Finished record samples and project data forms

core/utils/samples.py

@@ -174,11 +174,11 @@ def save_recorded_samples(samples_data, req_user, app_name):
             )
 
         # If only recorded set sample to completed state
-        if sample["only_recorded"]:
+        if sample["only_recorded"] and sample["sample_project"] == "None":
             sample["sample_state"] = "Completed"
             sample["completed_date"] = datetime.datetime.now()
         # If no sample project data needed set to defined
-        elif sample["sample_project"] == "None":
+        elif sample["sample_project"] is None:
             sample["sample_state"] = "Defined"
         else:
             sample["sample_state"] = "Pre-Defined"
@@ -327,6 +327,40 @@ def validate_sample_data(sample_data, req_user, app_name):
     return validation
 
 
+def validate_project_data(project_data, project_name):
+    """Sample data validation
+
+    Parameters
+    ----------
+    project_data
+        project data formatted in json obtained from jspreadsheet
+
+    Returns
+    -------
+        validation
+            list with validation info for each sample with format:
+            [{"Sample Name": "test 01",
+              "Validate": True,
+              "Validation error": None
+              },
+              {"Sample Name": "test 02",
+              "Validate": False,
+              "Validation error": "Mandatory field is missing."
+              }]
+    """
+    validation = []
+    for sample in project_data:
+        sample_dict = {}
+        sample_dict["Sample name"] = sample["sample_name"]
+        sample_dict["Project name"] = project_name
+        sample_dict["Validate"] = True
+        sample_dict["Validation error"] = ""
+
+        validation.append(sample_dict)
+
+    return validation
+
+
 def save_project_data(excel_data, project_info):
     """Saves the project form data for each sample
 
@@ -341,16 +375,16 @@ def save_project_data(excel_data, project_info):
     Returns
     -------
         Same project info adding keys
-         - project_data: field_value information for each sample
          - success: True/False
          - error: error message
     """
     for sample in excel_data:
+        sample_id = core.models.Samples.objects.get(
+            sample_code_id__exact=sample["sample_code_id"]
+        )
         for field in project_info["sample_project_fields"]:
             field_value = {}
-            field_value["sample_id"] = core.models.Samples.objects.get(
-                sample_code_id__exact=sample["sample_code_id"]
-            )
+            field_value["sample_id"] = sample_id
             field_value[
                 "sample_project_field_id"
             ] = core.models.SampleProjectsFields.objects.get(
@@ -359,25 +393,24 @@ def save_project_data(excel_data, project_info):
                 ),
                 sample_project_field_name__exact=field["sample_project_field_name"],
             )
-            field_value["sample_project_field_value"] = next(
-                (
-                    sample[field["sample_project_name"]]
-                    for sample in excel_data
-                    if sample["sample_code_id"] == sample["sample_code_id"]
-                ),
-                None,
-            )
+            field_value["sample_project_field_value"] = sample[
+                field["sample_project_field_name"]
+            ]
             try:
                 core.models.SampleProjectsFieldsValue.objects.create_project_field_value(
                     field_value
                 )
-                field_value["sample_id"].set_state("Defined")
                 project_info["success"] = True
             except Exception:
                 project_info["success"] = False
                 project_info["error"] = "Error saving any of the project fields"
-                field_value["sample_id"].set_state("Pre-Defined")
-                raise
+
+        if project_info["success"] and sample["only_recorded"]:
+            sample_id.set_state("Completed")
+        elif project_info["success"]:
+            sample_id.set_state("Defined")
+        else:
+            sample_id.set_state("Pre-Defined")
 
     return project_info
 

django_utils/templatetags/common.py

@@ -0,0 +1,8 @@
+from django import template
+
+register = template.Library()
+
+
+@register.filter
+def get(mapping, key):
+    return mapping.get(key, "")

wetlab/api/serializers.py

@@ -98,6 +98,7 @@ class Meta:
 
 class SampleSerializer(serializers.ModelSerializer):
     lab_request = serializers.StringRelatedField(many=False, label="Laboratory")
+    sample_state = serializers.StringRelatedField(many=False, label="Sample state")
     sample_project = serializers.StringRelatedField(many=False, label="Sample Project")
     project_values = ProjectValuesSerializers(many=True)
     sample_type = serializers.StringRelatedField(many=False, label="Sample type")
@@ -126,7 +127,11 @@ def to_representation(self, instance):
                         data[key] = data[key].split("T")[0]
                 # Change id to label for api rest output
                 if output_label:
-                    data_update[self.fields[key].label] = data[key]
+                    # output both label and value
+                    label_value = {}
+                    label_value["label"] = self.fields[key].label
+                    label_value["value"] = data[key]
+                    data_update[key] = label_value
                 else:
                     data_update[key] = data[key]
         return data_update
@@ -135,12 +140,14 @@ class Meta:
         model = core.models.Samples
         fields = [
             "sample_name",
+            "sample_code_id",
             "lab_request",
             "sample_type",
             "species",
             "sample_project",
             "sample_entry_date",
             "collection_sample_date",
+            "sample_state",
             "project_values",
         ]