Merge branch 'master' into add-nallo-metrics-deliver

Clinical-Genomics · Jan 27, 2025 · 6e9b12f · 6e9b12f
2 parents 6923bcf + e7621a7
commit 6e9b12f
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 67.0.2
+current_version = 67.0.5
 commit = True
 tag = True
 tag_name = v{new_version}

diff --git a/cg/__init__.py b/cg/__init__.py
@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "67.0.2"
+__version__ = "67.0.5"
diff --git a/cg/resources/raredisease_bundle_filenames.yaml b/cg/resources/raredisease_bundle_filenames.yaml
@@ -798,151 +798,151 @@
   tag: regions
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_1.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_1.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_2.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_2.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_3.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_3.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_4.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_4.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_5.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_5.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_6.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_6.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_7.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_7.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_8.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_8.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_9.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_9.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_10.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_10.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_11.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_11.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_12.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_12.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_13.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_13.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_14.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_14.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_15.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_15.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_16.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_16.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_17.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_17.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_18.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_18.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_19.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_19.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_20.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_20.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_21.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_21.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_22.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_22.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_X.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_X.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_Y.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_Y.png
   path_index: ~
   step: chromograph_upd
   tag: sites
 - format: png
   id: SAMPLEID
-  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID__upd_sites_M.png
+  path: PATHTOCASE/annotate_snv/genome/SAMPLEID_chromograph_sites/SAMPLEID_upd_sites_M.png
   path_index: ~
   step: chromograph_upd
   tag: sites

diff --git a/cg/services/orders/submitter/ticket_handler.py b/cg/services/orders/submitter/ticket_handler.py
@@ -119,14 +119,12 @@ def add_sample_case_name_to_message(message: str, case_name: str | None) -> str:
     def add_existing_sample_info_to_message(
         self, message: str, customer_id: str, internal_id: str, case_name: str
     ) -> str:
-
         existing_sample: Sample = self.status_db.get_sample_by_internal_id(internal_id=internal_id)
 
         sample_customer = ""
         if existing_sample.customer_id != customer_id:
             sample_customer = " from " + existing_sample.customer.internal_id
-
-        message += f"{existing_sample.name}, application: {existing_sample.application_version.application.tag}, case: {case_name} (already existing sample{sample_customer}), priority: {existing_sample.priority}"
+        message += f"{existing_sample.name}, application: {existing_sample.application_version.application.tag}, case: {case_name} (already existing sample{sample_customer}), priority: {existing_sample.priority.name.lower()}"
         return message
 
     @staticmethod
@@ -180,6 +178,7 @@ def create_case_xml_sample_list(self, order, message: str) -> str:
             if not case.is_new:
                 db_case = self.status_db.get_case_by_internal_id(case.internal_id)
                 for sample in db_case.samples:
+                    message += self.NEW_LINE
                     message = self.add_existing_sample_info_to_message(
                         message=message,
                         customer_id=sample.customer.internal_id,
@@ -189,6 +188,7 @@ def create_case_xml_sample_list(self, order, message: str) -> str:
             else:
                 for sample in case.samples:
                     if not sample.is_new:
+                        message += self.NEW_LINE
                         message = self.add_existing_sample_info_to_message(
                             message=message,
                             customer_id=order.customer,

diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "cg"
-version = "67.0.2"
+version = "67.0.5"
 description = "Clinical Genomics command center"
 readme = {file = "README.md", content-type = "text/markdown"}
 homepage = "https://github.com/Clinical-Genomics/cg"