From a2841739d027c4253f0fa7f2798207d16773c680 Mon Sep 17 00:00:00 2001
From: Sebastian Diaz <juan.sebastian.diaz.boada@scilifelab.se>
Date: Wed, 7 Aug 2024 12:01:55 +0200
Subject: [PATCH] Add sequencing times for PacBio run (#3530)(patch)

## Description
Add the following fields to the `PacBioSequencingRun` db model:
- run_started_at
- run_completed_at

Remove `movie_time_hours`

Create the alembic migration
---
 ...17cf7fea40d_add_sequencing_times_pacbio.py | 37 +++++++++++++++++++
 cg/store/models.py                            |  3 +-
 2 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100644 alembic/versions/2024_08_07_817cf7fea40d_add_sequencing_times_pacbio.py

diff --git a/alembic/versions/2024_08_07_817cf7fea40d_add_sequencing_times_pacbio.py b/alembic/versions/2024_08_07_817cf7fea40d_add_sequencing_times_pacbio.py
new file mode 100644
index 0000000000..6820adfa47
--- /dev/null
+++ b/alembic/versions/2024_08_07_817cf7fea40d_add_sequencing_times_pacbio.py
@@ -0,0 +1,37 @@
+"""Add sequencing times PacBio
+
+Revision ID: 817cf7fea40d
+Revises: 601a2f272754
+Create Date: 2024-08-07 10:19:57.450266
+
+"""
+
+import sqlalchemy as sa
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "817cf7fea40d"
+down_revision = "601a2f272754"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.add_column(
+        "pacbio_sequencing_run", sa.Column("run_started_at", sa.DateTime(), nullable=True)
+    )
+    op.add_column(
+        "pacbio_sequencing_run",
+        sa.Column("run_completed_at", sa.DateTime(), nullable=True),
+    )
+    op.drop_column("pacbio_sequencing_run", "movie_time_hours")
+
+
+def downgrade():
+    op.add_column(
+        "pacbio_sequencing_run",
+        sa.Column("movie_time_hours", sa.Integer(), nullable=True),
+    )
+    op.drop_column("pacbio_sequencing_run", "run_completed_at")
+    op.drop_column("pacbio_sequencing_run", "run_started_at")
diff --git a/cg/store/models.py b/cg/store/models.py
index 0a266ac1d9..be739d2fd3 100644
--- a/cg/store/models.py
+++ b/cg/store/models.py
@@ -1089,7 +1089,8 @@ class PacBioSequencingRun(InstrumentRun):
     id: Mapped[int] = mapped_column(ForeignKey("instrument_run.id"), primary_key=True)
     well: Mapped[Str32]
     plate: Mapped[int]
-    movie_time_hours: Mapped[int]
+    started_at: Mapped[datetime | None]
+    completed_at: Mapped[datetime | None]
     movie_name: Mapped[Str32]
     hifi_reads: Mapped[BigInt]
     hifi_yield: Mapped[BigInt]