From fee423fe7a046c9f818a6a05ac4bf5b0b958a16f Mon Sep 17 00:00:00 2001
From: Ruge Li <91452427+rugeli@users.noreply.github.com>
Date: Tue, 26 Sep 2023 17:10:11 -0700
Subject: [PATCH] add upload_results as a config option (#191)

* upload local recipes to S3

* update README and add boto3 into requirements

* lint

* rerange import order

* add save_file for S3 uploads and url generation

* delete redundant error msg

* add "upload_results" in config files as an option

* conditionally call post_and_open_file

* add check `number_of_packings`

* update conditional statement

* update
---
 cellpack/autopack/loaders/config_loader.py                   | 1 +
 cellpack/autopack/writers/__init__.py                        | 5 ++++-
 cellpack/tests/packing-configs/test_parallel_config.json     | 3 ++-
 .../tests/packing-configs/test_variable_count_config.json    | 3 ++-
 examples/packing-configs/pcna_parallel_packing_config.json   | 3 ++-
 examples/packing-configs/peroxisome_packing_config.json      | 3 ++-
 .../packing-configs/peroxisome_parallel_packing_config.json  | 5 +++--
 examples/packing-configs/run.json                            | 3 ++-
 8 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/cellpack/autopack/loaders/config_loader.py b/cellpack/autopack/loaders/config_loader.py
index 252a03be5..7b071af21 100644
--- a/cellpack/autopack/loaders/config_loader.py
+++ b/cellpack/autopack/loaders/config_loader.py
@@ -43,6 +43,7 @@ class ConfigLoader(object):
         "show_sphere_trees": False,
         "show_progress_bar": False,
         "spacing": None,
+        "upload_results": False,
         "use_periodicity": False,
         "version": 1.0,
     }
diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
index d67a91928..0d1893124 100644
--- a/cellpack/autopack/writers/__init__.py
+++ b/cellpack/autopack/writers/__init__.py
@@ -185,7 +185,10 @@ def save_as_simularium(self, env, all_ingr_as_array, compartments):
         file_name = env.helper.writeToFile(
             env.result_file, env.boundingBox, env.name, env.version
         )
-        autopack.helper.post_and_open_file(file_name)
+        if env.config_data.get(
+            "upload_results", env.config_data.get("number_of_packings", 1) <= 1
+        ):
+            autopack.helper.post_and_open_file(file_name)
 
     def save_Mixed_asJson(
         self,
diff --git a/cellpack/tests/packing-configs/test_parallel_config.json b/cellpack/tests/packing-configs/test_parallel_config.json
index 162f1cab4..e7b528e3c 100644
--- a/cellpack/tests/packing-configs/test_parallel_config.json
+++ b/cellpack/tests/packing-configs/test_parallel_config.json
@@ -14,5 +14,6 @@
     "number_of_packings": 5,
     "spacing":  null,
     "use_periodicity": false,
-    "show_sphere_trees": true
+    "show_sphere_trees": true,
+    "upload_results": false
 }
\ No newline at end of file
diff --git a/cellpack/tests/packing-configs/test_variable_count_config.json b/cellpack/tests/packing-configs/test_variable_count_config.json
index 013bb3ab9..564400e5f 100644
--- a/cellpack/tests/packing-configs/test_variable_count_config.json
+++ b/cellpack/tests/packing-configs/test_variable_count_config.json
@@ -13,5 +13,6 @@
     "spacing": null,
     "parallel": false,
     "use_periodicity": false,
-    "show_sphere_trees": true
+    "show_sphere_trees": true,
+    "upload_results": false
 }
\ No newline at end of file
diff --git a/examples/packing-configs/pcna_parallel_packing_config.json b/examples/packing-configs/pcna_parallel_packing_config.json
index 8b7c00af5..ffc847fee 100644
--- a/examples/packing-configs/pcna_parallel_packing_config.json
+++ b/examples/packing-configs/pcna_parallel_packing_config.json
@@ -16,5 +16,6 @@
     "show_progress_bar": true,
     "spacing": 2.5,
     "use_periodicity": false,
-    "show_sphere_trees": false
+    "show_sphere_trees": false,
+    "upload_results": false
 }
\ No newline at end of file
diff --git a/examples/packing-configs/peroxisome_packing_config.json b/examples/packing-configs/peroxisome_packing_config.json
index a7ff885a4..461705aec 100644
--- a/examples/packing-configs/peroxisome_packing_config.json
+++ b/examples/packing-configs/peroxisome_packing_config.json
@@ -14,5 +14,6 @@
     "spacing": 2.5,
     "use_periodicity": false,
     "show_sphere_trees": false,
-    "load_from_grid_file": false
+    "load_from_grid_file": true,
+    "upload_results": false
 }
\ No newline at end of file
diff --git a/examples/packing-configs/peroxisome_parallel_packing_config.json b/examples/packing-configs/peroxisome_parallel_packing_config.json
index b6bcd5a1c..d20a272cd 100644
--- a/examples/packing-configs/peroxisome_parallel_packing_config.json
+++ b/examples/packing-configs/peroxisome_parallel_packing_config.json
@@ -18,7 +18,8 @@
     "show_sphere_trees": false,
     "image_export_options": {
         "hollow": false,
-        "voxel_size": [1,1,1],
+        "voxel_size": [1, 1, 1],
         "projection_axis": "z"
-    }
+    },
+    "upload_results": false
 }
\ No newline at end of file
diff --git a/examples/packing-configs/run.json b/examples/packing-configs/run.json
index 18f658e12..7a10d021b 100644
--- a/examples/packing-configs/run.json
+++ b/examples/packing-configs/run.json
@@ -13,5 +13,6 @@
     "use_periodicity": false,
     "show_sphere_trees": false,
     "load_from_grid_file": false,
-    "save_converted_recipe": true
+    "save_converted_recipe": true,
+    "upload_results": true
 }
\ No newline at end of file