Fixed email module

CHANGELOG.md

@@ -54,6 +54,7 @@ Code contributions to the release:
 - Modified the module logic to dynamically select and render email templates based on user input. [#349](https://github.com/BU-ISCIII/relecov-tools/pull/349)
 - Enhanced email formatting and added a default CC to bioinformatica@isciii.es. [#349](https://github.com/BU-ISCIII/relecov-tools/pull/349)
 - Validate module now takes an optional argument to select the name of the sheet to check in excel file [#357](https://github.com/BU-ISCIII/relecov-tools/pull/357)
+- Fixed email module [#361](https://github.com/BU-ISCIII/relecov-tools/pull/361)
 
 #### Fixes
 

relecov_tools/__main__.py

@@ -271,7 +271,7 @@ def validate(json_file, json_schema, metadata, out_folder, excel_sheet):
     "--validate-file",
     required=True,
     type=click.Path(exists=True),
-    help="Path to the validation file (validate.json)",
+    help="Path to the validation summary json file (validate_log_summary.json)",
 )
 @click.option(
     "-r",
@@ -286,14 +286,22 @@ def validate(json_file, json_schema, metadata, out_folder, excel_sheet):
     type=click.Path(exists=True),
     help="Path to file",
 )
+@click.option(
+    "-t",
+    "--template_path",
+    type=click.Path(exists=True),
+    required=True,
+    default=None,
+    help="Path to relecov-tools templates folder",
+)
 @click.option(
     "-p",
     "--email-psswd",
     help="Password for bioinformatica@isciii.es",
     required=False,
     default=None,
 )
-def send_mail(validate_file, receiver_email, attachments, email_psswd):
+def send_mail(validate_file, receiver_email, attachments, template_path, email_psswd):
     """
     Send a sample validation report by mail.
     """
@@ -305,6 +313,7 @@ def send_mail(validate_file, receiver_email, attachments, email_psswd):
         )
 
     validate_data = relecov_tools.utils.read_json_file(validate_file)
+    batch = os.path.basename(os.path.dirname(os.path.abspath(validate_file)))
 
     if not validate_data:
         raise ValueError("Error: Validation data could not be loaded.")
@@ -313,7 +322,7 @@ def send_mail(validate_file, receiver_email, attachments, email_psswd):
 
     invalid_count = relecov_tools.log_summary.LogSum.get_invalid_count(validate_data)
 
-    email_sender = relecov_tools.mail.EmailSender(config)
+    email_sender = relecov_tools.mail.EmailSender(config, template_path)
 
     template_choice = click.prompt(
         "Select the type of template:\n1. Validation with errors\n2. Validation successful",
@@ -349,6 +358,7 @@ def send_mail(validate_file, receiver_email, attachments, email_psswd):
         invalid_count=invalid_count,
         submitting_institution_code=submitting_institution_code,
         template_name=template_name,
+        batch=batch,
     )
 
     if email_body is None:
@@ -369,9 +379,13 @@ 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 - {institution_name}"
+    subject = (
+        f"RELECOV - Informe de Validación de Muestras {batch} - {institution_name}"
+    )
     try:
-        email_sender.send_email(final_receiver_email, subject, email_body, attachments)
+        email_sender.send_email(
+            final_receiver_email, subject, email_body, attachments, email_psswd
+        )
     except Exception as e:
         log.exception(f"EXCEPTION FOUND: {e}")
         raise

relecov_tools/mail.py

@@ -13,9 +13,9 @@
 
 
 class EmailSender:
-    def __init__(self, config):
+    def __init__(self, config, template_path):
         self.config = config
-        self.template_path = self.config.get("delivery_template_path_file")
+        self.template_path = template_path
         self.yaml_cred_path = self.config.get("yaml_cred_path")
 
         if not self.config:
@@ -49,6 +49,7 @@ def render_email_template(
         invalid_count=None,
         submitting_institution_code=None,
         template_name=None,
+        batch=None,
     ):
 
         institution_info = self.get_institution_info(submitting_institution_code)
@@ -65,6 +66,7 @@ def render_email_template(
                 else 0
             ),
             "additional_info": additional_info,
+            "batch": batch,
         }
 
         templates_base_dir = os.path.dirname(self.template_path)
@@ -74,7 +76,7 @@ def render_email_template(
 
         return email_template
 
-    def send_email(self, receiver_email, subject, body, attachments):
+    def send_email(self, receiver_email, subject, body, attachments, email_psswd):
 
         if not isinstance(receiver_email, list):
             raise ValueError(
@@ -90,7 +92,10 @@ def send_email(self, receiver_email, subject, body, attachments):
             return
 
         sender_email = self.config["email_host_user"]
-        email_password = credentials.get("email_password")
+
+        email_password = (
+            email_psswd if email_psswd else credentials.get("email_password")
+        )
 
         if not email_password:
             print("The e-mail password could not be found.")

relecov_tools/templates/jinja_template_with_errors.j2

@@ -1,16 +1,14 @@
-
-Asunto: Informe de Validación de Muestras - {{ submitting_institution }}
-
 Estimado/a responsable de la subida de datos de secuenciación del {{ submitting_institution }},
 
-Le informamos que tras el proceso de validación de los datos enviados, el número de muestras que ha sido imposible validar es de {{ invalid_count }}.
+Le informamos que tras el proceso de validación de los datos procesados a fecha {{ batch }}, el número de muestras que no ha sido posible validar es de {{ invalid_count }}.
 Las muestras no han superado el proceso de validación debido a errores o faltas de información en los datos proporcionados. Le solicitamos que revise los detalles de cada muestra para subsanar los problemas.
 Adjunto a este correo encontrará un documento en formato Excel con información detallada sobre los errores o la información faltante para cada muestra. Le pedimos que proceda a realizar las correcciones necesarias y a reenviar los datos.
+En la carpete del SFTP existe una carpeta llamada {{ batch }}_invalid_samples con un excel de metadatos a subsanar con los errores mencionados en el excel adjunto al correo y los .fastq asociados. Una vez subsanados los errores, se puede renombrar la carpeta quitando `_invalid_samples` del nombre, o notificarnoslo en respuesta a este correo para que nos encarguemos nosotros.
 
-{{additional_info}}
+Notas adicionales: {{additional_info}}
 
-En caso de cualquier duda o aclaración, no dude en ponerse en contacto con el equipo técnico.
+En caso de cualquier duda o aclaración, no dude en ponerse en contacto con el equipo técnico empleando este mismo hilo de correos.
 
 Atentamente,
 
-Equipo Relecov
+Equipo RELECOV