Merge pull request #118 from databio/dev

Release 0.7.1

Author: khoroshevskyi

bedboss/_version.py

@@ -1 +1 @@
-__version__ = "0.7.0"
+__version__ = "0.7.1"

bedboss/bedboss.py

@@ -466,6 +466,8 @@ def insert_pep(
     m.print_error(f"Failed samples: {failed_samples}")
     if stop_pipeline:
         pm.stop_pipeline()
+
+    m.print_success(f"Processing of '{pep.name}' completed successfully")
     return None
 
 

bedboss/bedmaker/bedmaker.py

@@ -13,21 +13,17 @@
 
 from bedboss.bedclassifier.bedclassifier import get_bed_classification
 from bedboss.bedmaker.const import (
-    BED_TO_BIGBED_PROGRAM,
     BEDGRAPH_TEMPLATE,
     BIGBED_FILE_NAME,
     BIGBED_TEMPLATE,
     BIGBED_TO_BED_PROGRAM,
     BIGWIG_TEMPLATE,
-    QC_FOLDER_NAME,
     WIG_TEMPLATE,
 )
 from bedboss.const import MAX_FILE_SIZE, MAX_REGION_NUMBER, MIN_REGION_WIDTH
 from bedboss.bedmaker.models import BedMakerOutput, InputTypes
 from bedboss.bedmaker.utils import get_chrom_sizes
-from bedboss.bedqc.bedqc import bedqc
 from bedboss.exceptions import BedBossException, RequirementsException, QualityException
-from bedboss.utils import cleanup_pm_temp
 
 _LOGGER = logging.getLogger("bedboss")
 
@@ -132,7 +128,7 @@ def make_bed(
             bed_obj = bbclient.add_bed_to_cache(input_file)
             bed_id = bed_obj.identifier
             output_path = bbclient.seek(bed_id)
-        except FileNotFoundError as e:
+        except BaseException as e:
             raise BedBossException(f"File not found: {input_file} Error: {e}")
 
     else:

bedboss/cli.py

@@ -197,6 +197,14 @@ def run_pep(
     """
     from bedboss.bedboss import insert_pep
 
+    pm = create_pm(
+        outfolder=outfolder,
+        multi=multi,
+        recover=recover,
+        dirty=dirty,
+        pipeline_name=pep.replace("/", "_").replace(":", "_"),
+    )
+
     insert_pep(
         bedbase_config=bedbase_config,
         output_folder=outfolder,
@@ -218,15 +226,11 @@ def run_pep(
         standardize_pep=standardize_pep,
         lite=lite,
         rerun=rerun,
-        pm=create_pm(
-            outfolder=outfolder,
-            multi=multi,
-            recover=recover,
-            dirty=dirty,
-            pipeline_name=pep.replace("/", "_").replace(":", "_"),
-        ),
+        pm=pm,
     )
 
+    pm.stop_pipeline()
+
 
 @app.command(help="Run unprocessed files, or reprocess them")
 def reprocess_all(

requirements/requirements-all.txt

@@ -5,7 +5,7 @@ peppy>=0.40.7
 yacman>=0.8.4
 requests>=2.28.2
 piper>=v0.14.3
-bbconf>=0.11.0
+bbconf>=0.11.1
 # bbconf @ git+https://github.com/databio/bbconf.git@new_bed_compilance#egg=bbconf
 refgenconf>=0.12.2
 pandas>=2.0.0

scripts/bbuploader/main.py

@@ -40,12 +40,12 @@ def another_test():
 
     time1 = time.time()
     upload_gse(
-        gse="gse261411",
+        # gse="gse261411",
         # gse="gse261536",
         # gse="gse274130",
         # Genome hg19 and mm10
         # gse="gse280839",
-        # gse="gse246900",  ## -- this is good. allways using it
+        gse="gse246900",  ## -- this is good. allways using it
         # gse="gse106049",  # This is interesting reference genome.
         # gse="gse292153",  # This is interesting reference genome.
         # gse="gse247593", # Big dataset
@@ -60,7 +60,7 @@ def another_test():
         bedbase_config="/home/bnt4me/virginia/repos/bbuploader/config_db_local.yaml",
         outfolder="/home/bnt4me/virginia/repos/bbuploader/data",
         # genome="HG38",
-        # rerun=True,
+        rerun=True,
         run_failed=True,
         run_skipped=True,
         reinit_skipper=True,
@@ -73,11 +73,12 @@ def another_test():
 
 
 if __name__ == "__main__":
-    runn()
+    # runn()
 
-    # another_test()
+    another_test()
     # upload_time()
 
 ## cmd
 # bedboss geo upload-all --outfolder /home/bnt4me/virginia/repos/bbuploader/data --start-date 2025/02/23 --end-date 2025/02/26 --no-use-skipper --lite --bedbase-config /home/bnt4me/virginia/repos/bbuploader/config_db_local.yaml --no-use-skipper --no-preload
 ##
+# bedboss run-pep --pep databio/excluderanges:default --outfolder /home/bnt4me/virginia/bedbase_output/ --bedbase-config /home/bnt4me/virginia/repos/bbuploader/config_db_local.yaml