Merge branch 'master' into dev-pacbio-flow

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 62.0.24
+current_version = 62.0.25
 commit = True
 tag = True
 tag_name = v{new_version}

alembic/versions/2024_07_29_0ca61967d364_add_comment_column_to_analysis_table.py

@@ -0,0 +1,28 @@
+"""Add comment column to analysis table
+
+Revision ID: 0ca61967d364
+Revises: 77a75121be31
+Create Date: 2024-07-29 10:43:06.444590
+
+"""
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "0ca61967d364"
+down_revision = "77a75121be31"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.add_column(
+        table_name="analysis",
+        column=sa.Column("comment", sa.Text(), nullable=True),
+    )
+
+
+def downgrade():
+    op.drop_column(table_name="analysis", column_name="comment")

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "62.0.24"
+__version__ = "62.0.25"

cg/meta/report/report_api.py

@@ -330,6 +330,7 @@ def get_case_analysis_data(self, case: Case, analysis: Analysis) -> DataAnalysis
             else None
         )
         return DataAnalysisModel(
+            comment=analysis.comment,
             customer_workflow=case.data_analysis,
             data_delivery=case.data_delivery,
             delivered_files=delivered_files,

cg/meta/report/templates/macros/data_analysis/data_analysis.html

@@ -53,12 +53,14 @@ <h4 class="mt-4 mb-3">Dataanalys</h4>
         <td>{{ workflow }} (v{{ case.data_analysis.workflow_version }})</td>
         <td>{{ case.data_analysis.genome_build }}</td>
         <td>{% if "balsamic" in workflow %} {{ case.data_analysis.type }} {% endif %}</td>
-        <td>{% if "balsamic" in workflow and case.data_analysis.pons != "N/A" %} {{ case.data_analysis.pons }} {% endif %}</th>
+        <td>{% if "balsamic" in workflow and case.data_analysis.pons != "N/A" %} {{ case.data_analysis.pons }} {% endif %}</td>
         <td class="text-start">{% if workflow in ("balsamic", "balsamic-umi") %} {{ case.data_analysis.variant_callers }} {% endif %}</td>
         <td>{% if workflow in ("mip-dna", "raredisease", "rnafusion", "tomte") %} {{ case.data_analysis.panels }} {% endif %}</td>
       </tr>
     </tbody>
   </table>
+	<!--Data analysis comment warning -->
+  {{ data_analysis_comment_alert(comment=case.data_analysis.comment) }}
   <!-- Data analysis alert component -->
   {{ data_analysis_alert(case=case) }}
 {% endmacro %}
@@ -97,3 +99,11 @@ <h4 class="mt-4 mb-3">Dataanalys</h4>
     </div>
   {% endif %}
 {% endmacro %}
+
+{% macro data_analysis_comment_alert(comment) %}
+	{% if comment != "N/A" %}
+	  <div class="alert alert-warning" role="alert">
+	    {{ comment }}
+	  </div>
+	{% endif %}
+{% endmacro %}

cg/models/report/report.py

@@ -62,6 +62,7 @@ class DataAnalysisModel(BaseModel):
     Model that describes the workflow attributes used for the data analysis
 
     Attributes:
+        comment: prod bioinfo comment regarding the data analysis; source: StatusDB/analysis/comment
         customer_workflow: data analysis requested by the customer; source: StatusDB/family/data_analysis
         data_delivery: data delivery requested by the customer; source: StatusDB/family/data_delivery
         delivered_files: list of analysis case files to be delivered
@@ -75,6 +76,7 @@ class DataAnalysisModel(BaseModel):
         workflow_version: workflow version; source: statusDB/analysis/workflow_version
     """
 
+    comment: Annotated[str, BeforeValidator(get_report_string)] = NA_FIELD
     customer_workflow: Annotated[str, BeforeValidator(get_report_string)] = NA_FIELD
     data_delivery: Annotated[str, BeforeValidator(get_report_string)] = NA_FIELD
     delivered_files: Annotated[

cg/server/admin.py

@@ -424,7 +424,7 @@ class AnalysisView(BaseView):
     """Admin view for Model.Analysis"""
 
     column_default_sort = ("created_at", True)
-    column_editable_list = ["is_primary"]
+    column_editable_list = ["is_primary", "comment"]
     column_filters = ["workflow", "workflow_version", "is_primary"]
     column_formatters = {"case": CaseView.view_case_link}
     column_searchable_list = [

cg/store/models.py

@@ -274,10 +274,9 @@ class Analysis(Base):
     cleaned_at: Mapped[datetime | None]
     # primary analysis is the one originally delivered to the customer
     is_primary: Mapped[bool | None] = mapped_column(default=False)
-
     created_at: Mapped[datetime] = mapped_column(default=datetime.now)
+    comment: Mapped[Text | None]
     case_id: Mapped[int] = mapped_column(ForeignKey("case.id", ondelete="CASCADE"))
-
     case: Mapped["Case"] = orm.relationship(back_populates="analyses")
 
     def __str__(self):

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "62.0.24"
+version = "62.0.25"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"