FIX: Pass output arguments into Analysis and use them

octue/resources/analysis.py

@@ -86,6 +86,7 @@ def __init__(self, twine, handle_monitor_message=None, **kwargs):
 
         # Non-strands.
         self.output_location = kwargs.pop("output_location", None)
+        self.use_signed_urls_for_output_datasets = kwargs.pop("use_signed_urls_for_output_datasets", True)
 
         self._calculate_strand_hashes(strands=strand_kwargs)
         self._periodic_monitor_message_sender_threads = []
@@ -136,14 +137,14 @@ def set_up_periodic_monitor_message(self, create_monitor_message, period=60):
         self._periodic_monitor_message_sender_threads.append(thread)
         logger.info("Periodic monitor message set up to send every %ss.", period)
 
-    def finalise(self, upload_output_datasets_to=None, use_signed_urls=True):
+    def finalise(self, upload_output_datasets_to=None, use_signed_urls=None):
         """Validate the output values and output manifest and, if the analysis produced an output manifest, upload its
         output datasets to a unique subdirectory within the analysis's output location. This output location can be
         overridden by providing a different cloud path via the `upload_output_datasets_to` parameter. Either way, the
         dataset paths in the output manifest are replaced with signed URLs for easier, expiring access.
 
         :param str|None upload_output_datasets_to: If not provided but an output location was provided at instantiation, upload any output datasets into a unique subdirectory within this output location; if provided, upload into this location instead. The output manifest is updated with the upload locations.
-        :param bool use_signed_urls: if `True`, use signed URLs instead of cloud URIs for dataset paths in the output manifest
+        :param bool|None use_signed_urls: if `True`, use signed URLs instead of cloud URIs for dataset paths in the output manifest; if `None`, use the value of `use_signed_urls_for_output_datasets` given at instantiation
         :return None:
         """
         serialised_strands = {"output_values": None, "output_manifest": None}
@@ -163,6 +164,8 @@ def finalise(self, upload_output_datasets_to=None, use_signed_urls=True):
         if self.output_location and not upload_output_datasets_to:
             upload_output_datasets_to = storage.path.join(self.output_location, coolname.generate_slug())
 
+        use_signed_urls = use_signed_urls or self.use_signed_urls_for_output_datasets
+
         # If there isn't both an output manifest and upload location, nothing is uploaded.
         if not (upload_output_datasets_to and hasattr(self, "output_manifest")):
             return

octue/runner.py

@@ -255,6 +255,8 @@ def run(
                 id=analysis_id,
                 twine=self.twine,
                 handle_monitor_message=handle_monitor_message,
+                output_location=self.output_location,
+                use_signed_urls_for_output_datasets=self.use_signed_urls_for_output_datasets,
                 **self.configuration,
                 **inputs,
                 **outputs_and_monitors,