From 7d4f4df2e5bc063946077c95d5936ba51f0ee231 Mon Sep 17 00:00:00 2001
From: kedhammar <alfred.kedhammar@scilifelab.se>
Date: Tue, 9 Apr 2024 17:25:33 +0200
Subject: [PATCH] wip, perform demux and increase test cov by 5%

---
 taca/illumina/Standard_Runs.py  | 2 +-
 tests/analysis/test_analysis.py | 7 ++++++-
 tests/conftest.py               | 2 ++
 3 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/taca/illumina/Standard_Runs.py b/taca/illumina/Standard_Runs.py
index 08d6fdbc..ae49eaa2 100755
--- a/taca/illumina/Standard_Runs.py
+++ b/taca/illumina/Standard_Runs.py
@@ -429,7 +429,7 @@ def demultiplex_run(self):
                         f"started for run {os.path.basename(self.id)} on {datetime.now()}"
                     )
 
-                # Demutiplexing done for one mask type and scripts will continue
+                # Demultiplexing done for one mask type and scripts will continue
                 # Working with the next type. Command counter should increase by 1
                 bcl_cmd_counter += 1
         return True
diff --git a/tests/analysis/test_analysis.py b/tests/analysis/test_analysis.py
index c372e4f6..745402c6 100644
--- a/tests/analysis/test_analysis.py
+++ b/tests/analysis/test_analysis.py
@@ -392,7 +392,7 @@ def create_illumina_run_dir(
     if os.path.exists(run_path):
         shutil.rmtree(run_path)
     os.makedirs(run_path)
-    os.makedirs(os.path.join(run_path, "Demultiplexing"))
+    # os.makedirs(os.path.join(run_path, "Demultiplexing")) TODO
 
     # Set up files
     if completed:
@@ -562,3 +562,8 @@ def test_get_runObj(create_dirs):
     software = "bcl2fastq"
 
     _run_obj = analysis.get_runObj(run_path, software)
+
+    _mock_upload_to_db = patch("taca.analysis.analysis._upload_to_statusdb").start()
+    with patch("subprocess.Popen") as mock_Popen:
+        mock_Popen.start()
+        analysis.run_preprocessing(run_path, software)
diff --git a/tests/conftest.py b/tests/conftest.py
index 620bba93..2e7d02d5 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -17,6 +17,7 @@ def create_dirs():
         │   ├── transfer_minion_qc.tsv
         │   ├── transfer_minion.tsv
         │   └── transfer_promethion.tsv
+        │   └── transfer.tsv
         ├── miarka
         │   ├── minion
         │   │   └── qc
@@ -85,6 +86,7 @@ def create_dirs():
     open(f"{tmp.name}/log/transfer_promethion.tsv", "w").close()
     open(f"{tmp.name}/log/transfer_minion.tsv", "w").close()
     open(f"{tmp.name}/log/transfer_minion_qc.tsv", "w").close()
+    open(f"{tmp.name}/log/transfer.tsv", "w").close()
 
     # Analysis server destination dirs
     os.makedirs(f"{tmp.name}/miarka/promethion")