Converted get_invalid_count to a static method in log_summary.py

relecov_tools/__main__.py

@@ -289,6 +289,10 @@ def send_mail(validate_file, receiver_email, attachments, email_psswd):
     if not validate_data:
         raise ValueError(
                     "Error: Validation data could not be loaded.")
+
+    submitting_institution_code = list(validate_data.keys())[0]
+
+    invalid_count = relecov_tools.log_summary.LogSum.get_invalid_count(validate_data)
 
     email_sender = relecov_tools.mail.EmailSender(config)
 
@@ -299,8 +303,10 @@ def send_mail(validate_file, receiver_email, attachments, email_psswd):
     if add_info:
         additional_info = click.prompt("Enter additional information")
 
-    email_body, email_receiver_from_json = email_sender.render_email_template(
-        additional_info
+    email_body, email_receiver_from_json, institution_name = email_sender.render_email_template(
+        additional_info,
+        invalid_count=invalid_count,
+        submitting_institution_code = submitting_institution_code
     )
 
     if email_body is None:
@@ -313,7 +319,7 @@ def send_mail(validate_file, receiver_email, attachments, email_psswd):
     if not final_receiver_email:
         raise ValueError("Error: Could not obtain the recipient's email address.")
 
-    subject = f"Informe de Validación de Muestras - {email_receiver_from_json}"
+    subject = f"Informe de Validación de Muestras - {institution_name}"
 
     email_sender.send_email(final_receiver_email, subject, email_body, attachments)
 

relecov_tools/log_summary.py

@@ -308,3 +308,26 @@ def create_error_summary(
                 log.error("Error exporting logs to file: %s", str(e))
                 f.write(str(final_logs))
         return
+
+    @staticmethod
+    def get_invalid_count(validation_logs):
+        """
+        Counts the number of invalid samples in the logs data by checking the `valid` field.
+        
+        Args:
+            validation_logs (dict): Dictionary containing the validation logs.
+    
+        Returns:
+            dict: Dictionary with entry_key as keys and counts of invalid samples as values.
+        """
+        invalid_counts = {}
+        for entry_key, entry_value in validation_logs.items():
+            if "samples" in entry_value:
+                samples = entry_value["samples"]
+                for sample_key, sample_value in samples.items():
+                    if "valid" in sample_value and not sample_value["valid"]:
+                        if invalid_counts.get(entry_key):
+                            invalid_counts[entry_key] += 1
+                        else:
+                            invalid_counts[entry_key] = 1
+        return invalid_counts

relecov_tools/mail.py

@@ -25,17 +25,6 @@ def __init__(self, config):
             raise FileNotFoundError(
                 f"The template file could not be found in path {self.template_path}.")
 
-    def get_invalid_count(self):
-        invalid_count = 0
-
-        for entry_key, entry_value in self.validate_data.items():
-            if "samples" in entry_value:
-                samples = entry_value["samples"]
-                for sample_key, sample_value in samples.items():
-                    if "valid" in sample_value and not sample_value["valid"]:
-                        invalid_count += 1
-        return invalid_count
-
     def get_institution_info(
         self, institution_code, institutions_file="institutions.json"
     ):
@@ -53,11 +42,10 @@ def get_institution_info(
             print(f"No information found for code {institution_code}")
             return None
 
-    def render_email_template(self, additional_info="", validate_data=None):
-
-        submitting_institution_code = list(self.validate_data.keys())[0]
-        invalid_count = self.get_invalid_count()
-
+    def render_email_template(self, additional_info="",
+                              invalid_count= None,
+                              submitting_institution_code=None):
+
         institution_info = self.get_institution_info(submitting_institution_code)
         if not institution_info:
             print("Error: The information could not be obtained from the institution.")
@@ -75,7 +63,7 @@ def render_email_template(self, additional_info="", validate_data=None):
             additional_info=additional_info,
         )
 
-        return email_template, email_receiver
+        return email_template, email_receiver, institution_name
 
     def send_email(self, receiver_email, subject, body, attachments):
         credentials = relecov_tools.utils.read_yml_file(self.yaml_cred_path)