Refactor EARBotReviewer to handle merged but unreviewed reports (#130)

* Refactor EARBotReviewer to support merged but not reviewed reports

* Update comment notification for YAML file addition in EARBotReviewer

ear_bot/ear_bot_reviewer.py

@@ -455,26 +455,14 @@ def closed_pr(self):
                 for file in pr.get_files()
                 if file.filename.lower().endswith(".pdf")
             )
+            self._add_yaml_file(EAR_pdf.filename)
             EAR_pdf_url = re.sub(r"/blob/[\w\d]+/", "/blob/main/", EAR_pdf.blob_url)
             slack_post = (
                 f":tada: *New Assembly Finished!* :tada:\n\n"
                 f"Congratulations to {researcher_name} and the {institution} team for the high-quality assembly of _{species}_\n\n"
                 f"The assembly was reviewed by {reviewer_name}, and the process supervised by {supervisor_name}. The EAR can be found in the following link:\n"
                 f"{EAR_pdf_url}"
             )
-            EARpdf_to_yaml_path = os.path.join(root_folder, "EARpdf_to_yaml.py")
-            EAR_pdf_file = os.path.join(root_folder, EAR_pdf.filename)
-            output_pdf_to_yaml = subprocess.run(
-                f"python {EARpdf_to_yaml_path} {EAR_pdf_file}",
-                shell=True,
-                capture_output=True,
-                text=True,
-            )
-            yaml_file = EAR_pdf_file.replace(".pdf", ".yaml")
-            with open(yaml_file, "r") as file:
-                yaml_content = file.read()
-            commit(self.repo, yaml_file, "Add YAML file", yaml_content)
-            print(output_pdf_to_yaml.stdout, output_pdf_to_yaml.stderr)
             self._create_slack_post(slack_post)
         elif not merged:
             supervisor = pr.assignee.login
@@ -485,8 +473,16 @@ def closed_pr(self):
             )
             pr.add_to_labels("ERROR!")
         else:
+            EAR_pdf_filename = next(
+                file.filename
+                for file in pr.get_files()
+                if file.filename.lower().endswith(".pdf")
+            )
+            self._add_yaml_file(EAR_pdf_filename)
             print("No review has been found for this merged PR.")
-            sys.exit(1)
+            pr.create_issue_comment(
+                "The YAML file has been updated based on the new EAR.pdf"
+            )
 
     def _search_comment_user(self, pr, text_to_check):
         comment_user = []
@@ -569,6 +565,21 @@ def _create_slack_post(self, content):
         print(f"Slack post created: {link}")
         return True
 
+    def _add_yaml_file(self, EAR_pdf_filename):
+        EARpdf_to_yaml_path = os.path.join(root_folder, "EARpdf_to_yaml.py")
+        EAR_pdf_file = os.path.join(root_folder, EAR_pdf_filename)
+        output_pdf_to_yaml = subprocess.run(
+            f"python {EARpdf_to_yaml_path} {EAR_pdf_file}",
+            shell=True,
+            capture_output=True,
+            text=True,
+        )
+        yaml_file = EAR_pdf_file.replace(".pdf", ".yaml")
+        with open(yaml_file, "r") as file:
+            yaml_content = file.read()
+        commit(self.repo, yaml_file, "Add YAML file", yaml_content)
+        print(output_pdf_to_yaml.stdout, output_pdf_to_yaml.stderr)
+
 
 if __name__ == "__main__":
     parser = ArgumentParser(description="EAR bot!")