Merge pull request #74 from databio/dev

Release v0.10.1

bbconf/_version.py

@@ -1 +1 @@
-__version__ = "0.10.0"
+__version__ = "0.10.1"

bbconf/db_utils.py

@@ -445,6 +445,7 @@ class GeoGseStatus(Base):
     gsm_status_mapper: Mapped[List["GeoGsmStatus"]] = relationship(
         "GeoGsmStatus", back_populates="gse_status_mapper"
     )
+    error: Mapped[str] = mapped_column(nullable=True, comment="Error message")
 
 
 class GeoGsmStatus(Base):
@@ -464,6 +465,12 @@ class GeoGsmStatus(Base):
     gse_status_mapper: Mapped["GeoGseStatus"] = relationship(
         "GeoGseStatus", back_populates="gsm_status_mapper"
     )
+    submission_date: Mapped[datetime.datetime] = mapped_column(
+        default=deliver_update_date, onupdate=deliver_update_date
+    )
+    bed_id: Mapped[str] = mapped_column(
+        nullable=True, index=True, comment="Bed identifier"
+    )
 
 
 class BaseEngine:

docs/changelog.md

@@ -2,44 +2,63 @@
 
 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.
 
+## [0.10.1] - 2025-01-07
 
-# [0.9.1] - 2024-XX-XX
-## Added
-- Search neighbours files for bed record
+### Changed:
+- Updated `geo_gsm_status` and `geo_gse_status` tables to include additional information.
 
 
-## Changed
-- Added trackHub file creation to bedset
+## [0.10.0] - 2025-01-03
 
-# [0.9.0] - 2024-11-06
-## Changed
-- Fixed bug with uploading tss dist plot
+### Added:
 
-## Added
+* Added a new method `get_neighbours` in `bbconf/modules/bedfiles.py` to retrieve the nearest neighbors of a bed file from Qdrant.
+* Added a new method `sql_search` in `bbconf/modules/bedfiles.py` for performing SQL exact searches on bed files.
+* Added a new method `get_track_hub_file` in `bbconf/modules/bedsets.py` to generate track hub files for bedsets.
+* Added `processed` for uploading bed files and bedsets
+* Added `update` bedfile method
+
+### Changed:
+* Updated exception handling in the `create` method of `bbconf/modules/bedsets.py` to provide more specific error messages.
+
+## [0.9.0] - 2024-11-07
+
+### Changed
+- Fixed bug with uploading tss dist plot\
+
+### Added
 - Added annotations to bedsets (author, source)
 - get_genome_list method to bedfiles, that lists all available genomes
 - Added method that lists all missing plots for bedfiles (get_missing_plots)
 
-# [0.8.0] - 2024-10-23
-## Changed
-- Updated text to bed search (now using bivec)
 
-## Added 
-- Creating a raw pep from bedset metadata
+## [0.8.0] - 2024-10-23
+## Added:
+- New text2vec search (bivec search)
+- Added get_pep to bedset methods
 
-# [0.7.0] - 2024-09-20
-## Added 
+## [0.7.1] - 2024-10-15
+
+### Added:
+- Added table with standardized bed annotation
+- Added table with bed reference genome prediction values.
+
+### Changed:
+- Updated requirements
+
+## [0.7.0] - 2024-09-20
+### Added 
 - Table and methods for reference genome validator
 - Table with standard metadata schema
 - Bed file opening improvements
 
-# [0.6.1] - 2024-08-21
-## Added 
+## [0.6.1] - 2024-08-21
+### Added 
 
 - DB tables for GEO uploader status
 
-# [0.6.0] - 2024-05-01
-## Added
+## [0.6.0] - 2024-05-01
+### Added
 
 - Added tokenized files and universes.
 - Added bed embedding get endpoint to the API #50
@@ -50,14 +69,14 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Many other small bug fixes
 
 
-# [0.5.1] - 2024-04-09
-## Changed
+## [0.5.1] - 2024-04-09
+### Changed
 
 - updated qdrant uploader
 - bedset bedfile list query improvement
 - other minor fixes in uploading
 
-# [0.5.0] - 2024-04-08
+## [0.5.0] - 2024-04-08
 ### Changed
 
 - Rebuild bbconf
@@ -129,4 +148,4 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [0.0.1] - 2020-02-05
 ### Added
-- initial project release
+- initial project release