Merge pull request #73 from databio/dev

Release 0.4.0

Author: khoroshevskyi

MANIFEST.in

@@ -9,4 +9,5 @@ include bedboss/qdrant_index/*
 include bedboss/bedbuncher/*
 include bedboss/bedbuncher/tools/*
 include bedboss/bedclassifier/*
-include bedboss/tokens/*
+include bedboss/tokens/*
+include bedboss/bbuploader/*

bedboss/__init__.py

@@ -1,13 +1,12 @@
 """ Package-level data """
 
-import logmuse
-import coloredlogs
 import logging
 
+import coloredlogs
+import logmuse
 
 from bedboss._version import __version__
 
-
 __package_name__ = "bedboss"
 
 __author__ = [

bedboss/__main__.py

@@ -1,4 +1,5 @@
 import sys
+
 import logmuse
 
 from bedboss.cli import app

bedboss/_version.py

@@ -1 +1 @@
-__version__ = "0.3.0"
+__version__ = "0.4.0"

bedboss/bbuploader/__init__.py

@@ -0,0 +1,13 @@
+""" Package-level data """
+
+import coloredlogs
+import logmuse
+
+from bedboss.bbuploader.constants import PKG_NAME
+
+_LOGGER = logmuse.init_logger(PKG_NAME)
+coloredlogs.install(
+    logger=_LOGGER,
+    datefmt="%H:%M:%S",
+    fmt="[%(levelname)s] [%(asctime)s] [BBUPLOADER] %(message)s",
+)

bedboss/bbuploader/cli.py

@@ -0,0 +1,110 @@
+import typer
+from bedboss._version import __version__
+
+app_bbuploader = typer.Typer(
+    pretty_exceptions_short=False,
+    pretty_exceptions_show_locals=False,
+    help="Automatic BEDbase uploader for GEO data",
+)
+
+
+@app_bbuploader.command(
+    help="Run bedboss uploading pipeline for specified genome in specified period of time."
+)
+def upload_all(
+    bedbase_config: str = typer.Option(..., help="Path to bedbase config file"),
+    outfolder: str = typer.Option(..., help="Path to output folder"),
+    start_date: str = typer.Option(
+        None, help="The earliest date when opep was updated [Default: 2000/01/01]"
+    ),
+    end_date: str = typer.Option(
+        None, help="The latest date when opep was updated [Default: today's date]"
+    ),
+    search_limit: int = typer.Option(
+        10, help="Limit of projects to be searched. [Default: 10]"
+    ),
+    search_offset: int = typer.Option(
+        0, help="Limit of projects to be searched. [Default: 0]"
+    ),
+    download_limit: int = typer.Option(
+        100, help="Limit of projects to be downloaded [Default: 100]"
+    ),
+    genome: str = typer.Option(
+        None,
+        help="Reference genome [Default: None] (e.g. hg38) - if None, all genomes will be processed",
+    ),
+    create_bedset: bool = typer.Option(
+        True, help="Create bedset from bed files. [Default: True]"
+    ),
+    rerun: bool = typer.Option(True, help="Re-run all the samples. [Default: False]"),
+    run_skipped: bool = typer.Option(
+        True, help="Run skipped projects. [Default: False]"
+    ),
+    run_failed: bool = typer.Option(True, help="Run failed projects. [Default: False]"),
+):
+    from .main import upload_all as upload_all_function
+
+    upload_all_function(
+        bedbase_config=bedbase_config,
+        outfolder=outfolder,
+        start_date=start_date,
+        end_date=end_date,
+        search_limit=search_limit,
+        search_offset=search_offset,
+        download_limit=download_limit,
+        genome=genome,
+        create_bedset=create_bedset,
+        rerun=rerun,
+        run_skipped=run_skipped,
+        run_failed=run_failed,
+    )
+
+
+@app_bbuploader.command(help="Run bedboss uploading pipeline for GSE.")
+def upload_gse(
+    bedbase_config: str = typer.Option(..., help="Path to bedbase config file"),
+    outfolder: str = typer.Option(..., help="Path to output folder"),
+    gse: str = typer.Option(
+        ..., help="GSE number that can be found in pephub. eg. GSE123456"
+    ),
+    create_bedset: bool = typer.Option(
+        True, help="Create bedset from bed files. [Default: True]"
+    ),
+    genome: str = typer.Option(
+        None,
+        help=" reference genome to upload to database. If None, all genomes will be processed",
+    ),
+    rerun: bool = typer.Option(True, help="Re-run all the samples. [Default: False]"),
+    run_skipped: bool = typer.Option(
+        True, help="Run skipped projects. [Default: False]"
+    ),
+    run_failed: bool = typer.Option(True, help="Run failed projects. [Default: False]"),
+):
+    from .main import upload_gse as upload_gse_function
+
+    upload_gse_function(
+        bedbase_config=bedbase_config,
+        outfolder=outfolder,
+        gse=gse,
+        create_bedset=create_bedset,
+        genome=genome,
+        rerun=rerun,
+        run_skipped=run_skipped,
+        run_failed=run_failed,
+    )
+
+
+def version_callback(value: bool):
+    if value:
+        typer.echo(f"Bedboss version: {__version__}")
+        raise typer.Exit()
+
+
+@app_bbuploader.callback()
+def common(
+    ctx: typer.Context,
+    version: bool = typer.Option(
+        None, "--version", "-v", callback=version_callback, help="App version"
+    ),
+):
+    pass

bedboss/bbuploader/constants.py

@@ -0,0 +1,13 @@
+PKG_NAME = "bbuploader"
+
+FILE_FOLDER_NAME = "files"
+
+DEFAULT_GEO_TAG = "samples"
+
+
+class STATUS:
+    SUCCESS = "SUCCESS"
+    FAIL = "FAIL"
+    PARTIAL = "PARTIAL"
+    PROCESSING = "PROCESSING"
+    SKIPPED = "SKIPPED"