add support for seg map and meshes

.gitignore

@@ -151,4 +151,6 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-bla.py
+bla.py
+
+tmp/*

README.md

@@ -20,9 +20,6 @@ user = User(auth_token=auth_token)
 bucket = DataProxyBucket(user, "MY_BUCKET_NAME")
 
 proxy = EbrainsDataproxyHttpReplicatorAccessor(dataproxybucket=bucket, prefix="bigbrain_2015")
-io = get_IO_for_existing_dataset(bigbrain_accessor)
-import json
-proxy.store_file("info", json.dumps(io.info).encode("utf-8"))
 bigbrain_accessor.mirror_to(proxy)
 ```
 

chunk_replicator/accessor.py

@@ -1,4 +1,4 @@
-from typing import Set
+from typing import List, Set
 from neuroglancer_scripts.accessor import Accessor, _CHUNK_PATTERN_FLAT
 from neuroglancer_scripts.http_accessor import HttpAccessor
 from neuroglancer_scripts.precomputed_io import get_IO_for_existing_dataset
@@ -10,6 +10,7 @@
 
 from .dataproxy import DataProxyBucket
 from .util import retry
+from .logger import logger
 
 try:
     WORKER_THREADS = int(os.getenv("WORKER_THREADS", "16"))
@@ -30,14 +31,62 @@ class HttpMirrorSrcAccessor(HttpAccessor, MirrorSrcAccessor):
     def mirror_chunk(self, dst: Accessor, key: str, chunk_coords):
         chunk = self.fetch_chunk(key, chunk_coords)
         dst.store_chunk(chunk, key, chunk_coords)
+
+    def mirror_file(self, dst: Accessor, relative_path: str, mime_type="application/octet-stream"):
+        file_content = self.fetch_file(relative_path)
+        dst.store_file(relative_path, file_content, mime_type)
+        if relative_path.endswith(":0"):
+            dst.store_file(relative_path[:-2], file_content, mime_type)
+
 
-    def mirror_to(self, dst: Accessor):
+    def mirror_to(self, dst: Accessor, *, mesh_indicies: List[int]=None):
         assert dst.can_write
         io = get_IO_for_existing_dataset(self)
 
-        print("Begin mirroring. Got info:", io.info)
+        logger.debug("Begin mirroring. Got info:", io.info)
+
+        if mesh_indicies is not None:
+            logger.debug("mesh_indicies provided, mirroring meshes...")
+            mesh_dir = io.info.get("mesh")
+            assert mesh_dir, f"expecting mesh key defined in info, but is not."
+
+            with ThreadPoolExecutor(max_workers=WORKER_THREADS) as executor:
+                for progress in tqdm(
+                    executor.map(
+                        self.mirror_file,
+                        repeat(dst),
+                        (f"{mesh_dir}/{str(idx)}:0" for idx in mesh_indicies),
+                        repeat("application/json")
+                    ),
+                    total=len(mesh_indicies),
+                    desc="Fetching and writing mesh metadata...",
+                    unit="files",
+                    leave=True,
+                ):
+                    ...
+
+            fragments = [f"{mesh_dir}/{frag}"
+                        for idx in mesh_indicies
+                        for frag in json.loads(
+                            dst.fetch_file(f"{mesh_dir}/{str(idx)}:0").decode("utf-8")
+                        ).get("fragments")]
+
+            with ThreadPoolExecutor(max_workers=WORKER_THREADS) as executor:
+                for progress in tqdm(
+                    executor.map(
+                        self.mirror_file,
+                        repeat(dst),
+                        fragments,
+                    ),
+                    total=len(fragments),
+                    desc="Fetching and writing meshes...",
+                    unit="meshes",
+                    leave=True
+                ):
+                    ...
+
 
-        print("Mirroring info ...")
+        logger.debug("Mirroring info ...")
         dst.store_file("info", json.dumps(io.info).encode("utf-8"))
 
         for scale in io.info.get('scales'):
@@ -74,7 +123,7 @@ def mirror_to(self, dst: Accessor):
                 if not should_check_chunk_exists or not dst.chunk_exists(key, chunk_coord)
             ]
 
-            print(f"Mirroring data for key {key}")
+            logger.debug(f"Mirroring data for key {key}")
 
             with ThreadPoolExecutor(max_workers=WORKER_THREADS) as executor:
                 for progress in tqdm(
@@ -153,7 +202,7 @@ def store_chunk(self, buf, key, chunk_coords, mime_type="application/octet-strea
     def chunk_exists(self, key, chunk_coords):
         if not self._existing_obj_name_set:
 
-            print(f"Checking existing objects. Listing existing objects for {self.prefix}...")
+            logger.debug(f"Checking existing objects. Listing existing objects for {self.prefix}...")
 
             for obj in tqdm(
                 self.dataproxybucket.iterate_objects(prefix=self.prefix),

chunk_replicator/logger.py

@@ -0,0 +1,4 @@
+import logging
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)