From 99698bd4189985c3d5f2bfcc5b6a36bfcffa4f76 Mon Sep 17 00:00:00 2001
From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com>
Date: Thu, 1 Feb 2024 15:47:01 -0500
Subject: [PATCH] add upload_pephub cli argument
 https://github.com/databio/bedboss/issues/31

---
 bedboss/bedboss.py         |  3 +++
 bedboss/bedstat/bedstat.py |  1 -
 bedboss/cli.py             | 10 ++++++++++
 3 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/bedboss/bedboss.py b/bedboss/bedboss.py
index faf0ea5..bc83dd6 100644
--- a/bedboss/bedboss.py
+++ b/bedboss/bedboss.py
@@ -223,6 +223,7 @@ def insert_pep(
     no_db_commit: bool = False,
     force_overwrite: bool = False,
     upload_s3: bool = False,
+    upload_pephub: bool = False,
     pm: pypiper.PipelineManager = None,
     *args,
     **kwargs,
@@ -244,6 +245,7 @@ def insert_pep(
     :param bool no_db_commit: whether the JSON commit to the database should be skipped
     :param bool force_overwrite: whether to overwrite the existing record
     :param bool upload_s3: whether to upload to s3
+    :param bool upload_pephub: whether to push bedfiles and metadata to pephub (default: False)
     :param pypiper.PipelineManager pm: pypiper object
     :return: None
     """
@@ -295,6 +297,7 @@ def insert_pep(
             force_overwrite=force_overwrite,
             skip_qdrant=skip_qdrant,
             upload_s3=upload_s3,
+            upload_pephub=upload_pephub,
             pm=pm,
         )
         pep.samples[i].record_identifier = bed_id
diff --git a/bedboss/bedstat/bedstat.py b/bedboss/bedstat/bedstat.py
index 727c0b4..4e1e1f1 100755
--- a/bedboss/bedstat/bedstat.py
+++ b/bedboss/bedstat/bedstat.py
@@ -59,7 +59,6 @@ def load_to_pephub(
     """
 
     if is_registry_path(pep_registry_path):
-
         parsed_pep_list = parse_registry_path(pep_registry_path)
 
         # Combine data into a dict for sending to pephub
diff --git a/bedboss/cli.py b/bedboss/cli.py
index 2d161ef..116f57f 100644
--- a/bedboss/cli.py
+++ b/bedboss/cli.py
@@ -166,6 +166,11 @@ def build_argparser() -> ArgumentParser:
         action="store_true",
         help="whether to skip qdrant indexing",
     )
+    sub_all.add_argument(
+        "--upload-pephub",
+        action="store_true",
+        help="upload to pephub",
+    )
 
     # all-pep
     sub_all_pep.add_argument(
@@ -245,6 +250,11 @@ def build_argparser() -> ArgumentParser:
         "Before uploading you have to set up all necessury env vars: "
         "AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, and AWS_ENDPOINT_URL. [Default: False]",
     )
+    sub_all_pep.add_argument(
+        "--upload-pephub",
+        action="store_true",
+        help="upload to pephub",
+    )
 
     # bed_qc
     sub_qc.add_argument(