Merge remote-tracking branch 'origin' into retry

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 5.25.2
+current_version = 5.26.0
 commit = True
 tag = True
 

.gitignore

@@ -118,3 +118,5 @@ notebooks/
 *.mp4
 *.tiff
 .idea/
+
+

caveclient/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "5.25.2"
+__version__ = "5.26.0"
 
 from .frameworkclient import CAVEclient
 from .session_config import SESSION_DEFAULTS

caveclient/auth.py

@@ -3,6 +3,7 @@
 import os
 import urllib
 import webbrowser
+from typing import Optional
 
 import requests
 
@@ -44,13 +45,21 @@ def write_token(token, filepath, key, overwrite=True):
         json.dump(secrets, f)
 
 
+def server_token_filename(server_address):
+    server = urllib.parse.urlparse(server_address).netloc
+    server_file = server + "-cave-secret.json"
+    server_file_path = os.path.join(default_token_location, server_file)
+    return os.path.expanduser(server_file_path)
+
+
 class AuthClient(object):
     def __init__(
         self,
         token_file=None,
         token_key=None,
         token=None,
         server_address=default_global_server_address,
+        local_server=None,
     ):
         """Client to find and use auth tokens to access the dynamic annotation framework services.
 
@@ -71,11 +80,11 @@ def __init__(
         server_address : str, optional,
             URL to the auth server. By default, uses a default server address.
         """
+        self._server_address = server_address
+        self._local_server = local_server
+
         if token_file is None:
-            server = urllib.parse.urlparse(server_address).netloc
-            server_file = server + "-cave-secret.json"
-            self._server_file_path = os.path.join(default_token_location, server_file)
-            self._server_file_path = os.path.expanduser(self._server_file_path)
+            self._server_file_path = server_token_filename(self._server_address)
             if os.path.isfile(self._server_file_path):
                 token_file = self._server_file_path
             else:
@@ -102,7 +111,6 @@ def __init__(
                         break
         self._token = token
 
-        self._server_address = server_address
         self._default_endpoint_mapping = {"auth_server_address": self._server_address}
 
     @property
@@ -215,12 +223,12 @@ def get_new_token(self, open=False, no_text=False):
 
     def save_token(
         self,
-        token=None,
-        token_key=default_token_key,
-        overwrite=False,
-        token_file=None,
-        switch_token=True,
-        write_to_server_file=True,
+        token: Optional[str] = None,
+        token_key: str = default_token_key,
+        overwrite: bool = False,
+        token_file: Optional[str] = None,
+        switch_token: bool = True,
+        write_to_server_file: bool = True,
     ):
         """Conveniently save a token in the correct format.
 
@@ -313,3 +321,38 @@ def request_header(self):
             return auth_header
         else:
             return {}
+
+    @property
+    def local_server(self):
+        return self._local_server
+
+    @local_server.setter
+    def local_server(self, new_val):
+        self._local_server = new_val
+        self._synchronize_local_server_file()
+
+    @property
+    def local_server_filepath(self):
+        if self.local_server:
+            return server_token_filename(self.local_server)
+        else:
+            return None
+
+    def _synchronize_local_server_file(self):
+        if self.local_server:
+            if os.path.exists(self.local_server_filepath):
+                local_token = self._load_token(
+                    self.local_server_filepath, self._token_key
+                )
+                if local_token != self.token:
+                    self.save_token(
+                        token=self.token,
+                        token_file=self.local_server_filepath,
+                        overwrite=True,
+                    )
+            else:
+                self.save_token(
+                    token=self.token,
+                    token_file=self.local_server_filepath,
+                    overwrite=True,
+                )

caveclient/endpoints.py

@@ -25,6 +25,11 @@
     + "/aligned_volume/{aligned_volume_name}/table/{table_name}/count",
 }
 
+annotation_api_versions = {0: annotation_endpoints_legacy, 2: annotation_endpoints_v2}
+
+# -------------------------------
+# ------ MaterializationEngine endpoints
+# -------------------------------
 
 materialization_common = {
     "get_api_versions": "{me_server_address}/materialize/api/versions"
@@ -94,8 +99,6 @@
     3: materialization_endpoints_v3,
 }
 
-annotation_api_versions = {0: annotation_endpoints_legacy, 2: annotation_endpoints_v2}
-
 # -------------------------------
 # ------ Infoservice endpoints
 # -------------------------------
@@ -284,3 +287,23 @@
     "get_info": "{ngl_url}/version.json",
     "fallback_ngl_url": fallback_ngl_endpoint,
 }
+
+# -------------------------------
+# ------ Skeleton endpoints
+# -------------------------------
+
+skeletonservice_common = {}
+
+skeleton_common = "{skeleton_server_address}/skeletoncache/api"
+skeleton_v1 = "{skeleton_server_address}/skeletoncache/api/v1"
+skeletonservice_endpoints_v1 = {
+    "get_version": skeleton_common + "/version",
+    "skeleton_info": skeleton_v1 + "/{datastack_name}/precomputed/skeleton/info",
+    "get_skeleton_via_rid": skeleton_v1
+    + "/{datastack_name}/precomputed/skeleton/{root_id}",
+    "get_skeleton_via_skvn_rid": skeleton_v1
+    + "/{datastack_name}/precomputed/skeleton/{skeleton_version}/{root_id}",
+    "get_skeleton_via_skvn_rid_fmt": skeleton_v1
+    + "/{datastack_name}/precomputed/skeleton/{skeleton_version}/{root_id}/{output_format}",
+}
+skeletonservice_api_versions = {1: skeletonservice_endpoints_v1}

caveclient/frameworkclient.py

@@ -11,6 +11,7 @@
 from .jsonservice import JSONService, JSONServiceV1
 from .l2cache import L2CacheClient, L2CacheClientLegacy
 from .materializationengine import MaterializationClient, MaterializationClientType
+from .skeletonservice import SkeletonClient
 
 
 class GlobalClientError(Exception):
@@ -52,6 +53,7 @@ def __new__(
         - `client.info` is an `InfoServiceClient` (see [client.info](../client_api/info.md))
         - `client.l2cache` is an `L2CacheClient` (see [client.l2cache](../client_api/l2cache.md))
         - `client.materialize` is a `MaterializationClient` (see [client.materialize](../client_api/materialize.md))
+        - `client.skeleton` is a `SkeletonClient` (see [client.skeleton](../client_api/skeleton.md))
         - `client.schema` is a `SchemaClient` (see [client.schema](../client_api/schema.md))
         - `client.state` is a neuroglancer `JSONService` (see [client.state](../client_api/state.md))
 
@@ -312,6 +314,9 @@ def chunkedgraph(self) -> None:
     def datastack_name(self) -> None:
         return None
 
+    def __repr__(self):
+        return f"CAVEclient<datastack=None, server_address={self.server_address}>"
+
 
 class CAVEclientFull(CAVEclientGlobal):
     def __init__(
@@ -346,6 +351,7 @@ def __init__(
         - `client.info` is an `InfoServiceClient` (see [client.info](../client_api/info.md))
         - `client.l2cache` is an `L2CacheClient` (see [client.l2cache](../client_api/l2cache.md))
         - `client.materialize` is a `MaterializationClient` (see [client.materialize](../client_api/materialize.md))
+        - `client.skeleton` is a `SkeletonClient` (see [client.skeleton](../client_api/skeleton.md))
         - `client.schema` is a `SchemaClient` (see [client.schema](../client_api/schema.md))
         - `client.state` is a neuroglancer `JSONService` (see [client.state](../client_api/state.md))
 
@@ -399,9 +405,12 @@ def __init__(
         self._chunkedgraph = None
         self._annotation = None
         self._materialize = None
+        self._skeleton = None
         self._l2cache = None
         self.desired_resolution = desired_resolution
         self.local_server = self.info.local_server()
+        self.auth.local_server = self.local_server
+
         av_info = self.info.get_aligned_volume_info()
         self._aligned_volume_name = av_info["name"]
 
@@ -444,6 +453,7 @@ def _reset_services(self):
         self._chunkedgraph = None
         self._annotation = None
         self._materialize = None
+        self._skeleton = None
         self._l2cache = None
 
     @property
@@ -513,6 +523,24 @@ def materialize(self) -> MaterializationClientType:
             )
         return self._materialize
 
+    @property
+    def skeleton(self) -> SkeletonClient:
+        """
+        A client for the skeleton service. See [client.skeleton](../client_api/skeleton.md)
+        for more information.
+        """
+        if self._skeleton is None:
+            self._skeleton = SkeletonClient(
+                server_address=self.local_server,
+                auth_client=self.auth,
+                datastack_name=self._datastack_name,
+                max_retries=self._max_retries,
+                pool_maxsize=self._pool_maxsize,
+                pool_block=self._pool_block,
+                over_client=self,
+            )
+        return self._skeleton
+
     @property
     def state(self) -> JSONServiceV1:
         """
@@ -553,3 +581,6 @@ def l2cache(self) -> L2CacheClientLegacy:
                 over_client=self,
             )
         return self._l2cache
+
+    def __repr__(self):
+        return f"CAVEclient<datastack_name={self.datastack_name}, server_address={self.server_address}>"

caveclient/jsonservice.py

@@ -2,6 +2,7 @@
 import numbers
 import os
 import re
+from typing import Optional
 
 import numpy as np
 
@@ -251,7 +252,12 @@ def upload_state_json(self, json_state, state_id=None, timestamp=None):
         return int(response_re.groups()[0])
 
     @_check_version_compatibility(">=0.4.0")
-    def upload_property_json(self, property_json, state_id=None, timestamp=None):
+    def upload_property_json(
+        self,
+        property_json,
+        state_id=None,
+        max_size: Optional[int] = 2_500_000,
+    ):
         """Upload a Neuroglancer JSON state
 
         Parameters
@@ -261,8 +267,9 @@ def upload_property_json(self, property_json, state_id=None, timestamp=None):
         state_id : int
             ID of a JSON state uploaded to the state service.
             Using a state_id is an admin feature.
-        timestamp: time.time
-            Timestamp for json state date. Requires state_id.
+        max_size: int
+            Maximum size in bytes for the data to upload. Default is 2.5MB. Set to None
+            for no limit.
 
         Returns
         -------
@@ -278,12 +285,23 @@ def upload_property_json(self, property_json, state_id=None, timestamp=None):
             url_mapping["state_id"] = state_id
             url = self._endpoints["upload_properties_w_id"].format_map(url_mapping)
 
+        data = json.dumps(
+            property_json,
+            default=neuroglancer_json_encoder,
+        )
+
+        # get size in bytes of data to upload
+        data_size = len(data.encode("utf-8"))
+
+        if max_size is not None and data_size > max_size:
+            msg = f"Data size {data_size} exceeds maximum size of {max_size} bytes. "
+            msg += "Please reduce the size of the data or increase the `max_size` "
+            msg += "if your state server can handle larger inputs."
+            raise ValueError(msg)
+
         response = self.session.post(
             url,
-            data=json.dumps(
-                property_json,
-                default=neuroglancer_json_encoder,
-            ),
+            data=data,
         )
         handle_response(response, as_json=False)
         response_re = re.search(".*\/(\d+)", str(response.content))