Feat support s3 swcs (#141)

* feat: tools for reading from s3

* refactor: updated toml

* feat: s3 support for swcs functional

---------

Co-authored-by: anna-grim <[email protected]>

Author: anna-grim

src/segmentation_skeleton_metrics/utils/swc_util.py

@@ -426,15 +426,19 @@ def read_from_gcs_zip(self, bucket_name, path):
                         swc_dicts.append(result)
         return swc_dicts
 
-    def read_from_s3_swcs(self, s3_path):
+    def read_from_s3(self, s3_path):
         # List filenames
         bucket_name, prefix = parse_cloud_path(s3_path)
         swc_paths = util.list_s3_paths(bucket_name, prefix, extension=".swc")
 
         # Parse SWC files
         swc_dicts = deque()
         for path in swc_paths:
-            contents = util.read_txt_from_s3(bucket_name, path)
+            content = util.read_txt_from_s3(bucket_name, path).splitlines()
+            filename = os.path.basename(path)
+            result = self.parse(content, filename)
+            if result:
+                swc_dicts.append(result)
         return swc_dicts
 
     def confirm_read(self, filename):

src/segmentation_skeleton_metrics/utils/util.py

@@ -369,7 +369,7 @@ def read_txt_from_s3(bucket_name, path):
     """
     s3 = boto3.client("s3", config=Config(signature_version=UNSIGNED))
     obj = s3.get_object(Bucket=bucket_name, Key=path)
-    return obj['Body'].read().decode('utf-8').splitlines()
+    return obj['Body'].read().decode('utf-8')
 
 
 # --- Miscellaneous ---