str | list | None = None) -> BedListResult
```

Get bed files that are not processed.

**Parameters:**

- `limit` (*int*): Number of results to return. (default: `1000`)
- `offset` (*int*): Offset to start from. (default: `0`)
- `genome` (*str | list | None*): Genome alias or list of genome aliases to filter by. e.g. "hg38" or
  ["hg38", "mm10"]. By default None, which means no filtering by genome. (default: `None`)

**Returns:**

- *BedListResult*: List of bed file identifiers.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.reindex_hybrid_search"></a>

#### `reindex_hybrid_search`

```python
def reindex_hybrid_search(batch: int = 1000, purge: bool = False) -> None
```

Reindex all bed files for semantic database.

**Parameters:**

- `batch` (*int*): Number of files to upload in one batch. (default: `1000`)
- `purge` (*bool*): Resets indexed in database for all files to False. (default: `False`)

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.hybrid_search"></a>

#### `hybrid_search`

```python
def hybrid_search(query: str = 'liver', genome_alias: str = '', assay: str = '', limit: int = 100, offset: int = 0, with_metadata: bool = True) -> BedListSearchResult
```

Run semantic search for bed files using qdrant.
This is not bivec search, but usual qdrant search with sparse and dense embeddings.

**Parameters:**

- `query` (*str*): Text query to search for. (default: `'liver'`)
- `genome_alias` (*str*): Genome alias to filter results. (default: `''`)
- `assay` (*str*): Filter by assay type. (default: `''`)
- `limit` (*int*): Number of results to return. (default: `100`)
- `offset` (*int*): Offset to start from. (default: `0`)
- `with_metadata` (*bool*): If True, metadata will be returned in the results. Default is True. (default: `True`)

**Returns:**

- *BedListSearchResult*: List of bed file metadata.

<a id="bbconf.modules.bedfiles.BedAgentBedFile.search_external_file"></a>

#### `search_external_file`

```python
def search_external_file(source: str, accession: str) -> BedListSearchResult
```

Search for bed files by external source and accession number.
e.g. source='geo', accession='GSE12345'.

**Parameters:**

- `source` (*str*): External source, e.g. 'geo' or 'encode'.
- `accession` (*str*): Accession number, e.g. 'GSE12345' or 'ENCSR12345'.

**Returns:**

- *BedListSearchResult*: List of bed file metadata.

<a id="bbconf.modules.bedsets.BedAgentBedSet"></a>

## `BedAgentBedSet`

```python
class BedAgentBedSet(config: BedBaseConfig)
```

Class that represents Bedset in Database.

This class has method to add, delete, get files and metadata from the database.

Initialize BedAgentBedSet.

**Parameters:**

- `config` (*BedBaseConfig*): Config object.

### Attributes

- <a id="bbconf.modules.bedsets.BedAgentBedSet.config"></a>**`config`**

### Methods

<a id="bbconf.modules.bedsets.BedAgentBedSet.get"></a>

#### `get`

```python
def get(identifier: str, full: bool = False) -> BedSetMetadata
```

Get file metadata by identifier.

**Parameters:**

- `identifier` (*str*): Bed file identifier.
- `full` (*bool*): Return full record with stats, plots, files and metadata. (default: `False`)

**Returns:**

- *BedSetMetadata*: BED file metadata.

<a id="bbconf.modules.bedsets.BedAgentBedSet.get_plots"></a>

#### `get_plots`

```python
def get_plots(identifier: str) -> BedSetPlots
```

Get plots for bedset by identifier.

**Parameters:**

- `identifier` (*str*): Bedset identifier.

**Returns:**

- *BedSetPlots*: Bedset plots.

<a id="bbconf.modules.bedsets.BedAgentBedSet.get_objects"></a>

#### `get_objects`

```python
def get_objects(identifier: str) -> dict[str, FileModel]
```

Get objects for bedset by identifier.

**Parameters:**

- `identifier` (*str*): Bedset identifier.

**Returns:**

- *dict[str, FileModel]*: Bedset objects.

<a id="bbconf.modules.bedsets.BedAgentBedSet.get_statistics"></a>

#### `get_statistics`

```python
def get_statistics(identifier: str) -> BedSetStats
```

Get statistics for bedset by identifier.

**Parameters:**

- `identifier` (*str*): Bedset identifier.

**Returns:**

- *BedSetStats*: Bedset statistics.

<a id="bbconf.modules.bedsets.BedAgentBedSet.get_bedset_pep"></a>

#### `get_bedset_pep`

```python
def get_bedset_pep(identifier: str) -> dict
```

Create pep file for a bedset.

**Parameters:**

- `identifier` (*str*): Bedset identifier.

**Returns:**

- *dict*: Pep dict.

<a id="bbconf.modules.bedsets.BedAgentBedSet.get_track_hub_file"></a>

#### `get_track_hub_file`

```python
def get_track_hub_file(identifier: str) -> str
```

Get track hub file for bedset.

**Parameters:**

- `identifier` (*str*): Bedset identifier.

**Returns:**

- *str*: Track hub file.

<a id="bbconf.modules.bedsets.BedAgentBedSet.create"></a>

#### `create`

```python
def create(identifier: str, name: str, bedid_list: list[str], description: str | None = None, statistics: bool = False, annotation: dict | None = None, plots: dict | None = None, upload_s3: bool = False, local_path: str = '', no_fail: bool = False, overwrite: bool = False, processed: bool = True) -> None
```

Create bedset in the database.

**Parameters:**

- `identifier` (*str*): Bedset identifier.
- `name` (*str*): Bedset name.
- `description` (*str | None*): Bedset description. (default: `None`)
- `bedid_list` (*list[str]*): List of bed file identifiers.
- `statistics` (*bool*): Calculate statistics for bedset. (default: `False`)
- `annotation` (*dict | None*): Bedset annotation (author, source). (default: `None`)
- `plots` (*dict | None*): Dictionary with plots. (default: `None`)
- `upload_s3` (*bool*): Upload bedset to s3. (default: `False`)
- `local_path` (*str*): Local path to the output files. (default: `''`)
- `no_fail` (*bool*): Do not raise an error if bedset already exists. (default: `False`)
- `overwrite` (*bool*): Overwrite the record in the database. (default: `False`)
- `processed` (*bool*): Flag to indicate that bedset is processed. [Default: True]. (default: `True`)

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedsets.BedAgentBedSet.get_ids_list"></a>

#### `get_ids_list`

```python
def get_ids_list(query: str | None = None, limit: int = 10, offset: int = 0) -> BedSetListResult
```

Find (search) bedsets from the database.

Use `get(identifier)` to
    fetch a single bedset's member ids. `bedfile_count` is populated
    directly from the denormalized column, so it's free.

**Parameters:**

- `query` (*str | None*): Search query. (default: `None`)
- `limit` (*int*): Limit of results. (default: `10`)
- `offset` (*int*): Offset of results. (default: `0`)

**Returns:**

- *BedSetListResult*: List of bedsets.

<a id="bbconf.modules.bedsets.BedAgentBedSet.get_bedset_bedfiles"></a>

#### `get_bedset_bedfiles`

```python
def get_bedset_bedfiles(identifier: str) -> BedSetBedFiles
```

Get list of bedfiles in bedset.

**Parameters:**

- `identifier` (*str*): Bedset identifier.

**Returns:**

- *BedSetBedFiles*: List of bedfiles.

<a id="bbconf.modules.bedsets.BedAgentBedSet.delete"></a>

#### `delete`

```python
def delete(identifier: str) -> None
```

Delete bed file from the database.

**Parameters:**

- `identifier` (*str*): Bedset identifier.

**Returns:**

- *None*: None.

<a id="bbconf.modules.bedsets.BedAgentBedSet.exists"></a>

#### `exists`

```python
def exists(identifier: str) -> bool
```

Check if bedset exists in the database.

**Parameters:**

- `identifier` (*str*): Bedset identifier.

**Returns:**

- *bool*: True if bedset exists, False otherwise.

<a id="bbconf.modules.bedsets.BedAgentBedSet.get_unprocessed"></a>

#### `get_unprocessed`

```python
def get_unprocessed(limit: int = 100, offset: int = 0) -> BedSetListResult
```

Get unprocessed bedset from the database.

**Parameters:**

- `limit` (*int*): Limit of results. (default: `100`)
- `offset` (*int*): Offset of results. (default: `0`)

**Returns:**

- *BedSetListResult*: Bedset metadata.

<a id="bbconf.modules.bedsets.BedAgentBedSet.add_bedfile"></a>

#### `add_bedfile`

```python
def add_bedfile(identifier: str, bedfile: str) -> None
```

<a id="bbconf.modules.bedsets.BedAgentBedSet.delete_bedfile"></a>

#### `delete_bedfile`

```python
def delete_bedfile(identifier: str, bedfile: str) -> None
```

<a id="bbconf.modules.objects.BBObjects"></a>

## `BBObjects`

```python
class BBObjects(config: BedBaseConfig)
```

Initialize BBObjects.

**Parameters:**

- `config` (*BedBaseConfig*): Config object.

### Attributes

- <a id="bbconf.modules.objects.BBObjects.config"></a>**`config`**
- <a id="bbconf.modules.objects.BBObjects.bed"></a>**`bed`**
- <a id="bbconf.modules.objects.BBObjects.bedset"></a>**`bedset`**

### Methods

<a id="bbconf.modules.objects.BBObjects.get_thumbnail_uri"></a>

#### `get_thumbnail_uri`

```python
def get_thumbnail_uri(record_type: Literal['bed', 'bedset'], record_id: str, result_id: str, access_id: str = 'http') -> str
```

Create URL to access a bed- or bedset-associated thumbnail.

**Parameters:**

- `record_type` (*Literal['bed', 'bedset']*): Table name ["bed", "bedset"].
- `record_id` (*str*): Record identifier.
- `result_id` (*str*): Column name (result name).
- `access_id` (*str*): Access id (e.g. http, s3, etc.). (default: `'http'`)

**Returns:**

- *str*: String with thumbnail.

<a id="bbconf.modules.objects.BBObjects.get_object_uri"></a>

#### `get_object_uri`

```python
def get_object_uri(record_type: Literal['bed', 'bedset'], record_id: str, result_id: str, access_id: str) -> str
```

Create URL to access a bed- or bedset-associated file.

**Parameters:**

- `record_type` (*Literal['bed', 'bedset']*): Table name ["bed", "bedset"].
- `record_id` (*str*): Record identifier.
- `result_id` (*str*): Column name (result name).
- `access_id` (*str*): Access id (e.g. http, s3, etc.).

**Returns:**

- *str*: URI string for the object.

<a id="bbconf.modules.objects.BBObjects.get_drs_metadata"></a>

#### `get_drs_metadata`

```python
def get_drs_metadata(record_type: Literal['bed', 'bedset'], record_id: str, result_id: str, base_uri: str) -> DRSModel
```

Get DRS metadata for a bed- or bedset-associated file.

**Parameters:**

- `record_type` (*Literal['bed', 'bedset']*): Bed or bedset.
- `record_id` (*str*): Record identifier.
- `result_id` (*str*): Name of the result file to get metadata for.
- `base_uri` (*str*): Base uri to use for the self_uri field (server hostname of DRS broker).

**Returns:**

- *DRSModel*: DRS metadata.

<a id="bbconf.modules.objects.BBObjects.construct_drs_metadata"></a>

#### `construct_drs_metadata`

```python
def construct_drs_metadata(base_uri: str, object_id: str, record_metadata: FileModel, created_time: datetime.datetime | None = None, modified_time: datetime.datetime | None = None) -> DRSModel
```

Construct DRS metadata object.

**Parameters:**

- `base_uri` (*str*): Base uri to use for the self_uri field (server hostname of DRS broker).
- `object_id` (*str*): Record identifier.
- `record_metadata` (*FileModel*): Metadata of the record.
- `created_time` (*datetime.datetime | None*): Time of creation. (default: `None`)
- `modified_time` (*datetime.datetime | None*): Time of last modification. (default: `None`)

**Returns:**

- *DRSModel*: DRS metadata.

<a id="bbconf.modules.snapshots.BedAgentSnapshot"></a>

## `BedAgentSnapshot`

```python
class BedAgentSnapshot(config: BedBaseConfig)
```

Class that manages bulk-export snapshots (the `bed_snapshots` index).

One row per published artifact (metadata / bedsets / bedset_membership /
manifest). Adding a snapshot always uploads the file to S3 *and* records it
in the database; both writes live here in bbconf. This class also exposes
read (`list` / `get`) and `delete` helpers.

Initialize BedAgentSnapshot.

**Parameters:**

- `config` (*BedBaseConfig*): Config object.

### Attributes

- <a id="bbconf.modules.snapshots.BedAgentSnapshot.config"></a>**`config`**

### Methods

<a id="bbconf.modules.snapshots.BedAgentSnapshot.add"></a>

#### `add`

```python
def add(artifacts: BedSnapshotArtifact | list[BedSnapshotArtifact], creation_date: datetime | None = None) -> BedSnapshotListResult
```

Add snapshot artifacts: upload each to S3 and record it in the database.

Every artifact is uploaded under the fixed `snapshot/` prefix and then
recorded in `bed_snapshots`. The index rows are written only after all
uploads succeed, so a partial upload never leaves dangling rows.

**Parameters:**

- `artifacts` (*BedSnapshotArtifact | list[BedSnapshotArtifact]*): One artifact or a list of them. Each carries the local
  `path` to upload plus its `file_type` and file metadata.
- `creation_date` (*datetime | None*): Build date recorded on every row
  (defaults to now, UTC). (default: `None`)

**Returns:**

- *BedSnapshotListResult*: The created snapshot rows.

<a id="bbconf.modules.snapshots.BedAgentSnapshot.delete"></a>

#### `delete`

```python
def delete(id: int, remove_s3: bool = True) -> None
```

Delete a snapshot index row.

**Parameters:**

- `id` (*int*): Primary key of the snapshot row.
- `remove_s3` (*bool*): Also delete the underlying S3 object. (default: `True`)

**Returns:**

- *None*: None.

**Raises:**

- *SnapshotNotFoundError*: If no row with this id exists.

<a id="bbconf.modules.snapshots.BedAgentSnapshot.list"></a>

#### `list`

```python
def list(file_type: str | None = None, limit: int | None = 100, offset: int = 0) -> BedSnapshotListResult
```

List all snapshot index rows in the database, newest first.

**Parameters:**

- `file_type` (*str | None*): Optional filter on file type. (default: `None`)
- `limit` (*int | None*): Maximum number of rows to return. `None` returns all rows. (default: `100`)
- `offset` (*int*): Number of rows to skip. (default: `0`)

**Returns:**

- *BedSnapshotListResult*: List of snapshots and the total matching count.

<a id="bbconf.modules.snapshots.BedAgentSnapshot.get_by_filename"></a>

#### `get_by_filename`

```python
def get_by_filename(filename: str) -> BedSnapshotResult
```

Resolve a snapshot by its file name (the basename of its S3 key).

Returns the newest row whose `file_path` basename equals `filename`.
Used to round-trip an export's DRS object-id back to its row.

**Parameters:**

- `filename` (*str*): The bare file name, e.g.
  `bedbase_metadata_2026_08_03.parquet`.

**Returns:**

- *BedSnapshotResult*: The matching snapshot row.

**Raises:**

- *SnapshotNotFoundError*: If no row matches.

<a id="bbconf.modules.snapshots.BedAgentSnapshot.delete_by_checksum"></a>

#### `delete_by_checksum`

```python
def delete_by_checksum(checksum: str, remove_s3: bool = True) -> None
```

Delete snapshot index rows by their checksum.

Deletes every `bed_snapshots` row whose `checksum` matches (a checksum
identifies one file's content) and optionally removes the underlying S3
objects.

**Parameters:**

- `checksum` (*str*): SHA256 checksum of the snapshot file.
- `remove_s3` (*bool*): Also delete the underlying S3 object(s). (default: `True`)

**Returns:**

- *None*: None.

**Raises:**

- *SnapshotNotFoundError*: If no row matches the checksum.

<a id="bbconf.modules.snapshots.BedAgentSnapshot.get"></a>

#### `get`

```python
def get(id: int) -> BedSnapshotResult
```

Get a single snapshot index row by id.

**Parameters:**

- `id` (*int*): Primary key of the snapshot row.

**Returns:**

- *BedSnapshotResult*: The snapshot row.

**Raises:**

- *SnapshotNotFoundError*: If no row with this id exists.

<a id="bbconf.modules.analysis_files.BedAgentAnalysisFile"></a>

## `BedAgentAnalysisFile`

```python
class BedAgentAnalysisFile(config: BedBaseConfig)
```

Class that manages standalone analysis files (the `analysis_files` index).

One row per uploaded file (openSignalMatrix, models, other analysis inputs).
These files are global: they are not tied to any bed file or bedset. Adding
a file always uploads it to S3 *and* records it in the database; both writes
live here in bbconf. This class also exposes read (`list` / `get` /
`get_by_name` / `get_by_filename`) and `delete` helpers.

Initialize BedAgentAnalysisFile.

**Parameters:**

- `config` (*BedBaseConfig*): Config object.

### Attributes

- <a id="bbconf.modules.analysis_files.BedAgentAnalysisFile.config"></a>**`config`**

### Methods

<a id="bbconf.modules.analysis_files.BedAgentAnalysisFile.add"></a>

#### `add`

```python
def add(artifacts: AnalysisFileArtifact | list[AnalysisFileArtifact], creation_date: datetime | None = None) -> AnalysisFileListResult
```

Add analysis files: upload each to S3 and record it in the database.

Every artifact is uploaded under the fixed `analysis_files/` prefix and
then recorded in `analysis_files`. The index rows are written only
after all uploads succeed, so a partial upload never leaves dangling
rows.

**Parameters:**

- `artifacts` (*AnalysisFileArtifact | list[AnalysisFileArtifact]*): One artifact or a list of them. Each carries the local
  `path` to upload plus its `name` and file metadata.
- `creation_date` (*datetime | None*): Upload date recorded on every row
  (defaults to now, UTC). (default: `None`)

**Returns:**

- *AnalysisFileListResult*: The created analysis-file rows.

<a id="bbconf.modules.analysis_files.BedAgentAnalysisFile.delete"></a>

#### `delete`

```python
def delete(id: int, remove_s3: bool = True) -> None
```

Delete an analysis-file index row.

**Parameters:**

- `id` (*int*): Primary key of the analysis-file row.
- `remove_s3` (*bool*): Also delete the underlying S3 object. (default: `True`)

**Returns:**

- *None*: None.

**Raises:**

- *AnalysisFileNotFoundError*: If no row with this id exists.

<a id="bbconf.modules.analysis_files.BedAgentAnalysisFile.list"></a>

#### `list`

```python
def list(file_type: str | None = None, genome: str | None = None, tag: str | None = None, limit: int | None = 100, offset: int = 0) -> AnalysisFileListResult
```

List analysis-file index rows in the database, newest first.

**Parameters:**

- `file_type` (*str | None*): Optional filter on file type. (default: `None`)
- `genome` (*str | None*): Optional filter on genome/assembly. (default: `None`)
- `tag` (*str | None*): Optional filter; keep only rows whose `tags` contain this tag. (default: `None`)
- `limit` (*int | None*): Maximum number of rows to return. `None` returns all rows. (default: `100`)
- `offset` (*int*): Number of rows to skip. (default: `0`)

**Returns:**

- *AnalysisFileListResult*: List of analysis files and the total matching count.

<a id="bbconf.modules.analysis_files.BedAgentAnalysisFile.get"></a>

#### `get`

```python
def get(id: int) -> AnalysisFileResult
```

Get a single analysis-file index row by id.

**Parameters:**

- `id` (*int*): Primary key of the analysis-file row.

**Returns:**

- *AnalysisFileResult*: The analysis-file row.

**Raises:**

- *AnalysisFileNotFoundError*: If no row with this id exists.

<a id="bbconf.modules.analysis_files.BedAgentAnalysisFile.get_by_name"></a>

#### `get_by_name`

```python
def get_by_name(name: str, genome: str | None = None) -> AnalysisFileResult
```

Resolve an analysis file by its logical name (newest matching row).

**Parameters:**

- `name` (*str*): Logical name/key, e.g. `openSignalMatrix`.
- `genome` (*str | None*): Optional genome/assembly to disambiguate, e.g. `hg38`. (default: `None`)

**Returns:**

- *AnalysisFileResult*: The newest matching analysis-file row.

**Raises:**

- *AnalysisFileNotFoundError*: If no row matches.

<a id="bbconf.modules.analysis_files.BedAgentAnalysisFile.get_by_filename"></a>

#### `get_by_filename`

```python
def get_by_filename(filename: str) -> AnalysisFileResult
```

Resolve an analysis file by its file name (the basename of its S3 key).

Returns the newest row whose `file_path` basename equals `filename`.
Used to round-trip a DRS object-id back to its row.

**Parameters:**

- `filename` (*str*): The bare file name, e.g. `openSignalMatrix_hg38.txt.gz`.

**Returns:**

- *AnalysisFileResult*: The matching analysis-file row.

**Raises:**

- *AnalysisFileNotFoundError*: If no row matches.

<a id="bbconf.modules.analysis_files.BedAgentAnalysisFile.delete_by_checksum"></a>

#### `delete_by_checksum`

```python
def delete_by_checksum(checksum: str, remove_s3: bool = True) -> None
```

Delete analysis-file index rows by their checksum.

Deletes every `analysis_files` row whose `checksum` matches (a
checksum identifies one file's content) and optionally removes the
underlying S3 objects.

**Parameters:**

- `checksum` (*str*): SHA256 checksum of the analysis file.
- `remove_s3` (*bool*): Also delete the underlying S3 object(s). (default: `True`)

**Returns:**

- *None*: None.

**Raises:**

- *AnalysisFileNotFoundError*: If no row matches the checksum.