Merge branch 'feature-t/4566-warnings-clone-multiple-denominations' into 'dev'

Resolve "Warnings, avoir un nouveau wrning si un clone a plusiuers dénomination sur différents samples"

Closes #4566

See merge request !850

doc/warnings.md

@@ -58,4 +58,5 @@ Warnings which were implemented ([x]) have a fixed code that should not be chang
 ## Comparisons between several samples or patients (such as with clonedb)
 - [ ] W8x Potential contamination or public clone #1744 
 - [ ]     Known public clone 
+- [x] W81 Clone have different names between samples #4566
 

tools/fuse.py

@@ -222,8 +222,24 @@ class Window:
                 if key not in obj.d:
                     obj.d[key] = source.d[key]
 
+        # !! No name field if fuse with an empty clone
+        if "name" in self.d and "name" in other.d and self.d["name"] != other.d["name"]:
+            if obj.d["name"] == self.d["name"]:
+                name = other.d["name"]
+            else:
+                name = self.d["name"]
+
+            msg = "Clone have different names between samples: %s" % name
+            obj.addWarning(code="W81", msg=msg, level="warn")
         return obj
         
+    def addWarning(self, code, msg, level):
+        # init warn field if not already present
+        if not "warn" in self.d:
+            self.d["warn"] = []
+        self.d["warn"].append( {"code":code, "msg":msg, "level": level})
+        return
+
     def get_nb_reads(self, cid, point=0):
         return self[cid]["reads"][point]
 

tools/tests/data/warnings/w81_sample_1.vidjil

+{
+    "notes": "Sample with clone 1 and 3;", 
+    "clones": [
+        {"germline": "IGK", "id": "clone_1", "name": "clone_name_1", "reads": [500], "top": 1}, 
+        {"germline": "IGK", "id": "clone_3", "name": "clone_name_3", "reads": [500], "top": 2}], 
+    "clusters": [],
+    "germlines": {}, 
+    "producer": "vidjil fuse", 
+    "reads": {"germline": {"IGK": [9500]}, "segmented": [9500], "total": [9500]}, 
+    "samples": {
+         "commandline": ["cmdline_1"],
+         "log": ["log_1"], 
+         "number": 1, 
+         "original_names": ["seq_1"],
+         "producer": ["vidjil-algo 2018.02"], 
+         "run_timestamp": ["2018-03-28 10:26:11"],
+         "timestamp": ["2018-04-06 13:48:48"]}, 
+    "timestamp": "2019-04-08 15:18:00", 
+    "vidjil_json_version": "2016b", 
+    "warn": []
+ }

tools/tests/data/warnings/w81_sample_2.vidjil

+{
+  "notes": "Sample with clone 1-3; clone 3 have a variation in his name",
+  "clones": [
+    {"germline": "IGK", "id": "clone_1", "name": "clone_name_1", "reads": [500 ], "top": 1 },
+    {"germline": "IGK", "id": "clone_2", "name": "clone_name_2", "reads": [500 ], "top": 2 },
+    {"germline": "IGK", "id": "clone_3", "name": "clone_name_3b", "reads": [500 ], "top": 3 }
+  ],
+  "clusters": [],
+  "germlines": {},
+  "producer": "vidjil fuse",
+  "reads": {
+    "germline": {"IGK": [9500 ] }, "segmented": [9500 ], "total": [9500 ]
+  },
+  "samples": {
+    "commandline": ["cmdline_2"],
+    "log": ["log_2"],
+    "number": 1,
+    "original_names": ["seq_2"],
+    "producer": ["vidjil-algo 2018.02"],
+    "run_timestamp": ["2018-03-28 10:26:11"],
+    "timestamp": ["2018-04-06 13:48:48"]
+  },
+  "timestamp": "2019-04-08 15:18:00",
+  "vidjil_json_version": "2016b",
+  "warn": []
+}
\ No newline at end of file

tools/tests/should-get-tests/fuse_warnings.should-get

+!LAUNCH: python ../../fuse.py $FUSE_OPTIONS ../data/warnings/w81_sample_1.vidjil  ../data/warnings/w81_sample_2.vidjil -o fuse_warnings.vidjil ; cat fuse_warnings.vidjil
+
+$ Fuse the three files
+2: ListWindows: .9500, 9500.
+
+
+$ Middle file has the good 40-bp windows
+1: "id": "clone_1"
+1: "id": "clone_2"
+1: "id": "clone_3"
+
+$ fields 'warn' present 3 times (sample, clone, level)
+1: "level": "warn"
+
+$ Correct warning is present
+1: W81
+1: Clone have different names between samples: clone_name_3b
\ No newline at end of file