From d5908c7b61188a9fe6379fa1a35e0b091dc1c413 Mon Sep 17 00:00:00 2001
From: ericblanc20 <eric.blanc@bihealth.de>
Date: Wed, 30 Jun 2021 11:39:43 +0200
Subject: [PATCH] Enable generic & cancer dataset (#49)

---
 cubi_tk/snappy/pull_sheets.py  | 25 ++++++++++++++++++-------
 cubi_tk/sodar/pull_raw_data.py |  2 +-
 2 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/cubi_tk/snappy/pull_sheets.py b/cubi_tk/snappy/pull_sheets.py
index f16693be..6a4c5cc2 100644
--- a/cubi_tk/snappy/pull_sheets.py
+++ b/cubi_tk/snappy/pull_sheets.py
@@ -180,14 +180,20 @@ def on_visit_material(self, material, node_path, study=None, assay=None):
             sample = material
             characteristics = {c.name: c for c in source.characteristics}
             comments = {c.name: c for c in source.comments}
+            batch = characteristics.get("Batch", comments.get("Batch"))
+            family = characteristics.get("Family", comments.get("Family"))
+            father = characteristics.get("Father", comments.get("Father"))
+            mother = characteristics.get("Mother", comments.get("Mother"))
+            sex = characteristics.get("Sex", comments.get("Sex"))
+            affected = characteristics.get("Disease status", comments.get("Disease status"))
             self.sources[material.name] = Source(
-                family=characteristics["Family"].value[0],
+                family=family.value[0] if family else None,
                 source_name=source.name,
-                batch_no=characteristics.get("Batch", comments.get("Batch")).value[0],
-                father=characteristics["Father"].value[0],
-                mother=characteristics["Mother"].value[0],
-                sex=characteristics["Sex"].value[0],
-                affected=characteristics["Disease status"].value[0],
+                batch_no=batch.value[0] if batch else None,
+                father=father.value[0] if father else None,
+                mother=mother.value[0] if mother else None,
+                sex=sex.value[0] if sex else None,
+                affected=affected.value[0] if affected else None,
                 sample_name=sample.name,
             )
         elif material.type == "Library Name":
@@ -199,14 +205,19 @@ def on_visit_material(self, material, node_path, study=None, assay=None):
                 library_type = "WES"
             elif library.name.split("-")[-1].startswith("Panel_seq"):
                 library_type = "Panel_seq"
+            elif library.name.split("-")[-1].startswith("mRNA_seq"):
+                library_type = "mRNA_seq"
             else:
                 raise Exception("Cannot infer library type from %s" % library.name)
 
+            folder_name = first_value("Folder name", node_path)
+            if not folder_name:
+                folder_name = library.name
             self.samples[sample.name] = Sample(
                 source=self.sources[sample.name],
                 library_name=library.name,
                 library_type=library_type,
-                folder_name=first_value("Folder name", node_path),
+                folder_name=folder_name,
                 seq_platform=first_value("Platform", node_path),
                 library_kit=first_value("Library Kit", node_path),
             )
diff --git a/cubi_tk/sodar/pull_raw_data.py b/cubi_tk/sodar/pull_raw_data.py
index 999c4be9..5afc3c58 100644
--- a/cubi_tk/sodar/pull_raw_data.py
+++ b/cubi_tk/sodar/pull_raw_data.py
@@ -155,7 +155,7 @@ def execute(self) -> typing.Optional[int]:
         if not out_path.exists():
             out_path.mkdir(parents=True)
 
-        investigation = api.investigations.get(
+        investigation = api.samplesheet.retrieve(
             sodar_url=self.config.sodar_url,
             sodar_api_token=self.config.sodar_api_token,
             project_uuid=self.config.project_uuid,