diff --git a/bbconf/_version.py b/bbconf/_version.py index 3d26edf..df12433 100644 --- a/bbconf/_version.py +++ b/bbconf/_version.py @@ -1 +1 @@ -__version__ = "0.4.1" +__version__ = "0.4.2" diff --git a/bbconf/schemas/bedfiles_schema.yaml b/bbconf/schemas/bedfiles_schema.yaml index bfd1347..650c3b3 100644 --- a/bbconf/schemas/bedfiles_schema.yaml +++ b/bbconf/schemas/bedfiles_schema.yaml @@ -116,13 +116,12 @@ properties: $ref: "#/$defs/image" label: Open_chromatin description: Cell specific enrichment for open chromatin plot - added_to_qdrant: - type: boolean - label: Qdrant_status - description: whether the BED file is added to Qdrant other: type: object description: Other, not categorized BED file metadata + upload_status: + type: object + description: "Status of the upload to the databases: Dict[s3, qdrant, pephub]" $defs: diff --git a/docs/bbc_api.md b/docs/bbc_api.md deleted file mode 100644 index e933672..0000000 --- a/docs/bbc_api.md +++ /dev/null @@ -1,191 +0,0 @@ -Final targets: BedBaseConf, get_bedbase_cfg - - - - - -# Package `bbconf` Documentation - -## Class `BedBaseConf` -This class standardizes reporting of bedstat and bedbuncher results. It formalizes a way for these pipelines and downstream tools to communicate -- the produced results can easily and reliably become an input for the server. The object exposes API for interacting with the results and is backed by a [PostgreSQL](https://www.postgresql.org/) database. - - -```python -def __init__(self, config_path=None, database_only=False) -``` - -Initialize the object -#### Parameters: - -- `config_path` (`str`): path to the bedbase configuration file -- `database_only` (`bool`): whether the database managers should notkeep an in-memory copy of the data in the database - - - - -```python -def bed(self) -``` - -PipestatManager of the bedfiles table -#### Returns: - -- `pipestat.PipestatManager`: manager of the bedfiles table - - - - -```python -def bedset(self) -``` - -PipestatManager of the bedsets table -#### Returns: - -- `pipestat.PipestatManager`: manager of the bedsets table - - - - -```python -def config(self) -``` - -Config used to initialize the object -#### Returns: - -- `yacman.YacAttMap`: bedbase configuration file contents - - - - -```python -def get_bedbuncher_output_path(self, remote=False) -``` - -Get path to the output of the bedbuncher pipeline -#### Parameters: - -- `remote` (`bool`): whether to use remote url base - - -#### Returns: - -- `str`: path to the bedbuncher pipeline output - - - - -```python -def get_bedstat_output_path(self, remote=False) -``` - -Get path to the output of the bedstat pipeline -#### Parameters: - -- `remote` (`bool`): whether to use remote url base - - -#### Returns: - -- `str`: path to the bedstat pipeline output - - - - -```python -def remove_relationship(self, bedset_id, bedfile_ids=None) -``` - -Remove entries from the relationships table -#### Parameters: - -- `bedset_id` (`str`): id of the bedset to remove -- `bedfile_ids` (`list[str]`): ids of the bedfiles to remove for theselected bedset. If none provided, all the relationsips for the selected bedset will be removed. - - - - -```python -def report_relationship(self, bedset_id, bedfile_id) -``` - -Report a bedfile for bedset. - -Inserts the ID pair into the relationship table, which allows to -manage many to many bedfile bedset relationships -#### Parameters: - -- `bedset_id` (`int`): id of the bedset to report bedfile for -- `bedfile_id` (`int`): id of the bedfile to report - - - - -```python -def select_bedfiles_for_bedset(self, condition=None, condition_val=None, bedfile_col=None) -``` - -Select bedfiles that are part of a bedset that matches the query -#### Parameters: - -- `condition` (`str`): bedsets table query to restrict the results with,for instance `"id=%s"` -- `condition_val` (`list[str]`): values to populate the condition stringwith -- `bedfile_col` (`list[str] | str`): bedfile columns to include in theresult, if none specified all columns will be included - - -#### Returns: - -- `list[psycopg2.extras.DictRow]`: matched bedfiles table contents - - - - -```python -def get_bedbase_cfg(cfg=None) -``` - -Determine path to the bedbase configuration file - -The path can be either explicitly provided -or read from a $BEDBASE environment variable -#### Parameters: - -- `cfg` (`str`): path to the config file.Optional, the $BEDBASE config env var will be used if not provided - - -#### Returns: - -- `str`: configuration file path - - - - - - - -*Version Information: `bbconf` v0.1.0, generated by `lucidoc` v0.4.3* diff --git a/docs/changelog.md b/docs/changelog.md index 8c30fff..d15891c 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -2,10 +2,11 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. -## [0.4.2] - 2024-XX-XX +## [0.4.2] - 2024-03-12 ### Change - Updated logger - Updated requirements +- Added `upload_status` column to the `bedfile` table ## [0.4.1] - 2024-01-01