Merge branch 'master' into M_to_A_add_message

Needed master to test on stage.

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 6.4.0
+current_version = 6.5.0
 commit = True
 tag = True
 tag_name = v{new_version}

cg_lims/EPPs/udf/set/set_barcode.py

@@ -16,6 +16,7 @@ def get_barcode_set_udf(
     artifacts: List[Artifact],
     artifact_udf: str,
     container_type: str,
+    measurement: bool,
 ):
 
     """Assigning barcode to a barcode udf.
@@ -31,6 +32,14 @@ def get_barcode_set_udf(
     failed_samples = []
 
     for artifact in artifacts:
+        if measurement:
+            if len(artifact.samples) > 1:
+                LOG.info(f"Sample {str(artifact.id)} is a pool, and will be excluded")
+
+            else:
+                measurement_artifact = artifact
+                artifact = artifact.input_artifact_list()[0]
+
         try:
             art_container_type = artifact.container.type.name
 
@@ -51,9 +60,16 @@ def get_barcode_set_udf(
             # Sample has the correct "container_type".
             else:
                 barcode = get_barcode(artifact)
-                artifact.udf[artifact_udf] = barcode
-                artifact.put()
-                assigned_artifacts += 1
+
+                if measurement:
+                    measurement_artifact.udf[artifact_udf] = barcode
+                    measurement_artifact.put()
+                    assigned_artifacts += 1
+
+                else:
+                    artifact.udf[artifact_udf] = barcode
+                    artifact.put()
+                    assigned_artifacts += 1
 
         # Collects failed samples.
         except:
@@ -74,24 +90,27 @@ def get_barcode_set_udf(
 @click.command()
 @options.artifact_udf(help="The name of the barcode udf.")
 @options.input()
+@options.measurement()
 @options.container_type()
 @click.pass_context
 def assign_barcode(
     ctx: click.Context,
     artifact_udf: str,
     input: bool,
+    measurement: bool,
     container_type: str,
 ):
     """Assigned barcode to UDF"""
 
     LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
     process = ctx.obj["process"]
-    artifacts = get_artifacts(process=process, input=input)
+    artifacts = get_artifacts(process=process, input=input, measurement=measurement)
     try:
         get_barcode_set_udf(
             artifacts=artifacts,
             artifact_udf=artifact_udf,
-            container_type=container_type
+            container_type=container_type,
+            measurement=measurement,
         )
         message = "Barcodes were successfully generated."
         LOG.info(message)

cg_lims/__init__.py

@@ -1 +1 @@
-__version__ = "6.4.0"
+__version__ = "6.5.0"

tests/EPPs/udf/set/test_set_barcode.py

@@ -8,7 +8,7 @@
 from tests.conftest import server
 
 
-def test_with_tube(lims):
+def test_tube_barcode(lims):
     # GIVEN four artifacts, only two of them ACC9553A3PA1
     # and ACC9621A7PA1 have container type "Tube" and are the
     # only ones to be have assigned a barcode udf.
@@ -27,7 +27,7 @@ def test_with_tube(lims):
         del artifact.udf[barcode_udf]
 
     # WHEN running get_barcode_set_udf
-    get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type=container)
+    get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type=container, measurement=False)
 
     # THEN only tubes should get barcodes and be correct.
     for artifact in artifacts:
@@ -57,7 +57,7 @@ def test_plate_barcode(lims):
 
     # WHEN running get_barcode_set_udf
     with pytest.raises(MissingValueError) as error_message:
-        get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type=container)
+        get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type=container, measurement=False)
 
     # THEN InvalidValueError exception should be raised.
     # Because plate barcode has no specific barcode.
@@ -81,7 +81,7 @@ def test_pool_barcode(lims):
             exit()
 
     # WHEN running function get_barcode_set_udf.
-    get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type=container)
+    get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type=container, measurement=False)
 
     # THEN correct barcode should be assigned.
     for artifact in artifacts:        
@@ -108,7 +108,7 @@ def test_no_container_type(lims):
         del artifact.udf[barcode_udf]
 
     # WHEN running get_barcode_set_udf
-    get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type="")
+    get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type="", measurement=False)
 
     # THEN all artifacts should get barcodes and be correct.
     for artifact in artifacts:
@@ -125,7 +125,7 @@ def test_invalid_value(lims):
 
     # WHEN running function get_barcode_set_udf.
     with pytest.raises(InvalidValueError) as error_message:
-        get_barcode_set_udf(artifacts=artifact, artifact_udf=barcode_udf, container_type=container)
+        get_barcode_set_udf(artifacts=artifact, artifact_udf=barcode_udf, container_type=container, measurement=False)
 
     # THEN InvalidValueError should be triggered.
     assert (
@@ -150,7 +150,7 @@ def test_missing_value(lims):
 
     # WHEN running function get_barcode_set_udf.
     with pytest.raises(MissingValueError) as error_message:
-        get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type=container)
+        get_barcode_set_udf(artifacts=artifacts, artifact_udf=barcode_udf, container_type=container, measurement=False)
 
     # THEN no barcodes should be assigned and barcode_udf should not 
     # exists.
@@ -161,3 +161,60 @@ def test_missing_value(lims):
 
     with pytest.raises(KeyError):
         artifact.udf[barcode_udf]
+
+
+def test_container_on_measurement(lims):
+    # GIVEN measurements with different containers.
+    barcode_udf = 'Output Container Barcode'
+    container = 'Tube'
+    server("reception_control_wgs")
+    process = Process(lims, id="24-349794")
+    measurements = get_artifacts(process=process, measurement=True)
+
+    for measurement in measurements:
+        try:
+            del measurement.udf[barcode_udf]
+        except:
+            continue
+
+    # WHEN running get_barcode_set_udf
+    get_barcode_set_udf(artifacts=measurements, artifact_udf=barcode_udf, container_type=container, measurement=True)
+
+    # THEN barcodes should be assigned on measurement level only to samples with correct container.
+    for measurement in measurements:
+        if measurement.samples[0].artifact.container.type.name != container:
+            with pytest.raises(KeyError):
+                measurement.udf[barcode_udf]
+
+        else:
+            barcode = get_barcode(measurement.samples[0].artifact)
+            assert measurement.udf[barcode_udf] == barcode
+
+
+def test_missing_value_on_measurement(lims):
+    # GIVEN measurements with different containers.
+    barcode_udf = 'Output Container Barcode'
+    container = 'foobar'
+    server("reception_control_wgs")
+    process = Process(lims, id="24-349794")
+    measurements = get_artifacts(process=process, measurement=True)
+
+    for measurement in measurements:
+        try:
+            del measurement.udf[barcode_udf]
+        except:
+            continue
+
+    # WHEN running function get_barcode_set_udf.
+    with pytest.raises(MissingValueError) as error_message:
+        get_barcode_set_udf(artifacts=measurements, artifact_udf=barcode_udf, container_type=container, measurement=True)
+
+    # THEN no barcodes should be assigned and barcode_udf should not 
+    # exists.
+    assert (
+        f"No barcode assigned. Check parameters."
+        in error_message.value.message
+    )
+
+    with pytest.raises(KeyError):
+        measurement.udf[barcode_udf]