Fix module's error when no samples are involved in service

bu_isciii/bioinfo_doc.py

@@ -105,7 +105,7 @@ def __init__(
         self.service_folder = os.path.join(
             self.path, self.doc_conf["services_path"], year, self.resolution_folder
         )
-        self.samples = resolution_info["Samples"]
+        self.samples = resolution_info.get("Samples", None)
         self.user_data = resolution_info["Service"]["serviceUserId"]
         self.service = resolution_info["Service"]
         self.handled_services = None
@@ -192,19 +192,24 @@ def create_markdown(self, file_path):
         markdown_data["service"] = self.service
         markdown_data["user_data"] = self.user_data
         samples_in_service = {}
-        for sample_data in self.samples:
-            if sample_data["runName"] not in samples_in_service:
-                samples_in_service[sample_data["runName"]] = {}
-            if (
-                sample_data["projectName"]
-                not in samples_in_service[sample_data["runName"]]
-            ):
+
+        if self.samples is not None:
+            for sample_data in self.samples:
+                if sample_data["runName"] not in samples_in_service:
+                    samples_in_service[sample_data["runName"]] = {}
+                if (
+                    sample_data["projectName"]
+                    not in samples_in_service[sample_data["runName"]]
+                ):
+                    samples_in_service[sample_data["runName"]][
+                        sample_data["projectName"]
+                    ] = []
                 samples_in_service[sample_data["runName"]][
                     sample_data["projectName"]
-                ] = []
-            samples_in_service[sample_data["runName"]][
-                sample_data["projectName"]
-            ].append(sample_data["sampleName"])
+                ].append(sample_data["sampleName"])
+        else:
+            samples_in_service = {" N/A": {" N/A": ["No recorded samples"]}}
+
         markdown_data["samples"] = samples_in_service
 
         # Resolution related information

bu_isciii/clean.py

@@ -65,7 +65,6 @@ def __init__(self, resolution_id=None, path=None, ask_path=False, option=None):
         self.services_requested = self.resolution_info["Resolutions"][
             "availableServices"
         ]
-        self.service_samples = self.resolution_info["Samples"]
         if self.service_folder in self.path:
             self.full_path = self.path
         else:
@@ -81,7 +80,7 @@ def __init__(self, resolution_id=None, path=None, ask_path=False, option=None):
         self.delete_files = self.get_clean_items(self.services_to_clean, type="files")
         # self.delete_list = [item for item in self.delete_list if item]
         self.nocopy = self.get_clean_items(self.services_to_clean, type="no_copy")
-        self.service_samples = self.resolution_info["Samples"]
+        self.service_samples = self.resolution_info.get("Samples", None)
 
         if option is None:
             self.option = bu_isciii.utils.prompt_selection(
@@ -302,15 +301,18 @@ def purge_files(self):
         Params:
 
         """
-        files_to_delete = []
-        for sample_info in self.service_samples:
-            for file in self.delete_files:
-                file_to_delete = file.replace("sample_name", sample_info["sampleName"])
-                files_to_delete.append(file_to_delete)
-        path_content = self.scan_dirs(to_find=files_to_delete)
-        for file in path_content:
-            os.remove(file)
-            stderr.print("[green]Successfully removed " + file)
+        if self.service_samples is not None:
+            files_to_delete = []
+            for sample_info in self.service_samples:
+                for file in self.delete_files:
+                    file_to_delete = file.replace(
+                        "sample_name", sample_info["sampleName"]
+                    )
+                    files_to_delete.append(file_to_delete)
+            path_content = self.scan_dirs(to_find=files_to_delete)
+            for file in path_content:
+                os.remove(file)
+                stderr.print("[green]Successfully removed " + file)
         return
 
     def purge_folders(self, sacredtexts=["lablog", "logs"], add="", verbose=True):

bu_isciii/new_service.py

@@ -61,7 +61,7 @@ def __init__(
         self.services_requested = self.resolution_info["Resolutions"][
             "availableServices"
         ]
-        self.service_samples = self.resolution_info["Samples"]
+        self.service_samples = self.resolution_info.get("Samples", None)
         self.full_path = os.path.join(self.path, self.service_folder)
         #
         # resolutionFullData example
@@ -227,10 +227,18 @@ def create_symbolic_links(self):
                 stderr.print("Traceback: %s" % e)
 
     def create_new_service(self):
-        self.create_folder()
-        self.copy_template()
-        self.create_samples_id()
-        self.create_symbolic_links()
+        if self.service_samples is not None:
+            self.create_folder()
+            self.copy_template()
+            self.create_samples_id()
+            self.create_symbolic_links()
+        else:
+            stderr.print(
+                "[yellow]WARN: No samples recorded in service: " + self.resolution_id
+            )
+            bu_isciii.utils.prompt_yn_question("Do you want to proceed?: ")
+            self.create_folder()
+            self.copy_template()
 
     def get_resolution_id(self):
         return self.resolution_id