Source code for gen3.file

-import json
+import base64
+from dataclasses import dataclass, field
+
+import json
+from typing import List, Optional
+import numpy
 import requests
 import json
 import asyncio
 import aiohttp
 import aiofiles
 import time
-from tqdm import tqdm
+from tqdm.auto import tqdm
 from types import SimpleNamespace as Namespace
 import os
 import requests
@@ -53,7 +58,20 @@ 
Source code for gen3.file
 logging = get_logger("__name__")
 
 
+@dataclass
+class EmbeddingContent:
+    guid: str
+    embedding_id: str
+    embedding: numpy.ndarray
+    authz: list[str]
+    collection_id: int | None
+    self: str
+    metadata: dict[str, str] = field(default_factory=dict)
+
+
 MAX_RETRIES = 3
+DEFAULT_BATCH_SIZE = 500
+SUPPORTED_CONTENT_TYPES = ["gen3_embeddings"]
 
 
 

@@ -110,6 +128,217 @@ 
Source code for gen3.file
             return resp.text

 
 
+

+[docs]
+    def get_bulk_content(
+        self,
+        input_file=None,
+        guids=None,
+        batch_size=DEFAULT_BATCH_SIZE,
+        content_type=SUPPORTED_CONTENT_TYPES[0],
+    ) -> dict[str, EmbeddingContent]:
+        """
+        Retrieve bulk content for a set of GUIDs
+
+        Args:
+            input_file (str | None): Path to a file that contains one GUID per line.
+            guids (tuple[str, ...]): One or more GUIDs supplied
+            batch_size (int): How many GUIDs to send in each request to `/data/content`.
+            content_type (str): type of content of GUIDs, this determines how to parse.
+        """
+        if content_type not in SUPPORTED_CONTENT_TYPES:
+            raise ValueError(
+                f"Error: unsupported `content_type={content_type}`, not in supported: {SUPPORTED_CONTENT_TYPES}"
+            )
+
+        final_batch_size = min(batch_size, DEFAULT_BATCH_SIZE)
+        if final_batch_size != batch_size:
+            logging.warning(
+                f"Requested batch_size={batch_size} too large, using default: {DEFAULT_BATCH_SIZE}"
+            )
+
+        if input_file and guids:
+            raise ValueError("Error: provide either input_file or guids, not both.")
+
+        all_guids: List[str] = []
+
+        if input_file:
+            with open(input_file) as f:
+                for line in f:
+                    guid = line.strip()
+                    if guid:
+                        all_guids.append(guid)
+        elif guids:
+            all_guids.extend(guids)
+        else:
+            raise ValueError("Error: provide either input_file or guids")
+
+        if not all_guids:
+            logging.error("No valid GUIDs found in the supplied input.")
+            return {}
+
+        embeddings = {}
+
+        for start in range(0, len(all_guids), batch_size):
+            batch = all_guids[start : start + batch_size]
+            try:
+                batch_response = self.get_content(batch)
+            except Exception as exc:
+                logging.error(f"API error on batch starting at {batch[0]}: {exc}")
+                continue
+
+            if isinstance(batch_response, str):
+                logging.warning(
+                    f"Warning: received raw text response for batch starting with {batch[0]}. Skipping."
+                )
+                continue
+
+            if content_type == "gen3_embeddings":
+                embeddings_from_batch = self.get_embeddings_from_bulk_content(
+                    batch_response
+                )
+                embeddings.update(embeddings_from_batch)
+
+        logging.debug(f"Successfully retrieved {len(embeddings)} records!")
+        return embeddings

+
+
+

+[docs]
+    def get_content(self, guids: list) -> dict:
+        """
+        Bulk retrieve content for a list of GUIDs.
+
+        The Gen3 API provides the `/data/content` endpoint which accepts a JSON body with
+        an array of GUID strings.  This helper wraps that call and returns the parsed
+        response.
+
+        Args:
+            guids (list): A list or tuple of GUIDs for which to fetch content.
+
+        Returns:
+            dict | str: If the request succeeds and the body can be decoded as JSON, a mapping
+                from each provided GUID to its associated content is returned
+
+        Raises:
+            requests.HTTPError: If the HTTP status code indicates an error
+        """
+        api_url = f"{self._endpoint}/user/data/content"
+        body = {"guids": guids}
+        headers = {"Content-Type": "application/json"}
+
+        resp = requests.post(
+            api_url, auth=self._auth_provider, json=body, headers=headers
+        )
+        raise_for_status_and_print_error(resp)
+
+        return resp.json()

+
+
+

+[docs]
+    def get_embeddings_from_bulk_content(
+        self, batch_response: dict
+    ) -> dict[str, EmbeddingContent]:
+        """
+        Get a dict of parsed embeddings from a batch_resonse of GUIDs
+        which are all embeddings.
+        """
+        embeddings = {}
+        for guid, data in batch_response.get("guids", {}).items():
+            embeddings[guid] = self.get_embeddings_from_bulk_content_guid(guid, data)
+        return embeddings

+
+
+

+[docs]
+    def get_embeddings_from_bulk_content_guid(
+        self, guid: str, bulk_content_guid_data: dict
+    ) -> EmbeddingContent:
+        """
+        Return an EmbeddingContent by parsing the response data for a particular GUID in a Bulk Content
+        response which corresponds to a Gen3 EmbeddingContent.
+
+        Note: this handles base64 decoding if the API call used that. and note that the resulting
+            vector is a numpy array
+
+        Args:
+            guid (str): globally unique identifier for the blob of data provided
+            bulk_content_guid_data (dict): data from Bulk Content response.get("guids", {}).get(guid)
+                e.g. the data for the guid specified
+
+        Returns:
+            EmbeddingContent - a dataclass representation of the embedding
+        """
+        if not isinstance(bulk_content_guid_data, dict):
+            logging.info(f"Warning: did not find {guid} in output, adding empty row...")
+            return EmbeddingContent(
+                guid=guid,
+                embedding_id="",
+                embedding=numpy.array([]),
+                authz="",
+                collection_id=None,
+                self="",
+                metadata={},
+            )
+
+        embedding_id = bulk_content_guid_data.get(
+            "embedding_id", ""
+        ) or bulk_content_guid_data.get("id", "")
+        raw_vector = (
+            bulk_content_guid_data.get("vector")
+            or bulk_content_guid_data.get("embedding")
+            or []
+        )
+
+        embedding_vector = None
+
+        # handle vector if base64 version of API used
+        if not raw_vector and "vector_base64" in bulk_content_guid_data:
+            if "precision" not in bulk_content_guid_data:
+                raise Exception(
+                    f"`vector_base64` found but no `precision` specified. Unable to parse."
+                )
+
+            vector_data_type = (
+                numpy.float16
+                if bulk_content_guid_data["precision"] == "float16"
+                else numpy.float32
+            )
+
+            # endpoint may be using binary representation
+            vector_base64_str = bulk_content_guid_data["vector_base64"]
+
+            # re-pad the string to a multiple of 4 (handles any missing '=' signs)
+            padding_needed = -len(vector_base64_str) % 4
+            padded_b64 = vector_base64_str + ("=" * padding_needed)
+            decoded_bytes = base64.urlsafe_b64decode(padded_b64)
+
+            embedding_vector = numpy.frombuffer(decoded_bytes, dtype=vector_data_type)
+
+        if embedding_vector is None:
+            embedding_vector = numpy.array(raw_vector)
+
+        authz_val = bulk_content_guid_data.get("info", {}).get("authz", "")
+        collection_id_val = bulk_content_guid_data.get("info", {}).get(
+            "collection_id", ""
+        )
+
+        url_or_self = bulk_content_guid_data.get("info", {}).get("self")
+
+        metadata = bulk_content_guid_data.get("info", {}).get("metadata")
+
+        return EmbeddingContent(
+            guid=guid,
+            embedding_id=embedding_id,
+            embedding=embedding_vector,
+            authz=authz_val,
+            collection_id=collection_id_val,
+            self=url_or_self,
+            metadata=metadata,
+        )

+
+
 

 [docs]
     def delete_file(self, guid):
diff --git a/docs/_build/html/_modules/gen3/jobs.html b/docs/_build/html/_modules/gen3/jobs.html
index 850554d3d..8f19585f6 100644
--- a/docs/_build/html/_modules/gen3/jobs.html
+++ b/docs/_build/html/_modules/gen3/jobs.html
@@ -34,6 +34,7 @@ 
Source code for gen3.jobs
 """
 Contains class for interacting with Gen3's Job Dispatching Service(s).
 """
+
 import aiohttp
 import asyncio
 import backoff
diff --git a/docs/_build/html/_modules/gen3/metadata.html b/docs/_build/html/_modules/gen3/metadata.html
index c5a2cff9c..728c336ee 100644
--- a/docs/_build/html/_modules/gen3/metadata.html
+++ b/docs/_build/html/_modules/gen3/metadata.html
@@ -34,6 +34,7 @@ 
Source code for gen3.metadata
 """
 Contains class for interacting with Gen3's Metadata Service.
 """
+
 import aiohttp
 import backoff
 from datetime import datetime
diff --git a/docs/_build/html/_modules/gen3/tools/download/drs_download.html b/docs/_build/html/_modules/gen3/tools/download/drs_download.html
index 27f9b7d36..bfc0b07af 100644
--- a/docs/_build/html/_modules/gen3/tools/download/drs_download.html
+++ b/docs/_build/html/_modules/gen3/tools/download/drs_download.html
@@ -50,7 +50,6 @@ 
Source code for gen3.tools.download.drs_download

 
 """
 
-
 import re
 import os
 from dataclasses import dataclass, field
@@ -66,7 +65,7 @@ 
Source code for gen3.tools.download.drs_download

 from cdislogging import get_logger
 from dataclasses_json import dataclass_json, LetterCase, Undefined
 from dateutil import parser as date_parser
-from tqdm import tqdm
+from tqdm.auto import tqdm
 from urllib.parse import urlparse
 
 from gen3.auth import Gen3Auth, Gen3AuthError, decode_token
@@ -147,7 +146,7 @@ 
Source code for gen3.tools.download.drs_download

     @staticmethod
     def load(filename: Path) -> Optional[List["Downloadable"]]:
         """
-        Method to load a json manifest and return a list of Bownloadable object.
+        Method to load a json manifest and return a list of Downloadable object.
         This list is passed to the DownloadManager methods of download, and list
 
         Args:
@@ -929,9 +928,9 @@ 
Source code for gen3.tools.download.drs_download

         resolve_objects_drs_hostname(
             object_list,
             self.resolved_compact_drs,
-            mds_url=f"http://{self.hostname}/mds/aggregate/info"
-            if self.hostname
-            else None,
+            mds_url=(
+                f"http://{self.hostname}/mds/aggregate/info" if self.hostname else None
+            ),
             commons_url=self.commons_url,
         )
         progress_bar = (
diff --git a/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html
index 296f84d61..6cbdb2aee 100644
--- a/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html
+++ b/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html
@@ -53,6 +53,7 @@ 
Source code for gen3.tools.indexing.download_manifest
              To workaround this, we have each process write to a file and concat
               them all post-processing.
 """
+
 import asyncio
 import aiofiles
 import click
diff --git a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html
index 9a6cab6f0..4e5874f42 100644
--- a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html
+++ b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html
@@ -63,6 +63,7 @@ 
Source code for gen3.tools.indexing.index_manifest
    python index_manifest.py --commons_url https://giangb.planx-pla.net  --manifest_file path_to_manifest --auth "admin,admin" --replace_urls False --thread_num 10
     python index_manifest.py --commons_url https://giangb.planx-pla.net  --manifest_file path_to_manifest --api_key ./credentials.json --replace_urls False --thread_num 10
 """
+
 import os
 import csv
 import click
@@ -87,7 +88,7 @@ 
Source code for gen3.tools.indexing.index_manifest
PREV_GUID_STANDARD_KEY,
 )
 from gen3.utils import (
-    _standardize_str,
+    standardize_str,
     get_urls,
 )
 from gen3.tools.utils import get_and_verify_fileinfos_from_manifest
@@ -95,7 +96,6 @@ 
Source code for gen3.tools.indexing.index_manifest
from indexclient.client import Document
 from cdislogging import get_logger
 
-
 CURRENT_DIR = os.path.dirname(os.path.realpath(__file__))
 
 logging = get_logger("__name__")
@@ -187,7 +187,7 @@ 
Source code for gen3.tools.indexing.index_manifest
authz = (
             [
                 element.strip().replace("'", "").replace('"', "").replace("%20", " ")
-                for element in _standardize_str(fi[AUTHZ_STANDARD_KEY])
+                for element in standardize_str(fi[AUTHZ_STANDARD_KEY])
                 .strip()
                 .lstrip("[")
                 .rstrip("]")
@@ -209,7 +209,7 @@ 
Source code for gen3.tools.indexing.index_manifest
.replace("'", "")
                         .replace('"', "")
                         .replace("%20", " ")
-                        for element in _standardize_str(fi[ACL_STANDARD_KEY])
+                        for element in standardize_str(fi[ACL_STANDARD_KEY])
                         .strip()
                         .lstrip("[")
                         .rstrip("]")
@@ -224,7 +224,7 @@ 
Source code for gen3.tools.indexing.index_manifest
acl = []
 
         if FILENAME_STANDARD_KEY in fi:
-            file_name = _standardize_str(fi[FILENAME_STANDARD_KEY])
+            file_name = standardize_str(fi[FILENAME_STANDARD_KEY])
         else:
             file_name = ""
 
diff --git a/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html
index fcb339ac1..3e5ec1139 100644
--- a/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html
+++ b/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html
@@ -72,6 +72,7 @@ 
Source code for gen3.tools.indexing.verify_manifest
    MAX_CONCURRENT_REQUESTS (int): maximum number of desired concurrent requests across
         processes/threads
 """
+
 import aiohttp
 import asyncio
 import csv
@@ -81,7 +82,8 @@ 
Source code for gen3.tools.indexing.verify_manifest
import time
 
 from gen3.index import Gen3Index
-from gen3.utils import get_or_create_event_loop_for_thread
+from gen3.tools.utils import AUTHZ_STANDARD_KEY
+from gen3.utils import get_or_create_event_loop_for_thread, standardize_str
 
 MAX_CONCURRENT_REQUESTS = 24
 CURRENT_DIR = os.path.dirname(os.path.realpath(__file__))
@@ -169,7 +171,21 @@ 
Source code for gen3.tools.indexing.verify_manifest
    Returns:
         List[str]: authz resources for the indexd record
     """
-    return [item for item in row.get("authz", "").strip().split(" ") if item]
+    authz = (
+        [
+            element.strip().replace("'", "").replace('"', "").replace("%20", " ")
+            for element in standardize_str(row[AUTHZ_STANDARD_KEY])
+            .strip()
+            .lstrip("[")
+            .rstrip("]")
+            .split(" ")
+        ]
+        if AUTHZ_STANDARD_KEY in row
+        and row[AUTHZ_STANDARD_KEY] != "[]"
+        and row[AUTHZ_STANDARD_KEY]
+        else []
+    )
+    return authz
 
 
 def _get_urls_from_row(row):
diff --git a/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html b/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html
index 30d22538a..030bd18e3 100644
--- a/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html
+++ b/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html
@@ -52,6 +52,7 @@ 
Source code for gen3.tools.metadata.ingest_manifest
    MAX_CONCURRENT_REQUESTS (int): Maximum concurrent requests to mds for ingestion
 """
+
 import aiohttp
 import asyncio
 import csv
diff --git a/docs/_build/html/file.html b/docs/_build/html/file.html
index cb970d072..f7f515f54 100644
--- a/docs/_build/html/file.html
+++ b/docs/_build/html/file.html
@@ -103,6 +103,79 @@ 
Gen3 File Class
+

+get_bulk_content(input_file=None, guids=None, batch_size=500, content_type='gen3_embeddings') → dict[str, EmbeddingContent][source]

+
Retrieve bulk content for a set of GUIDs

+

+
Parameters:

+
    
+
  • input_file (str | None) – Path to a file that contains one GUID per line.
    • 
+
  • guids (tuple[str, ...]) – One or more GUIDs supplied
    • 
+
  • batch_size (int) – How many GUIDs to send in each request to /data/content.
    • 
+
  • content_type (str) – type of content of GUIDs, this determines how to parse.
    • 
+

+

+

+

+
+

+

+get_content(guids: list) → dict[source]

+
Bulk retrieve content for a list of GUIDs.

+
The Gen3 API provides the /data/content endpoint which accepts a JSON body with
+an array of GUID strings.  This helper wraps that call and returns the parsed
+response.

+

+
Parameters:

+
guids (list) – A list or tuple of GUIDs for which to fetch content.

+

+
Returns:

+

+
If the request succeeds and the body can be decoded as JSON, a mapping
from each provided GUID to its associated content is returned

+

+

+

+

+
Return type:

+
dict | str

+

+
Raises:

+
requests.HTTPError – If the HTTP status code indicates an error

+

+

+

+
+

+

+get_embeddings_from_bulk_content(batch_response: dict) → dict[str, EmbeddingContent][source]

+
Get a dict of parsed embeddings from a batch_resonse of GUIDs
+which are all embeddings.

+

+
+

+

+get_embeddings_from_bulk_content_guid(guid: str, bulk_content_guid_data: dict) → EmbeddingContent[source]

+
Return an EmbeddingContent by parsing the response data for a particular GUID in a Bulk Content
+response which corresponds to a Gen3 EmbeddingContent.

+

+
Note: this handles base64 decoding if the API call used that. and note that the resulting
vector is a numpy array

+

+

+

+
Parameters:

+
    
+
  • guid (str) – globally unique identifier for the blob of data provided
    • 
+
  • bulk_content_guid_data (dict) – data from Bulk Content response.get(“guids”, {}).get(guid)
+e.g. the data for the guid specified
    • 
+

+

+
Returns:

+
EmbeddingContent - a dataclass representation of the embedding

+

+

+

+
 

 

 get_presigned_url(guid, protocol=None)[source]

@@ -221,6 +294,10 @@ 
Gen3 SDK

 
  • Gen3File.delete_file()
    • 
 
  • Gen3File.delete_file_locations()
    • 
 
  • Gen3File.download_single()
    • 
+
  • Gen3File.get_bulk_content()
    • 
+
  • Gen3File.get_content()
    • 
+
  • Gen3File.get_embeddings_from_bulk_content()
    • 
+
  • Gen3File.get_embeddings_from_bulk_content_guid()
    • 
 
  • Gen3File.get_presigned_url()
    • 
 
  • Gen3File.upload_file()
    • 
 
  • Gen3File.upload_file_to_guid()
    • 
diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html
index fc7b36ca6..878765116 100644
--- a/docs/_build/html/genindex.html
+++ b/docs/_build/html/genindex.html
@@ -349,12 +349,20 @@ 
    G
    
       
  • get_aliases() (gen3.metadata.Gen3Metadata method)
 
    • 
       
  • get_all_records() (gen3.index.Gen3Index method)
+
    • 
+      
  • get_bulk_content() (gen3.file.Gen3File method)
+
    • 
+      
  • get_content() (gen3.file.Gen3File method)
 
    • 
       
  • get_dictionary_all() (gen3.submission.Gen3Submission method)
 
    • 
   
   
      
       
    • get_dictionary_node() (gen3.submission.Gen3Submission method)
+
      • 
+      
    • get_embeddings_from_bulk_content() (gen3.file.Gen3File method)
+
      • 
+      
    • get_embeddings_from_bulk_content_guid() (gen3.file.Gen3File method)
 
      • 
       
    • get_fresh_token() (gen3.tools.download.drs_download.DownloadManager method)
 
      • 
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index d329e8bcb..a61ccba7f 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -53,6 +53,10 @@ 
      Welcome to Gen3 SDK’s documentation!Gen3File.delete_file()
 
    • Gen3File.delete_file_locations()
      • 
 
    • Gen3File.download_single()
      • 
+
    • Gen3File.get_bulk_content()
      • 
+
    • Gen3File.get_content()
      • 
+
    • Gen3File.get_embeddings_from_bulk_content()
      • 
+
    • Gen3File.get_embeddings_from_bulk_content_guid()
      • 
 
    • Gen3File.get_presigned_url()
      • 
 
    • Gen3File.upload_file()
      • 
 
    • Gen3File.upload_file_to_guid()
      • 
diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv
index 8f2fb369e..82c42b951 100644
Binary files a/docs/_build/html/objects.inv and b/docs/_build/html/objects.inv differ
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index a1ce89060..e2651ee28 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/_build/html/tools/drs_pull.html b/docs/_build/html/tools/drs_pull.html
index 21e46086a..8cdf09927 100644
--- a/docs/_build/html/tools/drs_pull.html
+++ b/docs/_build/html/tools/drs_pull.html
@@ -387,7 +387,7 @@
 
      
 
      
 static load(filename: Path) → List[Downloadable] | None[source]
      
-
      Method to load a json manifest and return a list of Bownloadable object.
+
      Method to load a json manifest and return a list of Downloadable object.
 This list is passed to the DownloadManager methods of download, and list
      
 
      
 
      Parameters:
      
diff --git a/docs/tutorial/gen3_embeddings.ipynb b/docs/tutorial/gen3_embeddings.ipynb
new file mode 100644
index 000000000..f6b09d058
--- /dev/null
+++ b/docs/tutorial/gen3_embeddings.ipynb
@@ -0,0 +1,779 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# Gen3 Embeddings Demo\n",
+    "\n",
+    "> This will demonstrate how to create and retrieve embeddings in bulk from Gen3"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
+   "source": [
+    "First, let's install the Gen3 Python Software Development Kit (SDK), which includes a command line interface (CLI)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%pip install --upgrade pip\n",
+    "%pip install gen3 --upgrade"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# we also need pandas for some nice visualizations of output files\n",
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4",
+   "metadata": {},
+   "source": [
+    "If you are running Gen3 locally, you can set some variables to point to the right credentials file.\n",
+    "\n",
+    "If you are trying to interact with a production instance, just leave the default `ai`. e.g. don't uncomment - the default credentials setup should point you to the right place if you have your API key in the default location `~/.gen3/credentials.json`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "ai = \"ai\"\n",
+    "\n",
+    "# ai = \"--auth ~/.gen3/local_helm_test_user.json ai\"\n",
+    "# url_prefix = \"https://foobar-local.dev.planx-pla.net/ai\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6",
+   "metadata": {},
+   "source": [
+    "## Gen3 AI Embeddings CLI"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 ai embeddings --help"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!gen3 ai embeddings collections --help"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9",
+   "metadata": {},
+   "source": [
+    "Get a response from the service by reading collections. \n",
+    "\n",
+    "> IMPORTANT: You need appropriate permissions to read (and for future sections: write).\n",
+    "> So these commands may be empty or fail unless you have those authorizations in the environment your credentials are for."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings collections read"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "11",
+   "metadata": {},
+   "source": [
+    "## Create Embeddings Collections"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "12",
+   "metadata": {},
+   "source": [
+    "This will show creation of collections and embeddings. So you need write permission or this will fail. You can run the Gen3 Embeddings API locally to test this out. See the [Gen3 AI repo README](https://github.com/uc-cdis/gen3-ai) for more information."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "13",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings collections delete \"ctds-github-md\"\n",
+    "!gen3 $ai embeddings collections create \"ctds-github-md\" --dimensions 384 --description \"All markdown from CTDS Github\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "14",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings collections read \"ctds-github-md\" "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "15",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# try to delete collections that might already exist\n",
+    "!gen3 $ai embeddings collections delete \"test_expr\"\n",
+    "!gen3 $ai embeddings collections delete \"test_hist\"\n",
+    "!gen3 $ai embeddings collections delete \"test_summ\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "16",
+   "metadata": {},
+   "source": [
+    "Let's create some more example collections.\n",
+    "\n",
+    "> IMPORTANT: You need permission to create and manage these collections *before* running the commands. So ensure the Gen3 operator adds these resources to the `user.yaml` and provides your user permission to them. If you are running Gen3 yourself, you can see the [Gen3 AI repo README](https://github.com/uc-cdis/gen3-ai) for more information on how to set up appropriate auth."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "17",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings collections create \"test_expr\" --dimensions 256 --description \"test expr data\"\n",
+    "!gen3 $ai embeddings collections create \"test_hist\" --dimensions 1536 --description \"test hist data\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "18",
+   "metadata": {},
+   "source": [
+    "You can also create collections of larger dimensional size. This will use a `vector_type` of `halfvec` to fit it into the underlying database."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "19",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings collections create \"test_summ\" --dimensions 4096 --description \"test summ data\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "20",
+   "metadata": {},
+   "source": [
+    "## Publish Data into Embeddings Collections"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "21",
+   "metadata": {},
+   "source": [
+    "Now that we have created collections for embeddings, we can publish the actual embeddings into those collections.\n",
+    "\n",
+    "To do this, you need a Gen3 Embeddings Manifests. Conveniently, there are examples in the Gen3 Python SDK/CLI repo in the tests folder you can use."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "22",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings publish --help"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "23",
+   "metadata": {},
+   "source": [
+    "See the above help message to understand what we need to publish embeddings. \n",
+    "\n",
+    "**tl;dr** we need a manifest file with a row per embedding. That row needs to contain the vector (embedding), along with other metadata."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "24",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# here's a quick visualization of the columns/data of this input manifest\n",
+    "df = pd.read_csv('../../tests/embeddings_tests/test_expr.tsv', sep='\\t', nrows=3)\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "25",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings publish ../../tests/embeddings_tests/test_expr.tsv --default-collection test_expr"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "26",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# here's a quick visualization of the columns/data of this input manifest\n",
+    "df = pd.read_csv('../../tests/embeddings_tests/test_hist.tsv', sep='\\t', nrows=3)\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "27",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings publish ../../tests/embeddings_tests/test_hist.tsv --default-collection test_hist"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "28",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# here's a quick visualization of the columns/data of this input manifest\n",
+    "df = pd.read_csv('../../tests/embeddings_tests/test_summ.tsv', sep='\\t', nrows=3)\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "29",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings publish ../../tests/embeddings_tests/test_summ.tsv --default-collection test_summ"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "30",
+   "metadata": {},
+   "source": [
+    "## Convert Published Embeddings Manifests into Indexing Manifests"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "31",
+   "metadata": {},
+   "source": [
+    "Each of the `publish` commands above generated an output file `{input_filename}_output.tsv` (unless you overrode the output filename). \n",
+    "\n",
+    "Those outputs are manifests that now contain the final `embedding_id` and other Gen3 Embedding information that came back from creating embeddings through the Gen3 Embeddings API.\n",
+    "\n",
+    "We can **convert** those _outputted_ Published Gen3 Embeddings Manifests into Gen3 Indexing Manifests to _input_ into the Gen3 Indexing process. This will allow us to create persistent, indexed records with globally unique identifiers (GUIDs) in Gen3 through the Gen3 Indexing API.\n",
+    "\n",
+    "So first, let's convert to the expected format for indexing."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "32",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# here's a quick visualization of the columns/data of the output manifest from previous `publish` commands\n",
+    "# this is what we'll convert\n",
+    "df = pd.read_csv('../../tests/embeddings_tests/test_expr_output.tsv', sep='\\t', nrows=3)\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "33",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings convert --help"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "34",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 $ai embeddings convert ../../tests/embeddings_tests/test_expr_output.tsv --url-prefix $url_prefix\n",
+    "!gen3 $ai embeddings convert ../../tests/embeddings_tests/test_hist_output.tsv --url-prefix $url_prefix\n",
+    "!gen3 $ai embeddings convert ../../tests/embeddings_tests/test_summ_output.tsv --url-prefix $url_prefix"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "35",
+   "metadata": {},
+   "source": [
+    "That `convert` command created new `{original_filename}_converted.tsv` files. Let's take a look at those:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "36",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "df = pd.read_csv('../../tests/embeddings_tests/test_expr_output_converted.tsv', sep='\\t', nrows=3)\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "37",
+   "metadata": {},
+   "source": [
+    "## Create Gen3 Indexed Records with the Indexing Manifest"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "38",
+   "metadata": {},
+   "source": [
+    "The manifest we converted to above is a Gen3 Indexing Manifest with no GUIDs - we'll let the Gen3 Indexing command and backend generate those for us.\n",
+    "\n",
+    "The `md5` checksum and `size` in bytes columns above are of the JSON-stringified version of the vector (in other words, the \"data\" is the vector itself).\n",
+    "\n",
+    "`url` is a direct link to the Gen3 Embeddings API for that particular embedding.\n",
+    "\n",
+    "Now, before we index, let's validate our Gen3 Indexing manifest is correctly formatted:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "39",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 objects manifest validate-manifest-format --help"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "40",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 objects manifest validate-manifest-format ../../tests/embeddings_tests/test_expr_output_converted.tsv --allowed-protocols \"https http\"\n",
+    "!gen3 objects manifest validate-manifest-format ../../tests/embeddings_tests/test_hist_output_converted.tsv --allowed-protocols \"https http\"\n",
+    "!gen3 objects manifest validate-manifest-format ../../tests/embeddings_tests/test_summ_output_converted.tsv --allowed-protocols \"https http\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "41",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 objects manifest publish --help"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "42",
+   "metadata": {},
+   "source": [
+    "> IMPORTANT NOTE: Publishing the manifest through the Gen3 Indexing API requires permissions to write to that API. \n",
+    "\n",
+    "**For Gen3 Operators**: typically there is an `indexd_admin` policy. One option to provide the necessary permissions is to add the `/vectorstore/collection/` resource path to that. This will allow full administrative management of indexing records with `authz` beginning with that path.\n",
+    "\n",
+    "Example `user.yaml` snippet:\n",
+    "\n",
+    "```yaml\n",
+    "...\n",
+    "      - id: indexd_admin\n",
+    "        description: full access to indexd API\n",
+    "        role_ids:\n",
+    "          - indexd_admin\n",
+    "        resource_paths:\n",
+    "          - /programs\n",
+    "          - /vectorstore/collections       <----- THIS IS NEW\n",
+    "...\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "43",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 -v objects manifest publish ../../tests/embeddings_tests/test_expr_output_converted.tsv --out-manifest-file ../../tests/embeddings_tests/expr_output_converted_indexed.tsv --thread-num 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "44",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 objects manifest verify ../../tests/embeddings_tests/test_expr_output_converted_indexed.tsv --max-concurrent-requests 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "45",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 -v objects manifest publish ../../tests/embeddings_tests/test_hist_output_converted.tsv --out-manifest-file ../../tests/embeddings_tests/hist_output_converted_indexed.tsv --thread-num 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "46",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 objects manifest verify ../../tests/embeddings_tests/test_hist_output_converted_indexed.tsv --max-concurrent-requests 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "47",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 -v objects manifest publish ../../tests/embeddings_tests/test_summ_output_converted.tsv --out-manifest-file ../../tests/embeddings_tests/summ_output_converted_indexed.tsv --thread-num 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "48",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!gen3 objects manifest verify ../../tests/embeddings_tests/test_summ_output_converted_indexed.tsv --max-concurrent-requests 1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "49",
+   "metadata": {},
+   "source": [
+    "Now there are indexed records with GUIDs. The above tool output an `*_indexed.tsv` manifest. We can take a look and see that now the `guid` column is filled out! "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "50",
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "df = pd.read_csv('../../tests/embeddings_tests/test_expr_output_converted_indexed.tsv', sep='\\t', nrows=3)\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "51",
+   "metadata": {},
+   "source": [
+    "## Everything is in Gen3 now!\n",
+    "\n",
+    "Let's recap. We have:\n",
+    "\n",
+    "- Created Gen3 Embeddings Collections to store embeddings of different dimensionality\n",
+    "- Ingested Embeddings Manifests of embeddings through the Gen3 Embeddings API into the collections we created\n",
+    "- Converted output manifest from embedding creation into indexing manifests\n",
+    "- Ingested Indexing Manifests to create Gen3 Indexed Records with assigned GUIDs\n",
+    "\n",
+    "At this point, we have the embeddings themselves stored and we've created persistent identifiers (GUIDs). \n",
+    "\n",
+    "Now you can use those GUIDs the same way you use other Gen3 GUIDs for files. So if you have a Gen3 Data Model with nodes that point to sample files identified by GUIDs, you can now have a new \"embedding\" node with a GUID pointing to the embedding!\n",
+    "\n",
+    "This will allow traditional Gen3 search for data with embeddings.\n",
+    "\n",
+    "If you want to search the embeddings collections themselves, the Gen3 Embedding API exposes search functionality as well. This supports similarity search.\n",
+    "\n",
+    "## Bulk Retrieval of Gen3 Embeddings via their Indexed GUIDs\n",
+    "\n",
+    "Let's assume we've found GUIDs of interest via a search in Gen3 (and for simplicity, let's assume those GUIDs are ALL the GUIDs we have indexed previously in this notebook). Now, given **only** those GUIDs, we want to bulk retrieve the actual embeddings from Gen3 to do some AI/ML analysis."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "52",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\"\"\"\n",
+    "This just aggregates all the GUIDs from all our indexed files into a single file.\n",
+    "\n",
+    "This output file simulates (or rather, skips) the process of finding data of interest and getting the GUIDs.\n",
+    "\"\"\"\n",
+    "import glob\n",
+    "import pandas as pd\n",
+    "\n",
+    "file_pattern = \"../../tests/embeddings_tests/*_output_converted_indexed.tsv\"\n",
+    "output_file = \"../../tests/embeddings_tests/test_aggregated_guids.tsv\"\n",
+    "\n",
+    "all_files = glob.glob(file_pattern)\n",
+    "\n",
+    "df_list = []\n",
+    "for file in all_files:\n",
+    "    # usecols ensures we don't waste memory. only load guids\n",
+    "    df = pd.read_csv(file, sep=\"\\t\", usecols=[\"guid\"])\n",
+    "    df_list.append(df)\n",
+    "\n",
+    "combined_df = pd.concat(df_list, ignore_index=True)\n",
+    "combined_df.to_csv(output_file, sep=\"\\t\", index=False)\n",
+    "\n",
+    "print(f\"Done! Aggregated {len(all_files)} files into: {output_file}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "53",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df = pd.read_csv('../../tests/embeddings_tests/test_aggregated_guids.tsv', sep='\\t', nrows=3)\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "54",
+   "metadata": {},
+   "source": [
+    "## Bulk retrieve embeddings from Fence\n",
+    "\n",
+    "Now we can pretend we found a bunch of GUIDs of interest in Gen3.\n",
+    "\n",
+    "For this example, we'll use all the GUIDs we previously created.\n",
+    "\n",
+    "By providing a manifest of only GUIDs (or passing on the CLI), we can get the _content_ of the referenced data from the indexed record, e.g. the embedding itself.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "55",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from gen3.file import Gen3File\n",
+    "from gen3.auth import Gen3Auth\n",
+    "\n",
+    "auth = Gen3Auth()\n",
+    "gen3_file = Gen3File(auth.endpoint, auth_provider=auth)\n",
+    "\n",
+    "embeddings_contents = gen3_file.get_bulk_content(input_file=\"../../tests/embeddings_tests/test_aggregated_guids.tsv\")\n",
+    " \n",
+    "print(f\"Got all {len(embeddings_contents)} GUIDs\")\n",
+    "\n",
+    "for guid, embedding_content in embeddings_contents.items():\n",
+    "    # the GUIDs are already an efficient numpy array!\n",
+    "    print(type(embedding_content.embedding))\n",
+    "    print(embedding_content)\n",
+    "    break\n",
+    "\n",
+    "# do other AI/ML work with the embeddings!"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "56",
+   "metadata": {},
+   "source": [
+    "We have shown the full flow from original vectors -> storage in Gen3 -> retrieval from Gen3 in an efficient bulk pipeline. \n",
+    "\n",
+    "We've also shown that Gen3 Embeddings can be indexed like files to provide GUIDs which can be referenced and searched the same way file-based GUIDs are today."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "gen3-NXImaaEr-py3.13",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/gen3/ai.py b/gen3/ai.py
new file mode 100644
index 000000000..f8561c1a7
--- /dev/null
+++ b/gen3/ai.py
@@ -0,0 +1,294 @@
+import logging
+from typing import Any
+
+import backoff
+import httpx
+from cdislogging import get_logger
+
+from gen3.auth import Gen3Auth
+from gen3.utils import DEFAULT_BACKOFF_SETTINGS
+
+logger = get_logger("__name__")
+
+
+class EmbeddingsClient:
+    """
+    Client for interacting with the gen3_embeddings API.
+
+    For local:
+
+    ```python
+        auth = Gen3Auth(refresh_file="credentials.json")
+        embeddings_client = EmbeddingClient(
+            auth=auth,
+            endpoint="localhost:4143",
+            api_prefix="",
+        )
+    ````
+
+    """
+
+    def __init__(
+        self,
+        auth: Gen3Auth,
+        endpoint: str | None = None,
+        api_prefix: str = "ai",
+    ):
+        """
+        Initialize the embedding client.
+        """
+        # prefer provided endpoint and fallback on one in creds
+        endpoint = endpoint or auth.endpoint or ""
+        endpoint = endpoint.strip("/")
+
+        if not endpoint.endswith(api_prefix):
+            endpoint += "/" + api_prefix
+
+        self.endpoint = endpoint.rstrip("/")
+        self._auth = auth
+
+    def _get_headers(self) -> dict[str, str]:
+        """Get headers for API requests."""
+        auth_token = self._auth.get_access_token()
+
+        if not auth_token:
+            logger.warning(f"No auth token could be obtained.")
+
+        headers = {}
+        if auth_token:
+            headers["Authorization"] = f"Bearer {auth_token}"
+
+        return headers
+
+    @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS)
+    async def create_collection(
+        self,
+        collection_name: str,
+        dimensions: int,
+        description: str | None = None,
+    ) -> dict[str, Any]:
+        """
+        Create a new vectorstore collection.
+
+        Args:
+            collection_name (str): Name of the collection to create
+            dimensions (int): Number of dimensions for embeddings
+            description (str): Optional description for the collection
+
+        Returns:
+            Response from the API
+
+        Raises:
+            httpx.HTTPError: If the request fails
+        """
+        url = f"{self.endpoint}/vectorstore/collections"
+
+        payload = {
+            "collection_name": collection_name,
+            "dimensions": dimensions,
+        }
+
+        # TODO: remove when the service does this automatically
+        if dimensions > 2000:
+            payload["vector_type"] = "halfvec"
+
+        if description:
+            payload["description"] = description
+
+        async with httpx.AsyncClient() as client:
+            response = await client.post(
+                url,
+                json=payload,
+                headers=self._get_headers(),
+            )
+            response.raise_for_status()
+            return response.json()
+
+    @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS)
+    async def create_embeddings(
+        self,
+        collection_name: str,
+        embeddings_with_metadata: list[dict],
+        collection_id: int | None = None,
+        ai_model: str | None = None,
+    ) -> dict[str, Any]:
+        """
+        Create and add embeddings to an existing collection.
+
+        Args:
+            collection_name (str): Name of the collection to add embeddings to
+            embeddings_with_metadata (list[dict]): List of dictionaries containing the embedding and metadata
+            ai_model (str): Optional AI model name
+
+        Returns:
+            Response from the API
+
+        Raises:
+            httpx.HTTPError: If the request fails
+        """
+        url = f"{self.endpoint}/vectorstore/collections/{collection_name}/embeddings"
+        params = {}
+        if ai_model:
+            params["ai_model"] = ai_model
+
+        body = {"embeddings": embeddings_with_metadata}
+
+        async with httpx.AsyncClient() as client:
+            response = await client.post(
+                url,
+                json=body,
+                params=params,
+                headers=self._get_headers(),
+            )
+            response.raise_for_status()
+            return response.json()
+
+    @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS)
+    async def list_collections(
+        self, collection_name: str | None = None
+    ) -> list[dict[str, Any]]:
+        """
+        List all vectorstore collections.
+
+        Args:
+            collection_name (str): optional collection_name to retrieve, if not provided will list all
+
+        Returns:
+            List of collection information
+
+        Raises:
+            httpx.HTTPError: If the request fails
+        """
+        url = f"{self.endpoint}/vectorstore/collections"
+        collections = []
+
+        if collection_name:
+            url += f"/{collection_name}"
+
+        async with httpx.AsyncClient() as client:
+            response = await client.get(url, headers=self._get_headers())
+            response.raise_for_status()
+            response_json = response.json()
+
+        if collection_name:
+            collections = [response_json]
+        else:
+            collections = response_json.get("collections", [])
+
+        return collections
+
+    @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS)
+    async def list_embeddings(
+        self,
+        collection_name: str,
+        no_embeddings_info: bool = False,
+    ) -> list[dict[str, Any]]:
+        """
+        List all embeddings in an collection.
+
+        Args:
+            collection_name (str): Name of the collection
+            no_embeddings_info (bool): If True, omit info block in response to reduce payload size
+
+        Returns:
+            List of embedding information
+
+        Raises:
+            httpx.HTTPError: If the request fails
+        """
+        url = f"{self.endpoint}/vectorstore/collections/{collection_name}/embeddings"
+        params = {}
+        if no_embeddings_info:
+            params["no_embeddings_info"] = "true"
+
+        async with httpx.AsyncClient() as client:
+            response = await client.get(url, params=params, headers=self._get_headers())
+            response.raise_for_status()
+            return response.json()
+
+    @backoff.on_exception(backoff.expo, Exception, **DEFAULT_BACKOFF_SETTINGS)
+    async def delete_collection(self, collection_name: str) -> None:
+        """
+        Delete a vectorstore collection.
+
+        Args:
+            collection_name (str): Name of the collection to delete
+
+        Returns:
+            Response from the API
+
+        Raises:
+            httpx.HTTPError: If the request fails
+        """
+        url = f"{self.endpoint}/vectorstore/collections/{collection_name}"
+
+        async with httpx.AsyncClient() as client:
+            response = await client.delete(url, headers=self._get_headers())
+            response.raise_for_status()
+
+            # 204 on success, so no body
+            return None
+
+
+class LocalEmbeddingClient:
+    """
+    Client for local embedding generation using sentence-transformers.
+    """
+
+    def __init__(self, model_name: str = "all-MiniLM-L6-v2"):
+        """
+        Initialize the local embedding client.
+
+        Args:
+            model_name (str): Name of the sentence-transformers model to use
+        """
+        # lazy load. moved from top-level to avoid extensive loading at module load
+        # b/c we're lazy loading, we need to explicitly set the log level for this module
+        from sentence_transformers import SentenceTransformer
+
+        logging.getLogger("sentence_transformers").setLevel(logger.level)
+
+        self.model = SentenceTransformer(model_name)
+        self.dimensions = self.model.get_embedding_dimension()
+        logger.info(f"Loaded model: {model_name} (dimensions: {self.dimensions})")
+
+    def embed(
+        self,
+        texts_with_metadata: list[dict],
+        keep_original_text: bool = True,
+        show_progress_bar: bool = False,
+    ) -> list:
+        """
+        Generate embeddings for a list of texts.
+
+        Args:
+            texts_with_metadata (list[dict]): List of text strings to embed w/ metadata
+
+        Returns:
+            list of objects with embedding and metadata
+        """
+        texts = [item["text"] for item in texts_with_metadata]
+
+        embeddings = self.model.encode(
+            texts, convert_to_numpy=True, show_progress_bar=show_progress_bar
+        ).tolist()
+
+        # we can only have an embedding with metadata in the final output, so
+        # if we need to keep the original text, move it to the metadata
+        if not keep_original_text:
+            for item in texts_with_metadata:
+                item["metadata"].update({"text": item["text"]})
+                del item["text"]
+
+        # this format should be what the JSON body for bulk creation of embeddings
+        # expects
+        embeddings_with_metadata = [
+            {
+                "embedding": embedding,
+                "metadata": text_with_metadata["metadata"],
+                "authz": text_with_metadata.get("authz", ""),
+            }
+            for embedding, text_with_metadata in zip(embeddings, texts_with_metadata)
+        ]
+
+        return embeddings_with_metadata
diff --git a/gen3/cli/__main__.py b/gen3/cli/__main__.py
index 5a51be11b..3a3d4be26 100644
--- a/gen3/cli/__main__.py
+++ b/gen3/cli/__main__.py
@@ -15,6 +15,7 @@
 import gen3.cli.drs_pull as drs_pull
 import gen3.cli.users as users
 import gen3.cli.wrap as wrap
+import gen3.cli.ai.main as ai
 import gen3
 from gen3 import logging as sdklogging
 from gen3.cli import nih
@@ -112,26 +113,39 @@ def main(
         )
         # disables all logging
         logging.disable(logging.CRITICAL)
+        level = logging.NOTSET
     elif very_verbose_logs:
+        level = "DEBUG"
         logger = cdislogging.get_logger(
             __name__, format=gen3.LOG_FORMAT, log_level="debug"
         )
-        sdklogging.setLevel("DEBUG")
+        sdklogging.setLevel(level)
+
     elif verbose_logs:
+        level = "INFO"
         logger = cdislogging.get_logger(
             __name__, format=gen3.LOG_FORMAT, log_level="info"
         )
-        sdklogging.setLevel("INFO")
+        sdklogging.setLevel(level)
+
     elif only_error_logs:
+        level = "ERROR"
         logger = cdislogging.get_logger(
             __name__, format=gen3.LOG_FORMAT, log_level="error"
         )
-        sdklogging.setLevel("ERROR")
+        sdklogging.setLevel(level)
     else:
+        level = "WARNING"
         logger = cdislogging.get_logger(
             __name__, format=gen3.LOG_FORMAT, log_level="warning"
         )
-        sdklogging.setLevel("WARNING")
+        sdklogging.setLevel(level)
+
+    # set other module loggers to the same level as the SDK
+    # so modules like httpx, etc use the same level
+    for name in logging.root.manager.loggerDict:
+        logger = logging.getLogger(name)
+        logger.setLevel(level)
 
 
 main.add_command(auth.auth)
@@ -145,4 +159,5 @@ def main(
 main.add_command(nih.nih)
 main.add_command(users.users)
 main.add_command(wrap.run)
+main.add_command(ai.ai)
 main()
diff --git a/gen3/cli/ai/embeddings.py b/gen3/cli/ai/embeddings.py
new file mode 100644
index 000000000..4e71918a6
--- /dev/null
+++ b/gen3/cli/ai/embeddings.py
@@ -0,0 +1,709 @@
+import asyncio
+import csv
+import hashlib
+import json
+import os
+import sys
+import traceback
+
+import click
+from tqdm.auto import tqdm
+import indexclient.client as indexclient
+
+from gen3 import logging
+from gen3.ai import EmbeddingsClient, LocalEmbeddingClient
+from gen3.cli.ai.utils import chunk_text, get_all_nested_files
+from gen3.index import Gen3Index
+from gen3.utils import get_or_create_event_loop_for_thread
+
+COLLECTION_NAME_TO_ID_CACHE = {}
+
+
+@click.command(
+    "convert",
+    help=("""
+        Convert a Gen3 Embeddings Manifest into a Gen3 Indexing Manifest.
+
+        \b
+        The input manifest (Gen3 Embeddings Manifest) must contain at least the columns: 
+        \b
+            embedding: JSON-encoded list of floats
+            authz: single Gen3 authz resource path which will control authorization to this embedding
+            self: URL self-representation of the embedding in the Gen3 Embeddings API
+        \b
+        The output file (Gen3 Indexing Manifest) will have the columns:
+        \b
+            guid    md5    size    authz    acl    url
+        \b
+        The GUID is left blank (it will be generated by the indexing), `md5` and `size` are
+        derived from the JSON representation of the embedding vector, `authz` is
+        passed through from the input, and `url` is populated from a `self`
+        column.
+        \b
+        A new file named `_converted.tsv` is created in the same directory as
+        the source file.
+        \b
+        Example:
+            gen3 ai embeddings convert ./tests/embeddings_tests/test_summ.tsv
+        """),
+)
+@click.argument(
+    "manifest_file",
+    type=click.Path(exists=True, dir_okay=False),
+    required=True,
+)
+@click.option(
+    "--out-manifest-file",
+    "-o",
+    default=None,
+    help="Output filename for final manifest (default: originalfile_converted.tsv)",
+)
+@click.option(
+    "--url-prefix",
+    "-u",
+    default=None,
+    help=(
+        "Prefix for ALL `urls` in the output file. If a url provided doesn't have the prefix, it will be added. "
+        "This can be used to ensure an appropriate https://example.com/ai prefix if the input manifest doesn't have that "
+        "in all the `self` fields."
+    ),
+)
+@click.pass_context
+def convert_embeddings(
+    ctx,
+    manifest_file: str,
+    out_manifest_file: str | None,
+    url_prefix: str = "",
+):
+    """
+    Convert a Gen3 Embeddings Manifest into a Gen3 Indexing Manifest.
+
+    See above `help` for more details.
+    """
+    auth = ctx.obj["auth_factory"].get()
+    client: EmbeddingsClient = ctx.obj["client"]
+
+    # we need an indexing client as well
+    gen3_index = Gen3Index(auth.endpoint, auth_provider=auth)
+    manifest_file_name = click.format_filename(manifest_file)
+
+    # get a total line count without loading the whole file in memory
+    with open(manifest_file_name) as file:
+        # - 1 for header
+        total_rows = sum(1 for line in file) - 1
+
+    # get valid indexd guids and dump into the manifest
+    valid_guids = gen3_index.get_valid_guids(count=total_rows)
+
+    out_manifest_file = (
+        out_manifest_file
+        if out_manifest_file
+        else f"{os.path.splitext(manifest_file_name)[0]}_converted.tsv"
+    )
+    click.echo(f"Writing converted manifest to '{out_manifest_file}'")
+    fieldnames = ["guid", "md5", "size", "authz", "acl", "url"]
+
+    # open output file
+    with open(out_manifest_file, "w", newline="") as out_f:
+        writer = csv.DictWriter(out_f, fieldnames=fieldnames, delimiter="\t")
+        writer.writeheader()
+
+        # open input file and iterate over rows
+        with open(manifest_file_name) as f:
+            delimiter = "\t" if manifest_file_name.endswith(".tsv") else ","
+            reader = csv.DictReader(f, delimiter=delimiter)
+
+            row_number = 1
+            for row in tqdm(reader, desc="Converting rows", total=total_rows):
+                embedding_str = row.get("embedding", "[]")
+                try:
+                    # eliminate whitespace in the JSON representation for consistent hashing
+                    embedding_json = json.dumps(
+                        json.loads(embedding_str), separators=(",", ":")
+                    )
+                except Exception as exc:
+                    click.echo(
+                        f"Invalid embedding in row: {row}. Skipping. Error: {exc}",
+                        err=True,
+                    )
+                    continue
+
+                md5_hash = hashlib.md5(embedding_json.encode("utf-8")).hexdigest()
+                size_bytes = len(embedding_json.encode("utf-8"))
+                authz = row.get("authz", "")
+                url = row.get("self", "")
+
+                if not url:
+                    logging.error(
+                        f"Row #{row_number} did not contain REQUIRED `self` column contents. Continuing anyway..."
+                    )
+
+                if not authz:
+                    logging.error(
+                        f"Row #{row_number} did not contain REQUIRED `authz` column contents. Continuing anyway..."
+                    )
+
+                if not url.startswith(url_prefix):
+                    url = url_prefix + url
+
+                out_row = {
+                    "guid": valid_guids.pop(),
+                    "md5": md5_hash,
+                    "size": size_bytes,
+                    "authz": authz,
+                    "acl": "",
+                    "url": url,
+                }
+                writer.writerow(out_row)
+                row_number += 1
+
+    click.echo(
+        f"Done! Check for errors above. Gen3 Indexing Manifest: {out_manifest_file}"
+    )
+
+
+@click.command(
+    "publish",
+    help=("""
+        
+        Publish a manifest of already-embedded objects to a Gen3 collection.
+        The manifest must be a CSV/TSV with the following columns:
+
+        \b
+                              embedding: JSON-encoded list of floats
+        collection_id / collection_name: Target collection (use name to lookup id)
+                     **metadata columns: any additional columns are treated as metadata for the embedding
+
+        Example usage:
+
+        \b
+            gen3 ai embeddings publish --collection "ctds-github-md" --manifest_file embeddings.tsv
+        """),
+)
+@click.argument(
+    "manifest_file",
+    type=click.Path(exists=True, dir_okay=False),
+    required=True,
+)
+@click.option(
+    "--batch-size",
+    "batch_size",
+    help="max number of embeddings to collect before pushing to API in bulk per collection",
+    default=1000,
+)
+@click.option(
+    "--default-collection",
+    "default_collection",
+    help="Name of the default embeddings collection (used when rows don't specify).",
+)
+@click.option(
+    "--out-manifest-file",
+    "-o",
+    default=None,
+    help="Output filename for final manifest",
+)
+@click.pass_context
+def publish_embeddings(
+    ctx,
+    out_manifest_file: str | None,
+    manifest_file: str,
+    batch_size: int,
+    default_collection: str | None = None,
+):
+    """
+    Publish embeddings from a manifest file to a collection.
+
+    Args:
+        batch_size (int): max number of embeddings before pushing to API in bulk per collection.
+           NOTE: as this increases it requires a larger memory footprint locally (as each batch
+                 is stored in-memory before creating in the API and then flushing). The backend API
+                 also has limits.
+    """
+    auth = ctx.obj["auth_factory"].get()
+    client: EmbeddingsClient = ctx.obj["client"]
+
+    manifest_file_name = click.format_filename(manifest_file)
+    delimiter = "\t" if manifest_file_name.endswith(".tsv") else ","
+
+    # get a total line count without loading the whole file in memory
+    with open(manifest_file_name) as file:
+        # - 1 for header
+        total_rows = sum(1 for line in file) - 1
+
+    with open(manifest_file_name) as file:
+        reader = csv.DictReader(file, delimiter=delimiter)
+        out_manifest_file = (
+            out_manifest_file
+            if out_manifest_file
+            else f"{os.path.splitext(manifest_file_name)[0]}_output.tsv"
+        )
+
+        # clear out file if it exists and create if it doesn't, we'll append
+        # content later
+        open(out_manifest_file, "w").close()
+
+        # build metadata columns list (exclude embedding and collection fields)
+        excluded = {"embedding", "collection_id", "collection_name", "authz"}
+        metadata_cols = [
+            c for c in getattr(reader, "fieldnames", []) if c not in excluded
+        ]
+
+        pending_per_collection = {}
+        pending_count = 0
+        total_count = 0
+
+        all_metadata_keys = set()
+        output_header_written = False
+
+        with tqdm(
+            total=total_rows,
+            desc="Publishing Gen3 Embeddings Manifest",
+            mininterval=1.0,
+        ) as pbar:
+            for row in reader:
+                collection_id = row.get("collection_id")
+                collection_name = row.get("collection_name", "")
+                authz = row.get("authz")
+
+                if not collection_id:
+                    collection_id, collection_name = _get_collection_id_and_name(
+                        collection_name=collection_name,
+                        client=client,
+                        default_collection=default_collection,
+                    )
+
+                try:
+                    embedding = json.loads(row.get("embedding", "[]"))
+                except json.JSONDecodeError as exc:
+                    click.echo(
+                        f"Invalid embedding in row: {row}. Skipping. Error: {exc}",
+                        err=True,
+                    )
+                    pbar.update(1)
+                    continue
+
+                metadata = {k: row[k] for k in metadata_cols if k in row}
+                embedding_content = {"embedding": embedding, "metadata": metadata}
+
+                # this presumes that all rows have the same metadata keys since it's based
+                # on the overall columns of the manifest
+                all_metadata_keys.update(metadata.keys())
+
+                if authz:
+                    embedding_content.update({"authz": authz})
+
+                collection_group = pending_per_collection.setdefault(
+                    collection_id, {"name": collection_name, "embeddings": []}
+                )
+                collection_group["embeddings"].append(embedding_content)
+                pending_count += 1
+
+                # create the embeddings
+                if pending_count >= batch_size:
+                    for (
+                        collection_id,
+                        collection_group,
+                    ) in pending_per_collection.items():
+                        loop = get_or_create_event_loop_for_thread()
+                        created_embeddings_response = loop.run_until_complete(
+                            client.create_embeddings(
+                                collection_name=collection_group["name"],
+                                collection_id=collection_id,
+                                embeddings_with_metadata=collection_group["embeddings"],
+                            )
+                        )
+                        created_embeddings = created_embeddings_response.get(
+                            "embeddings", {}
+                        )
+
+                        _append_created_embeddings_to_file(
+                            created_embeddings,
+                            out_manifest_file,
+                            all_metadata_keys=all_metadata_keys,
+                            output_header_written=output_header_written,
+                        )
+                        output_header_written = True
+
+                    total_count += pending_count
+                    pbar.update(pending_count)
+                    pending_per_collection.clear()
+                    pending_count = 0
+
+            # get the last batch
+            if pending_per_collection:
+                for collection_id, collection_group in pending_per_collection.items():
+                    loop = get_or_create_event_loop_for_thread()
+                    created_embeddings_response = loop.run_until_complete(
+                        client.create_embeddings(
+                            # ignore unbound type error here because we know it will be bound
+                            collection_name=collection_group["name"],
+                            collection_id=collection_id,
+                            embeddings_with_metadata=collection_group["embeddings"],
+                        )
+                    )
+                    created_embeddings = created_embeddings_response.get(
+                        "embeddings", {}
+                    )
+
+                    _append_created_embeddings_to_file(
+                        created_embeddings,
+                        out_manifest_file,
+                        all_metadata_keys=all_metadata_keys,
+                        output_header_written=output_header_written,
+                    )
+                    output_header_written = True
+
+                total_count += pending_count
+                pbar.update(pending_count)
+                pending_per_collection.clear()
+                pending_count = 0
+
+    click.echo(f"Published {total_count} embeddings.")
+    click.echo(f"Wrote output manifest: {out_manifest_file}.")
+
+
+def _append_created_embeddings_to_file(
+    created_embeddings: dict,
+    out_manifest_file: str,
+    all_metadata_keys: set,
+    output_header_written: bool,
+):
+    """
+    Append the provided created_embeddings to the output file. Allows calling multiple times
+    """
+    logging.info(f"Writing batch of created embeddings to '{out_manifest_file}'...")
+    # write to manifest file
+    fieldnames = ["embedding_id", "embedding", "collection_id", "authz", "self"]
+    fieldnames.extend(sorted(list(all_metadata_keys)))
+
+    with open(out_manifest_file, "a") as f:
+        writer = csv.DictWriter(f, fieldnames=fieldnames, delimiter="\t")
+
+        if not output_header_written:
+            writer.writeheader()
+            output_header_written = True
+
+        for item in created_embeddings:
+            row = {
+                "embedding_id": item["embedding_id"],
+                "embedding": json.dumps(item["vector"]),
+                "authz": item.get("info", {}).get("authz", ""),
+                "collection_id": item.get("info", {}).get("collection_id", ""),
+                "self": item.get("info", {}).get("self", ""),
+            }
+            row.update(item.get("info", {}).get("metadata", {}))
+            writer.writerow(row)
+
+
+def _get_collection_id_and_name(
+    collection_name: str,
+    client: EmbeddingsClient,
+    default_collection: str | None = None,
+) -> tuple[str, str]:
+    """
+    Gets collection id by hitting service with name and extracting ID, stores
+    in in-mem cache.
+    """
+    global COLLECTION_NAME_TO_ID_CACHE
+
+    if collection_name and collection_name in COLLECTION_NAME_TO_ID_CACHE:
+        # cache hit
+        collection_id = COLLECTION_NAME_TO_ID_CACHE[collection_name]
+    elif collection_name:
+        # cache miss
+        # resolve collection id if a name was supplied
+        collection = asyncio.run(
+            client.list_collections(collection_name=collection_name)
+        )
+        if not collection:
+            click.echo(
+                f"Failed to resolve a collection. Given collection_name:'{collection_name}' / default_collection:'{default_collection}'"
+            )
+            sys.exit(1)
+        collection_id = collection[0]["id"]
+
+        # update in-mem cache
+        COLLECTION_NAME_TO_ID_CACHE[collection_name] = collection_id
+
+    elif default_collection:
+        # resolve collection id using default_collection if provided
+        collection_name = default_collection
+        collection = asyncio.run(
+            client.list_collections(collection_name=collection_name)
+        )
+        if not collection:
+            click.echo(
+                f"Failed to resolve a collection. Given collection_name:'{collection_name}' / default_collection:'{default_collection}'"
+            )
+            sys.exit(1)
+        collection_id = collection[0]["id"]
+
+        # update in-mem cache
+        COLLECTION_NAME_TO_ID_CACHE[collection_name] = collection_id
+    else:
+        click.echo(
+            f"Failed to resolve a collection. Given collection_name:'{collection_name}' / default_collection:'{default_collection}'"
+        )
+        sys.exit(1)
+
+    return collection_id, collection_name
+
+
+@click.command(
+    "delete",
+    help="[Not Implemented Yet] Deletes specified embeddings data in local files from Gen3 instance.",
+)
+@click.pass_context
+def delete_embeddings(ctx):
+    """
+    Deletes specified embeddings data in local files from Gen3 instance.
+    """
+    raise NotImplementedError("`gen3 ai embeddings delete` is not implemented yet.")
+
+
+@click.command()
+# TODO: Eventually, this could first check the Gen3 AI Model Repo / Inference API(s) to see if this
+#       model is available and require some explicit --local flag to allow sentence-transformers?
+@click.option(
+    "--model",
+    "-m",
+    default="all-MiniLM-L6-v2",
+    help="Sentence-transformers model name (default: all-MiniLM-L6-v2)",
+)
+@click.option(
+    "--out-manifest-file",
+    "-o",
+    default="output.tsv",
+    help="Output filename for final manifest (default: output.tsv)",
+)
+@click.option(
+    "--collection-name",
+    type=str,
+    required=False,
+    help="collection_name for all processed files (ends up in output)",
+)
+@click.option(
+    "--collection-id",
+    type=str,
+    required=False,
+    help="collection_id for all processed files (ends up in output)",
+)
+@click.option(
+    "--chunk-size",
+    default=512,
+    type=int,
+    help="Number of characters per chunk (default: 512)",
+)
+@click.option(
+    "--chunk-overlap",
+    default=50,
+    type=int,
+    help="Number of characters to overlap between chunks (default: 50)",
+)
+@click.option(
+    "--strategy",
+    "-s",
+    default="text",
+    type=str,
+    help="Embedding strategy: text / file. File attempts to embed the entire file instead of chunking the text within (default: text)",
+)
+@click.option(
+    "--recursive",
+    "-r",
+    is_flag=True,
+    help="Recursively process directories",
+)
+@click.option(
+    "--file-extensions",
+    "-f",
+    multiple=True,
+    help="File extensions to process. Can be supplied multiple times. ex: -f .txt -f .md -f .sql",
+    default=[".txt", ".md", ".tsv", ".csv"],
+)
+@click.option(
+    "--keep-text",
+    is_flag=True,
+    help="Whether or not to include the original text (non-embedded) in the final output.",
+)
+@click.option(
+    "--keep-folder-paths",
+    is_flag=True,
+    help="Whether or not to include the original folder paths in the final output metadata.",
+)
+@click.argument("paths", nargs=-1, type=click.Path(exists=True))
+@click.pass_context
+def chunk_and_embed_text(
+    ctx: click.Context,
+    out_manifest_file: str,
+    model: str,
+    collection_name: str,
+    collection_id: str,
+    chunk_size: int,
+    chunk_overlap: int,
+    strategy: str,
+    recursive: bool,
+    file_extensions: list,
+    keep_text: bool,
+    keep_folder_paths: bool,
+    paths: list[str],
+) -> None:
+    """
+    Chunk files and create embeddings locally, then submit to the service.
+
+    PATHS: One or more files or directories to chunk and embed
+
+    Embed files in a directory and output a manifest to publish
+    collection is used to get model / dimensions
+    this requires CPU/GPU for the actual embedding process and is not optimized for
+    production-level and extensive embedding, it's really for small-size and local testing.
+
+    To scale this, you need to write your own pipeline to generate the manifest file format and
+    then use the `gen3 ai embeddings publish` command to create records in Gen3.
+
+    chunk-size is used when strategy = text. If strategy = file, then this will attempt to pull the AI Model specified by the
+    collection and use it to embed the whole file.
+
+    ex:
+      gen3 ai embeddings embed ./directory/ --collection "ctds-github-md" --out-manifest-file ... --strategy "text" / "file" --chunk-size 1024
+    """
+    paths = [click.format_filename(path) for path in paths]
+    all_files = get_all_nested_files(
+        paths=paths, file_extensions=file_extensions, recursive=recursive
+    )
+
+    click.echo(f"Found {len(all_files)} file(s) to process")
+    click.echo(f"       Chunk size: {chunk_size} characters")
+    click.echo(f"    Chunk overlap: {chunk_overlap} characters")
+    click.echo(f"            Model: {model}")
+    click.echo(f"    Collection ID: {collection_id}")
+    click.echo(f"  Collection Name: {collection_name}")
+    click.echo(f"         Strategy: {strategy}")
+    click.echo(f"        Recursive: {recursive}")
+    click.echo(f"  File Extensions: {file_extensions}")
+    click.echo(f"        Keep Text: {keep_text}")
+    click.echo(f" Keep Folder Paths: {keep_folder_paths}")
+    click.echo(f"           Output: {out_manifest_file}")
+
+    if not all_files:
+        click.echo()
+        click.echo("No files found!", err=True)
+        sys.exit(1)
+
+    local_client = LocalEmbeddingClient(model_name=model)
+
+    # by default, remove the user directory from any file paths
+    # TODO: we could expose an option to the CLI to customize this
+    prefix_to_remove_from_filepath = os.path.expanduser("~") + "/"
+
+    # read and chunk all files
+    all_texts_with_metadata = _read_and_chunk_files(
+        all_files=all_files,
+        strategy=strategy,
+        chunk_size=chunk_size,
+        chunk_overlap=chunk_overlap,
+        keep_folder_paths=keep_folder_paths,
+        prefix_to_remove_from_filepath=prefix_to_remove_from_filepath,
+    )
+
+    click.echo()
+    click.echo(f"Total chunks to embed: {len(all_texts_with_metadata)}")
+    click.echo()
+
+    # generate embeddings locally
+    click.echo("Generating embeddings...")
+    try:
+        embeddings_with_metadata = local_client.embed(
+            all_texts_with_metadata,
+            keep_original_text=keep_text,
+            show_progress_bar=True,
+        )
+        click.echo(f"Generated {len(embeddings_with_metadata)} embeddings")
+    except Exception as exc:
+        click.echo(f"  Failed to generate embeddings: {exc}", err=True)
+        logging.error(traceback.format_exc())
+        sys.exit(1)
+
+    click.echo()
+    click.echo(f"Writing embeddings to '{out_manifest_file}'...")
+    click.echo()
+
+    # write to manifest file
+    fieldnames = ["embedding", "collection_name", "collection_id", "authz"]
+
+    all_metadata_keys = set()
+    for item in embeddings_with_metadata:
+        all_metadata_keys.update(item["metadata"].keys())
+
+    fieldnames.extend(sorted(list(all_metadata_keys)))
+
+    with open(out_manifest_file, "w") as f:
+        writer = csv.DictWriter(f, fieldnames=fieldnames, delimiter="\t")
+        writer.writeheader()
+        for item in embeddings_with_metadata:
+            row = {
+                "embedding": json.dumps(item["embedding"]),
+                "authz": item["authz"],
+                "collection_name": collection_name if collection_name else "",
+                "collection_id": collection_id if collection_id else "",
+            }
+            row.update(item["metadata"])
+            writer.writerow(row)
+
+    click.echo()
+    click.echo(
+        f"Successfully wrote {len(embeddings_with_metadata)} embeddings to {out_manifest_file}!"
+    )
+
+
+def _read_and_chunk_files(
+    all_files: list[str],
+    strategy: str,
+    chunk_size: int,
+    chunk_overlap: int,
+    keep_folder_paths: bool,
+    prefix_to_remove_from_filepath: str = "",
+):
+    """
+    Read and chunk all files
+    """
+    all_texts_with_metadata = []
+    for file_path in all_files:
+        try:
+            with open(file_path, "r") as f:
+                if not keep_folder_paths:
+                    file_path = os.path.basename(file_path)
+                file_path = file_path.removeprefix(prefix_to_remove_from_filepath)
+                content = f.read()
+                texts_with_metadata = []
+                if strategy == "text":
+                    chunks = chunk_text(content, chunk_size, chunk_overlap)
+                    texts_with_metadata.extend(
+                        [
+                            {
+                                "text": chunk,
+                                "metadata": {
+                                    "file": file_path,
+                                    "chunk_size": chunk_size,
+                                    "chunk_overlap": chunk_overlap,
+                                },
+                            }
+                            for chunk in chunks
+                        ]
+                    )
+                elif strategy == "file":
+                    texts_with_metadata.append(
+                        {
+                            "text": content,
+                            "metadata": {
+                                "file": file_path,
+                            },
+                        }
+                    )
+
+                all_texts_with_metadata.extend(texts_with_metadata)
+                click.echo(f"  {file_path}: {len(texts_with_metadata)} chunk(s)")
+        except Exception as exc:
+            click.echo(f"   {file_path}: {exc}", err=True)
+            sys.exit(1)
+
+    return all_texts_with_metadata
diff --git a/gen3/cli/ai/embeddings_collections.py b/gen3/cli/ai/embeddings_collections.py
new file mode 100644
index 000000000..2fa8fa9fa
--- /dev/null
+++ b/gen3/cli/ai/embeddings_collections.py
@@ -0,0 +1,109 @@
+import asyncio
+import sys
+
+import click
+import httpx
+
+from gen3.cli.ai.utils import click_echo_dict_format, click_echo_if_text
+
+
+@click.command("create")
+@click.option(
+    "--dimensions",
+    required=True,
+    type=int,
+    help="Number of dimensions for the embeddings",
+)
+@click.option(
+    "--description",
+    default=None,
+    help="Optional description for the collection",
+)
+@click.argument("collection_name")
+@click.pass_context
+def create_collection(
+    ctx: click.Context, dimensions: int, description: str | None, collection_name: str
+) -> None:
+    """
+    Create a new embeddings collection.
+
+    COLLECTION_NAME: Name for the new collection
+    """
+    client = ctx.obj["client"]
+
+    click.echo(
+        f"Creating collection '{collection_name}' with {dimensions} dimensions..."
+    )
+
+    try:
+        result = asyncio.run(
+            client.create_collection(collection_name, dimensions, description)
+        )
+        click.echo(f"Collection created successfully!")
+        click_echo_dict_format(result, format="pretty_json")
+    except httpx.HTTPError as exc:
+        click.echo(f"Failed to create collection: {exc}", err=True)
+        sys.exit(1)
+
+
+@click.command("read")
+@click.option(
+    "--format",
+    help="Format of collections output: `json` / `pretty_json` / `text`. Defeault is `text`",
+    default="text",
+)
+@click.argument("collection_name", required=False)
+@click.pass_context
+def read_collections(
+    ctx: click.Context, format: str, collection_name: str | None
+) -> None:
+    """
+    Read embeddings collections. If no collection name provided, list all.
+
+    COLLECTION_NAME: Optional specific collection name to filter by
+    """
+    client = ctx.obj["client"]
+
+    if collection_name is not None:
+        click_echo_if_text(
+            f"Reading embeddings collection {collection_name}...", format=format
+        )
+        try:
+            collections = asyncio.run(
+                client.list_collections(collection_name=collection_name)
+            )
+            click_echo_if_text(f"Found {collection_name} collection", format=format)
+            click_echo_dict_format(input_dict=collections, format=format)
+        except httpx.HTTPError as exc:
+            click.echo(f"Failed to find collection: {exc}", err=True)
+            sys.exit(1)
+    else:
+        click_echo_if_text("Listing all embeddings collections...", format=format)
+        try:
+            collections = asyncio.run(client.list_collections())
+            click_echo_if_text(f"Found {len(collections)} collection(s)", format=format)
+            click_echo_dict_format(input_dict=collections, format=format)
+        except httpx.HTTPError as exc:
+            click.echo(f"Failed to list collections: {exc}", err=True)
+            sys.exit(1)
+
+
+@click.command("delete")
+@click.argument("collection_name", required=False)
+@click.pass_context
+def delete_collection(ctx: click.Context, collection_name: str | None) -> None:
+    """
+    Delete a embeddings collection.
+
+    COLLECTION_NAME: collection name to delete
+    """
+    client = ctx.obj["client"]
+
+    click_echo_if_text(f"Deleting collection '{collection_name}'...")
+    try:
+        asyncio.run(client.delete_collection(collection_name))
+    except httpx.HTTPError as exc:
+        click.echo(f"Failed to delete collection: {exc}", err=True)
+        sys.exit(1)
+
+    click_echo_if_text(f"Successfully deleted collection '{collection_name}'!")
diff --git a/gen3/cli/ai/main.py b/gen3/cli/ai/main.py
new file mode 100644
index 000000000..c916812d7
--- /dev/null
+++ b/gen3/cli/ai/main.py
@@ -0,0 +1,97 @@
+"""
+CLI for Gen3 AI support.
+
+Examples:
+
+# local testing
+`gen3 --auth ~/.gen3/local_helm_test_user.json --endpoint "http://127.0.0.1:4142" ai --api-prefix "" embeddings ...`
+
+# local testing CRUD on collections
+gen3 --auth ~/.gen3/local_helm_test_user.json --endpoint "http://127.0.0.1:4142" ai --api-prefix "" embeddings collections create "ctds-github-md" --dimensions 384 --description "All markdown from CTDS Github"
+gen3 --auth ~/.gen3/local_helm_test_user.json --endpoint "http://127.0.0.1:4142" ai --api-prefix "" embeddings collections read
+gen3 --auth ~/.gen3/local_helm_test_user.json --endpoint "http://127.0.0.1:4142" ai --api-prefix "" embeddings collections read "ctds-github-md"
+gen3 --auth ~/.gen3/local_helm_test_user.json --endpoint "http://127.0.0.1:4142" ai --api-prefix "" embeddings collections delete "ctds-github-md"
+
+# publish a manifest of already-embedded objects
+# manifest is a CSV/TSV with columns:
+# embedding: JSON list of floats serialized as a string
+# authz: authz resource path (optional, will default to collection)
+# collection_id / collection_name: collection embedding should be placed in (if name is provided, use list_collection(collection_name=provided) to determine the ID)
+# ** additional columns are interpretted as metadata
+
+gen3 --auth ~/.gen3/local_helm_test_user.json --endpoint "http://127.0.0.1:4142" ai --api-prefix "" embeddings publish ./tests/embeddings_tests/expr.tsv --default-collection expr
+
+gen3 ai embeddings publish ./tests/embeddings_tests/expr.tsv --default-collection expr
+gen3 ai embeddings publish ./tests/embeddings_tests/hist.tsv --default-collection hist
+gen3 ai embeddings publish ./tests/embeddings_tests/summ.tsv --default-collection summ
+
+# embed and get a manifest
+gen3 ai embeddings embed-files --recursive --chunk-size 1024 --chunk-overlap 256 --collection-name ctds-github-md --out-manifest-file embeddings_manifest.tsv ~/Documents/repos/gen3-discovery-ai/bin/library/library_.github_README.md ~/Documents/repos/gen3-discovery-ai/bin/library/library_arborist_README.md
+gen3 ai embeddings embed-files --recursive --chunk-size 1024 --chunk-overlap 256 --collection-name ctds-github-md --out-manifest-file embeddings_manifest.tsv ~/Documents/repos/gen3-discovery-ai/bin/library/
+
+# against running instance using defaults. 1st download credentials and store in "~/.gen3/credentials.json"
+`gen3 ai embeddings ...`
+"""
+
+import click
+
+from gen3.ai import EmbeddingsClient
+from gen3.cli.ai.embeddings import (
+    chunk_and_embed_text,
+    convert_embeddings,
+    delete_embeddings,
+    publish_embeddings,
+)
+from gen3.cli.ai.embeddings_collections import (
+    create_collection,
+    delete_collection,
+    read_collections,
+)
+
+
+@click.group()
+@click.option(
+    "--api-prefix",
+    default="ai",
+    help="Prefix after the domain for the AI-based services (default: ai).",
+)
+@click.pass_context
+def ai(ctx: click.Context, api_prefix: str) -> None:
+    """
+    For working with Gen3 AI
+    """
+    ctx.obj["ai_api_prefix"] = api_prefix
+
+
+@ai.group()
+@click.pass_context
+def embeddings(ctx: click.Context) -> None:
+    """
+    For working with embeddings
+    """
+    api_prefix = ctx.obj["ai_api_prefix"]
+    auth = ctx.obj["auth_factory"].get()
+    endpoint = ctx.obj["endpoint"] or auth.endpoint
+
+    ctx.obj["client"] = EmbeddingsClient(
+        auth=auth, endpoint=endpoint, api_prefix=api_prefix
+    )
+
+
+@embeddings.group()
+@click.pass_context
+def collections(ctx: click.Context) -> None:
+    """
+    For working with embeddings collections
+    """
+    pass
+
+
+embeddings.add_command(publish_embeddings, name="publish")
+embeddings.add_command(delete_embeddings, name="delete")
+embeddings.add_command(chunk_and_embed_text, name="embed-files")
+embeddings.add_command(convert_embeddings, name="convert")
+
+collections.add_command(create_collection, name="create")
+collections.add_command(read_collections, name="read")
+collections.add_command(delete_collection, name="delete")
diff --git a/gen3/cli/ai/utils.py b/gen3/cli/ai/utils.py
new file mode 100644
index 000000000..aa0478078
--- /dev/null
+++ b/gen3/cli/ai/utils.py
@@ -0,0 +1,122 @@
+import json
+import os
+
+import click
+
+
+def click_echo_if_text(message: str, format: str = "text") -> None:
+    """
+    If format is text, then echo. For one-liner prints with context on output
+
+    Args:
+        message: message to print
+        format: text or json, determines how it's printed. This will only print is format is text
+    """
+    if format == "text":
+        click.echo(message)
+
+
+def click_echo_dict_format(input_dict: dict, format: str = "pretty_json") -> None:
+    """
+    Prints input dict in specified format. For one-liner prints with context on how to output
+
+    Args:
+        input_dict: dict to print
+        format: pretty_json or json, determines how it's printed
+    """
+
+    def format_text_recursive(data, indent_level=0):
+        lines = []
+        indent = "  " * indent_level
+
+        if isinstance(data, dict):
+            for key, value in data.items():
+                if isinstance(value, (dict, list)):
+                    lines.append(f"{indent}{key}:")
+                    lines.append(format_text_recursive(value, indent_level + 1))
+                else:
+                    lines.append(f"{indent}{key}: {value}")
+        elif isinstance(data, list):
+            for item in data:
+                if isinstance(item, (dict, list)):
+                    item_str = format_text_recursive(item, indent_level + 1).lstrip()
+                    lines.append(f"{indent}- {item_str}")
+                else:
+                    lines.append(f"{indent}- {item}")
+
+        return "\n".join(lines)
+
+    output = ""
+    if format == "pretty_json":
+        output = json.dumps(input_dict, indent=2)
+    elif format == "json":
+        output = json.dumps(input_dict)
+    elif format == "text":
+        output = format_text_recursive(input_dict)
+    else:
+        raise Exception(f"Unsupported text output format: {format}")
+
+    click.echo(output)
+
+
+def chunk_text(text: str, chunk_size: int, chunk_overlap: int) -> list[str]:
+    """
+    Split text into overlapping chunks.
+
+    Args:
+        text: Text to chunk
+        chunk_size: Maximum characters per chunk
+        chunk_overlap: Number of characters to overlap between chunks
+
+    Returns:
+        List of text chunks
+    """
+    chunks = []
+    start = 0
+
+    while start < len(text):
+        end = start + chunk_size
+        chunk = text[start:end]
+
+        if not chunk:
+            break
+
+        if end < len(text):
+            # look for sentence boundaries
+            for delimiter in [".", "!", "?", "\n"]:
+                last_delimiter = chunk.rfind(delimiter)
+                # only break if delimiter is in the latter half
+                if last_delimiter > chunk_size * 0.5:
+                    end = start + last_delimiter + 1
+                    break
+
+        chunks.append(chunk.strip())
+        start = end - chunk_overlap
+
+    return chunks
+
+
+def get_all_nested_files(
+    paths: list[str], file_extensions: list[str], recursive: bool = True
+):
+    """
+    Get all nested files with the given extensions from a list of paths.
+
+    Args:
+       paths: List of paths to search
+       file_extensions: List of extensions to look for
+       recursive: Whether to search recursively
+    """
+    all_files = []
+    for path in paths:
+        if recursive and os.path.isdir(path):
+            # recursively find all text files
+            for root, _, files in os.walk(path):
+                for file in files:
+                    if file.endswith(tuple(file_extensions)):
+                        all_files.append(os.path.join(root, file))
+        else:
+            if os.path.isfile(path):
+                all_files.append(path)
+
+    return all_files
diff --git a/gen3/cli/auth.py b/gen3/cli/auth.py
index a7969f38f..fea22d904 100644
--- a/gen3/cli/auth.py
+++ b/gen3/cli/auth.py
@@ -72,7 +72,7 @@ def wts_list():
 
 @click.group()
 def auth():
-    """Commands for authentication and authorization"""
+    """For authentication and authorization"""
     pass
 
 
diff --git a/gen3/cli/content.py b/gen3/cli/content.py
new file mode 100644
index 000000000..4b2d6a176
--- /dev/null
+++ b/gen3/cli/content.py
@@ -0,0 +1,147 @@
+"""
+Tool for retrieving bulk content (not signed URLs) from a Gen3 commons.
+
+The command accepts either an input file that contains one GUID per line
+(`--input-file`) or a list of GUIDs passed on the command line (`--guids`).
+It then calls `Gen3File.get_content` in batches, normalises the response,
+and writes a TSV that is compatible with the *publish_embeddings* manifest.
+
+The output file format follows exactly what the `publish_embeddings`
+command generates for each row:
+
+    embedding_id   embedding   authz   collection_id   self
+"""
+
+import base64
+import csv
+import json
+from pathlib import Path
+from typing import Iterable, List
+
+import numpy
+from dataclasses import dataclass
+import click
+from cdislogging import get_logger
+import numpy
+
+from gen3.file import DEFAULT_BATCH_SIZE, SUPPORTED_CONTENT_TYPES, Gen3File
+
+
+@click.command(name="read")
+@click.option(
+    "--input-file",
+    "-i",
+    type=click.Path(exists=True),
+    help="Path to a file that contains one GUID per line.",
+)
+@click.option(
+    "--guids",
+    "-g",
+    multiple=True,
+    help="One or more GUIDs. Use this option instead of an input file.",
+)
+@click.option(
+    "--output-file",
+    "-o",
+    type=click.Path(),
+    default="content_output.tsv",
+    show_default=True,
+    help="Destination TSV file name.",
+)
+@click.option(
+    "--batch-size",
+    type=int,
+    default=DEFAULT_BATCH_SIZE,
+    show_default=True,
+    help="Number of GUIDs to request in each bulk API call.",
+)
+@click.option(
+    "--content-type",
+    type=str,
+    default="gen3_embeddings",
+    show_default=True,
+    help=(
+        "The type of content returned (to ensure formatting in output is "
+        "application/content specific). NOTE: ONLY supports `gen3_embeddings` for now!"
+    ),
+)
+@click.pass_context
+def get_bulk_content(ctx, input_file, guids, output_file, batch_size, content_type):
+    """Retrieve bulk content for a set of GUIDs and write to a TSV.
+
+    The function writes a TSV with columns:
+
+        embedding_id   embedding   authz   collection_id   self
+
+    which is identical to the manifest produced by `publish_embeddings`.
+
+    Args:
+        ctx (click.Context): Click context containing `auth_factory`.
+        input_file (str | None): Path to a file that contains one GUID per line.
+        guids (tuple[str, ...]): One or more GUIDs supplied on the command line.
+        output_file (str): Where the TSV will be written.
+        batch_size (int): How many GUIDs to send in each request to `/data/content`.
+    """
+    auth = ctx.obj["auth_factory"].get()
+
+    if content_type not in SUPPORTED_CONTENT_TYPES:
+        click.echo(
+            f"Error: unsupported `content_type={content_type}`, not in supported: {SUPPORTED_CONTENT_TYPES}"
+        )
+        ctx.exit(1)
+
+    if input_file and guids:
+        click.echo("Error: provide either --input-file or --guids, not both.", err=True)
+        ctx.exit(1)
+
+    gen3_file = Gen3File(auth.endpoint, auth_provider=auth)
+    embeddings = gen3_file.get_bulk_content(
+        input_file=input_file,
+        guids=guids,
+        batch_size=batch_size,
+        content_type=content_type,
+    )
+
+    rows = []
+    fieldnames = []
+    fieldnames = set(
+        [
+            "guid",
+            "embedding_id",
+            "embedding",
+            "authz",
+            "collection_id",
+            "self",
+            "metadata",
+        ]
+    )
+
+    for _, embedding in embeddings.items():
+        rows.append(
+            {
+                "guid": embedding.guid,
+                "embedding_id": embedding.embedding_id,
+                "embedding": embedding.embedding,
+                "authz": embedding.authz,
+                "collection_id": embedding.collection_id,
+                "self": embedding.self,
+                "metadata": embedding.metadata,
+            }
+        )
+
+    _write_output(output_file, rows, fieldnames=list(fieldnames))
+    click.echo(f"Successfully wrote {len(rows)} records to {output_file}")
+
+
+def _write_output(output_file: str, rows: List[dict], fieldnames: List[str]) -> None:
+    """Write rows to a TSV file.
+
+    Args:
+        output_file (str): Destination path for the output TSV.
+        rows (list[dict]): Each dictionary must contain the keys
+    """
+    with open(output_file, "w", newline="") as f:
+        writer = csv.DictWriter(f, fieldnames=fieldnames, delimiter="\t")
+        writer.writeheader()
+        for row in rows:
+            writer.writerow(row)
diff --git a/gen3/cli/discovery.py b/gen3/cli/discovery.py
index ea8359aaf..a82f7f6a2 100644
--- a/gen3/cli/discovery.py
+++ b/gen3/cli/discovery.py
@@ -20,7 +20,7 @@
 
 @click.group()
 def discovery():
-    """Commands for reading and editing discovery metadata"""
+    """For reading and editing discovery metadata"""
     pass
 
 
@@ -253,12 +253,10 @@ def objects():
     pass
 
 
-@click.command(
-    help="""
+@click.command(help="""
     Outputs a TSV with populated information. [DATASET_GUIDS] argument is
     a variable number of datasets, e.g. 'phs000001.v1.p1.c1 phs000002.v1.p1.c1'
-    """
-)
+    """)
 @click.argument(
     "dataset_guids",
     nargs=-1,
@@ -320,16 +318,14 @@ def discovery_objects_read(
             click.echo(obj["guid"])
 
 
-@click.command(
-    help="""
+@click.command(help="""
     Takes a TSV as input and writes the specified objects GUIDs and defined metadata into Gen3's
     Metadata API, under a Discovery Metadata record for the dataset. The specified content from
     the TSV goes into an 'objects' block of the dataset's metadata.
     If dataset_guid already exists, update, if it doesn't already exist, create it.
     Use 'discovery objects read --template' to get a TSV with the minimum required columns
     to publish.
-    """
-)
+    """)
 @click.argument(
     "file",
     required=True,
diff --git a/gen3/cli/drs_pull.py b/gen3/cli/drs_pull.py
index 80c655117..e51bab5e0 100644
--- a/gen3/cli/drs_pull.py
+++ b/gen3/cli/drs_pull.py
@@ -249,7 +249,7 @@ def download_objects(
 
 @click.group()
 def drs_pull():
-    """Commands for downloading and listing DRS objects and manifests"""
+    """For downloading and listing DRS objects and manifests"""
     pass
 
 
diff --git a/gen3/cli/file.py b/gen3/cli/file.py
index 194b14466..68e8ba0dd 100644
--- a/gen3/cli/file.py
+++ b/gen3/cli/file.py
@@ -6,13 +6,12 @@
 from gen3.file import Gen3File
 from gen3.utils import get_or_create_event_loop_for_thread
 
-
 logger = get_logger("__name__")
 
 
 @click.group()
 def file():
-    "Commands for asynchronously downloading files from a server"
+    "For asynchronously downloading files from a server"
     pass
 
 
diff --git a/gen3/cli/nih.py b/gen3/cli/nih.py
index a44bde47a..fa734c1b5 100644
--- a/gen3/cli/nih.py
+++ b/gen3/cli/nih.py
@@ -10,13 +10,13 @@
 
 @click.group()
 def nih():
-    """Commands for reading from NIH APIs"""
+    """For reading from NIH APIs"""
     pass
 
 
 @nih.group()
 def dbgap_study_registration():
-    """Commands for interacting with the dbgap study registration api"""
+    """For interacting with the dbgap study registration api"""
     pass
 
 
diff --git a/gen3/cli/objects.py b/gen3/cli/objects.py
index 80ca40d95..cf4a5b39e 100644
--- a/gen3/cli/objects.py
+++ b/gen3/cli/objects.py
@@ -18,11 +18,12 @@
     publish_crosswalk_metadata,
     read_crosswalk_metadata,
 )
+from gen3.cli.content import get_bulk_content
 
 
 @click.group()
 def objects():
-    """Commands for reading and editing objects"""
+    """For reading and editing objects"""
     pass
 
 
@@ -352,9 +353,7 @@ def objects_manifest_delete_all_guids(ctx, file):
 manifest.add_command(objects_manifest_delete_all_guids, name="delete-all-guids")
 
 
-@click.command(
-    help=(
-        """
+@click.command(help=("""
     Publishes specified crosswalk from local files to Gen3 instance and merges
     with existing crosswalk data already in Gen3.\n
 
@@ -364,9 +363,7 @@ def objects_manifest_delete_all_guids(ctx, file):
     \t\tcommons url | identifier type | identifier name\n
     
     \tYou can have any number of columns for mapping.\n
-    """
-    )
-)
+    """))
 @click.argument(
     "file",
     type=click.Path(writable=True),
@@ -445,3 +442,5 @@ def objects_crosswalk_delete(ctx):
 crosswalk.add_command(objects_crosswalk_read, name="read")
 crosswalk.add_command(objects_crosswalk_verify, name="verify")
 crosswalk.add_command(objects_crosswalk_delete, name="delete")
+
+objects.add_command(get_bulk_content, name="read")
diff --git a/gen3/cli/pfb.py b/gen3/cli/pfb.py
index 989c1db2b..a08498a5b 100644
--- a/gen3/cli/pfb.py
+++ b/gen3/cli/pfb.py
@@ -18,7 +18,7 @@ def main():
 
 @click.group()
 def pfb():
-    """Commands for working with Portable Format for Biomedical Data (PFB)"""
+    """For working with Portable Format for Biomedical Data (PFB)"""
     pass
 
 
diff --git a/gen3/cli/users.py b/gen3/cli/users.py
index 67ee2758d..c09d57538 100644
--- a/gen3/cli/users.py
+++ b/gen3/cli/users.py
@@ -19,7 +19,7 @@ def main():
 
 @click.group()
 def users():
-    """Commands for working with gen3users"""
+    """For working with gen3users"""
     pass
 
 
diff --git a/gen3/cli/wss.py b/gen3/cli/wss.py
index 8949631eb..1ceb21180 100644
--- a/gen3/cli/wss.py
+++ b/gen3/cli/wss.py
@@ -72,7 +72,7 @@ def copy(ctx, src, dest):
 
 @click.group()
 def wss():
-    """[unfinished] Commands for Workspace Storage Service"""
+    """[unfinished] For Workspace Storage Service"""
     pass
 
 
diff --git a/gen3/configure.py b/gen3/configure.py
index 5322cf6a4..7d1b0e25b 100644
--- a/gen3/configure.py
+++ b/gen3/configure.py
@@ -18,6 +18,7 @@
 min_shepherd_version=
 
 """
+
 import json
 from os.path import expanduser
 from pathlib import Path
diff --git a/gen3/doi.py b/gen3/doi.py
index 558dda0c1..91ce11a2c 100644
--- a/gen3/doi.py
+++ b/gen3/doi.py
@@ -5,6 +5,7 @@
 For collecting DOI Metadata, other classes (outside of the ones in this module)
 can interact with different APIs to gather the necessary metadata.
 """
+
 import backoff
 import requests
 import os
@@ -290,9 +291,9 @@ def persist_doi_metadata_in_gen3(
                     f"DOI {doi.identifier} is missing `version` in doi.optional_fields. "
                     f"Defaulting to `1`."
                 )
-            metadata[
-                prefix + "version_information"
-            ] = f"This is version {doi.optional_fields.get('version', '1')} of this {doi.doi_type_general}."
+            metadata[prefix + "version_information"] = (
+                f"This is version {doi.optional_fields.get('version', '1')} of this {doi.doi_type_general}."
+            )
         if additional_metadata.get("version_information"):
             del additional_metadata["version_information"]
 
@@ -305,9 +306,9 @@ def persist_doi_metadata_in_gen3(
                 "`additional_metadata` in doi.persist_metadata_in_gen3() call. "
                 f"Consider providing this. Default will be used: {DataCite.DEFAULT_DOI_ACCESS_INFORMATION}"
             )
-            metadata[
-                prefix + "access_information"
-            ] = DataCite.DEFAULT_DOI_ACCESS_INFORMATION
+            metadata[prefix + "access_information"] = (
+                DataCite.DEFAULT_DOI_ACCESS_INFORMATION
+            )
         if additional_metadata.get("access_information"):
             del additional_metadata["access_information"]
 
diff --git a/gen3/external/__init__.py b/gen3/external/__init__.py
index e93e5d8a0..e466efebf 100644
--- a/gen3/external/__init__.py
+++ b/gen3/external/__init__.py
@@ -6,4 +6,5 @@
 
 If you're adding a new metadata source, use the ExternalMetadataSourceInterface.
 """
+
 from gen3.external.external import ExternalMetadataSourceInterface
diff --git a/gen3/external/nih/dbgap_doi.py b/gen3/external/nih/dbgap_doi.py
index ea8366b86..8e0c56253 100644
--- a/gen3/external/nih/dbgap_doi.py
+++ b/gen3/external/nih/dbgap_doi.py
@@ -140,9 +140,9 @@ def get_metadata_for_ids(self, ids):
             doi_metadata["descriptions"] = dbgapDOI._get_doi_descriptions(
                 phsid, dbgap_fhir_metadata
             )
-            doi_metadata[
-                "alternateIdentifiers"
-            ] = dbgapDOI._get_doi_alternate_identifiers(phsid, dbgap_fhir_metadata)
+            doi_metadata["alternateIdentifiers"] = (
+                dbgapDOI._get_doi_alternate_identifiers(phsid, dbgap_fhir_metadata)
+            )
             doi_metadata["fundingReferences"] = dbgapDOI._get_doi_funding(
                 phsid, dbgap_fhir_metadata
             )
diff --git a/gen3/file.py b/gen3/file.py
index 751615744..3c3573f07 100644
--- a/gen3/file.py
+++ b/gen3/file.py
@@ -1,11 +1,16 @@
+import base64
+from dataclasses import dataclass, field
+
 import json
+from typing import List, Optional
+import numpy
 import requests
 import json
 import asyncio
 import aiohttp
 import aiofiles
 import time
-from tqdm import tqdm
+from tqdm.auto import tqdm
 from types import SimpleNamespace as Namespace
 import os
 import requests
@@ -20,7 +25,20 @@
 logging = get_logger("__name__")
 
 
+@dataclass
+class EmbeddingContent:
+    guid: str
+    embedding_id: str
+    embedding: numpy.ndarray
+    authz: list[str]
+    collection_id: int | None
+    self: str
+    metadata: dict[str, str] = field(default_factory=dict)
+
+
 MAX_RETRIES = 3
+DEFAULT_BATCH_SIZE = 500
+SUPPORTED_CONTENT_TYPES = ["gen3_embeddings"]
 
 
 class Gen3File:
@@ -72,6 +90,205 @@ def get_presigned_url(self, guid, protocol=None):
         except:
             return resp.text
 
+    def get_bulk_content(
+        self,
+        input_file=None,
+        guids=None,
+        batch_size=DEFAULT_BATCH_SIZE,
+        content_type=SUPPORTED_CONTENT_TYPES[0],
+    ) -> dict[str, EmbeddingContent]:
+        """
+        Retrieve bulk content for a set of GUIDs
+
+        Args:
+            input_file (str | None): Path to a file that contains one GUID per line.
+            guids (tuple[str, ...]): One or more GUIDs supplied
+            batch_size (int): How many GUIDs to send in each request to `/data/content`.
+            content_type (str): type of content of GUIDs, this determines how to parse.
+        """
+        if content_type not in SUPPORTED_CONTENT_TYPES:
+            raise ValueError(
+                f"Error: unsupported `content_type={content_type}`, not in supported: {SUPPORTED_CONTENT_TYPES}"
+            )
+
+        final_batch_size = min(batch_size, DEFAULT_BATCH_SIZE)
+        if final_batch_size != batch_size:
+            logging.warning(
+                f"Requested batch_size={batch_size} too large, using default: {DEFAULT_BATCH_SIZE}"
+            )
+
+        if input_file and guids:
+            raise ValueError("Error: provide either input_file or guids, not both.")
+
+        all_guids: List[str] = []
+
+        if input_file:
+            with open(input_file) as f:
+                for line in f:
+                    guid = line.strip()
+                    if guid:
+                        all_guids.append(guid)
+        elif guids:
+            all_guids.extend(guids)
+        else:
+            raise ValueError("Error: provide either input_file or guids")
+
+        if not all_guids:
+            logging.error("No valid GUIDs found in the supplied input.")
+            return {}
+
+        embeddings = {}
+
+        for start in range(0, len(all_guids), batch_size):
+            batch = all_guids[start : start + batch_size]
+            try:
+                batch_response = self.get_content(batch)
+            except Exception as exc:
+                logging.error(f"API error on batch starting at {batch[0]}: {exc}")
+                continue
+
+            if isinstance(batch_response, str):
+                logging.warning(
+                    f"Warning: received raw text response for batch starting with {batch[0]}. Skipping."
+                )
+                continue
+
+            if content_type == "gen3_embeddings":
+                embeddings_from_batch = self.get_embeddings_from_bulk_content(
+                    batch_response
+                )
+                embeddings.update(embeddings_from_batch)
+
+        logging.debug(f"Successfully retrieved {len(embeddings)} records!")
+        return embeddings
+
+    def get_content(self, guids: list) -> dict:
+        """
+        Bulk retrieve content for a list of GUIDs.
+
+        The Gen3 API provides the `/data/content` endpoint which accepts a JSON body with
+        an array of GUID strings.  This helper wraps that call and returns the parsed
+        response.
+
+        Args:
+            guids (list): A list or tuple of GUIDs for which to fetch content.
+
+        Returns:
+            dict | str: If the request succeeds and the body can be decoded as JSON, a mapping
+                from each provided GUID to its associated content is returned
+
+        Raises:
+            requests.HTTPError: If the HTTP status code indicates an error
+        """
+        api_url = f"{self._endpoint}/user/data/content"
+        body = {"guids": guids}
+        headers = {"Content-Type": "application/json"}
+
+        resp = requests.post(
+            api_url, auth=self._auth_provider, json=body, headers=headers
+        )
+        raise_for_status_and_print_error(resp)
+
+        return resp.json()
+
+    def get_embeddings_from_bulk_content(
+        self, batch_response: dict
+    ) -> dict[str, EmbeddingContent]:
+        """
+        Get a dict of parsed embeddings from a batch_resonse of GUIDs
+        which are all embeddings.
+        """
+        embeddings = {}
+        for guid, data in batch_response.get("guids", {}).items():
+            embeddings[guid] = self.get_embeddings_from_bulk_content_guid(guid, data)
+        return embeddings
+
+    def get_embeddings_from_bulk_content_guid(
+        self, guid: str, bulk_content_guid_data: dict
+    ) -> EmbeddingContent:
+        """
+        Return an EmbeddingContent by parsing the response data for a particular GUID in a Bulk Content
+        response which corresponds to a Gen3 EmbeddingContent.
+
+        Note: this handles base64 decoding if the API call used that. and note that the resulting
+            vector is a numpy array
+
+        Args:
+            guid (str): globally unique identifier for the blob of data provided
+            bulk_content_guid_data (dict): data from Bulk Content response.get("guids", {}).get(guid)
+                e.g. the data for the guid specified
+
+        Returns:
+            EmbeddingContent - a dataclass representation of the embedding
+        """
+        if not isinstance(bulk_content_guid_data, dict):
+            logging.info(f"Warning: did not find {guid} in output, adding empty row...")
+            return EmbeddingContent(
+                guid=guid,
+                embedding_id="",
+                embedding=numpy.array([]),
+                authz="",
+                collection_id=None,
+                self="",
+                metadata={},
+            )
+
+        embedding_id = bulk_content_guid_data.get(
+            "embedding_id", ""
+        ) or bulk_content_guid_data.get("id", "")
+        raw_vector = (
+            bulk_content_guid_data.get("vector")
+            or bulk_content_guid_data.get("embedding")
+            or []
+        )
+
+        embedding_vector = None
+
+        # handle vector if base64 version of API used
+        if not raw_vector and "vector_base64" in bulk_content_guid_data:
+            if "precision" not in bulk_content_guid_data:
+                raise Exception(
+                    f"`vector_base64` found but no `precision` specified. Unable to parse."
+                )
+
+            vector_data_type = (
+                numpy.float16
+                if bulk_content_guid_data["precision"] == "float16"
+                else numpy.float32
+            )
+
+            # endpoint may be using binary representation
+            vector_base64_str = bulk_content_guid_data["vector_base64"]
+
+            # re-pad the string to a multiple of 4 (handles any missing '=' signs)
+            padding_needed = -len(vector_base64_str) % 4
+            padded_b64 = vector_base64_str + ("=" * padding_needed)
+            decoded_bytes = base64.urlsafe_b64decode(padded_b64)
+
+            embedding_vector = numpy.frombuffer(decoded_bytes, dtype=vector_data_type)
+
+        if embedding_vector is None:
+            embedding_vector = numpy.array(raw_vector)
+
+        authz_val = bulk_content_guid_data.get("info", {}).get("authz", "")
+        collection_id_val = bulk_content_guid_data.get("info", {}).get(
+            "collection_id", ""
+        )
+
+        url_or_self = bulk_content_guid_data.get("info", {}).get("self")
+
+        metadata = bulk_content_guid_data.get("info", {}).get("metadata")
+
+        return EmbeddingContent(
+            guid=guid,
+            embedding_id=embedding_id,
+            embedding=embedding_vector,
+            authz=authz_val,
+            collection_id=collection_id_val,
+            self=url_or_self,
+            metadata=metadata,
+        )
+
     def delete_file(self, guid):
         """
         This method is DEPRECATED. Use delete_file_locations() instead.
diff --git a/gen3/jobs.py b/gen3/jobs.py
index fc156b54a..11525c6d7 100644
--- a/gen3/jobs.py
+++ b/gen3/jobs.py
@@ -1,6 +1,7 @@
 """
 Contains class for interacting with Gen3's Job Dispatching Service(s).
 """
+
 import aiohttp
 import asyncio
 import backoff
diff --git a/gen3/metadata.py b/gen3/metadata.py
index 32c11c73e..eea10618b 100644
--- a/gen3/metadata.py
+++ b/gen3/metadata.py
@@ -1,6 +1,7 @@
 """
 Contains class for interacting with Gen3's Metadata Service.
 """
+
 import aiohttp
 import backoff
 from datetime import datetime
diff --git a/gen3/tools/bundle/ingest_manifest.py b/gen3/tools/bundle/ingest_manifest.py
index 26196659f..3f6ecd645 100644
--- a/gen3/tools/bundle/ingest_manifest.py
+++ b/gen3/tools/bundle/ingest_manifest.py
@@ -9,7 +9,7 @@
 
 from drsclient.client import DrsClient
 from gen3.auth import Gen3Auth
-from gen3.utils import UUID_FORMAT, SIZE_FORMAT, _verify_format, _standardize_str
+from gen3.utils import UUID_FORMAT, SIZE_FORMAT, _verify_format, standardize_str
 from gen3.tools.utils import (
     GUID_COLUMN_NAMES,
     SIZE_COLUMN_NAMES,
@@ -130,9 +130,9 @@ def _verify_and_process_bundle_manifest(manifest_file, manifest_file_delimiter="
                         bundle_name = value
                         record["name"] = bundle_name
                         if bundle_name not in bundle_name_to_guid:
-                            bundle_name_to_guid[
-                                bundle_name
-                            ] = ""  # to keep track of the available bundles.
+                            bundle_name_to_guid[bundle_name] = (
+                                ""  # to keep track of the available bundles.
+                            )
                         else:
                             logging.error(
                                 "ERROR: bundle_name {} at row {} is not unique".format(
@@ -149,7 +149,7 @@ def _verify_and_process_bundle_manifest(manifest_file, manifest_file_delimiter="
                         pass_verification = False
                 elif key in IDS_COLUMN_NAME:
                     standard = (
-                        _standardize_str(value)
+                        standardize_str(value)
                         .strip()
                         .lstrip("[")
                         .rstrip("]")
@@ -193,7 +193,7 @@ def _verify_and_process_bundle_manifest(manifest_file, manifest_file_delimiter="
                     if not value:
                         continue
                     standard = (
-                        _standardize_str(value)
+                        standardize_str(value)
                         .strip()
                         .lstrip("[")
                         .rstrip("]")
diff --git a/gen3/tools/download/drs_download.py b/gen3/tools/download/drs_download.py
index 2a4ec04a2..2d19f9800 100644
--- a/gen3/tools/download/drs_download.py
+++ b/gen3/tools/download/drs_download.py
@@ -17,7 +17,6 @@
 
 """
 
-
 import re
 import os
 from dataclasses import dataclass, field
@@ -33,7 +32,7 @@
 from cdislogging import get_logger
 from dataclasses_json import dataclass_json, LetterCase, Undefined
 from dateutil import parser as date_parser
-from tqdm import tqdm
+from tqdm.auto import tqdm
 from urllib.parse import urlparse
 
 from gen3.auth import Gen3Auth, Gen3AuthError, decode_token
@@ -104,7 +103,7 @@ def create_object_list(manifest) -> List["Downloadable"]:
     @staticmethod
     def load(filename: Path) -> Optional[List["Downloadable"]]:
         """
-        Method to load a json manifest and return a list of Bownloadable object.
+        Method to load a json manifest and return a list of Downloadable object.
         This list is passed to the DownloadManager methods of download, and list
 
         Args:
@@ -868,9 +867,9 @@ def resolve_objects(self, object_list: List[Downloadable], show_progress: bool):
         resolve_objects_drs_hostname(
             object_list,
             self.resolved_compact_drs,
-            mds_url=f"http://{self.hostname}/mds/aggregate/info"
-            if self.hostname
-            else None,
+            mds_url=(
+                f"http://{self.hostname}/mds/aggregate/info" if self.hostname else None
+            ),
             commons_url=self.commons_url,
         )
         progress_bar = (
diff --git a/gen3/tools/download/external_file_download.py b/gen3/tools/download/external_file_download.py
index a73888eb9..032b7c59f 100644
--- a/gen3/tools/download/external_file_download.py
+++ b/gen3/tools/download/external_file_download.py
@@ -6,6 +6,7 @@
         See docs/howto/externalFileDownloading.md for more details
 
 """
+
 import json
 from pathlib import Path
 from typing import Any, Dict, List
diff --git a/gen3/tools/indexing/download_manifest.py b/gen3/tools/indexing/download_manifest.py
index 98a84e348..045b1a793 100644
--- a/gen3/tools/indexing/download_manifest.py
+++ b/gen3/tools/indexing/download_manifest.py
@@ -20,6 +20,7 @@
               To workaround this, we have each process write to a file and concat
               them all post-processing.
 """
+
 import asyncio
 import aiofiles
 import click
diff --git a/gen3/tools/indexing/index_manifest.py b/gen3/tools/indexing/index_manifest.py
index 8b377badf..0a319ad6d 100644
--- a/gen3/tools/indexing/index_manifest.py
+++ b/gen3/tools/indexing/index_manifest.py
@@ -30,6 +30,7 @@
     python index_manifest.py --commons_url https://giangb.planx-pla.net  --manifest_file path_to_manifest --auth "admin,admin" --replace_urls False --thread_num 10
     python index_manifest.py --commons_url https://giangb.planx-pla.net  --manifest_file path_to_manifest --api_key ./credentials.json --replace_urls False --thread_num 10
 """
+
 import os
 import csv
 import click
@@ -54,7 +55,7 @@
     PREV_GUID_STANDARD_KEY,
 )
 from gen3.utils import (
-    _standardize_str,
+    standardize_str,
     get_urls,
 )
 from gen3.tools.utils import get_and_verify_fileinfos_from_manifest
@@ -62,7 +63,6 @@
 from indexclient.client import Document
 from cdislogging import get_logger
 
-
 CURRENT_DIR = os.path.dirname(os.path.realpath(__file__))
 
 logging = get_logger("__name__")
@@ -151,7 +151,7 @@ def _index_record(
         authz = (
             [
                 element.strip().replace("'", "").replace('"', "").replace("%20", " ")
-                for element in _standardize_str(fi[AUTHZ_STANDARD_KEY])
+                for element in standardize_str(fi[AUTHZ_STANDARD_KEY])
                 .strip()
                 .lstrip("[")
                 .rstrip("]")
@@ -173,7 +173,7 @@ def _index_record(
                         .replace("'", "")
                         .replace('"', "")
                         .replace("%20", " ")
-                        for element in _standardize_str(fi[ACL_STANDARD_KEY])
+                        for element in standardize_str(fi[ACL_STANDARD_KEY])
                         .strip()
                         .lstrip("[")
                         .rstrip("]")
@@ -188,7 +188,7 @@ def _index_record(
             acl = []
 
         if FILENAME_STANDARD_KEY in fi:
-            file_name = _standardize_str(fi[FILENAME_STANDARD_KEY])
+            file_name = standardize_str(fi[FILENAME_STANDARD_KEY])
         else:
             file_name = ""
 
diff --git a/gen3/tools/indexing/merge_manifests.py b/gen3/tools/indexing/merge_manifests.py
index 56752ea43..1001bcc41 100644
--- a/gen3/tools/indexing/merge_manifests.py
+++ b/gen3/tools/indexing/merge_manifests.py
@@ -23,6 +23,7 @@
 into one.
 
 """
+
 import os
 from cdislogging import get_logger
 
diff --git a/gen3/tools/indexing/post_indexing_validation.py b/gen3/tools/indexing/post_indexing_validation.py
index 4f7626560..6adea7625 100644
--- a/gen3/tools/indexing/post_indexing_validation.py
+++ b/gen3/tools/indexing/post_indexing_validation.py
@@ -8,14 +8,12 @@
 | ACL | Bucket | Protocol | Presigned URL Status | Download Status | GUID |
 """
 
-
 import csv
 from cdislogging import get_logger, get_stream_handler
 from gen3.file import Gen3File
 import requests
 import re
 
-
 logger = get_logger(__name__)
 logger.addHandler(get_stream_handler())
 logger.setLevel("INFO")
diff --git a/gen3/tools/indexing/validate_manifest_format.py b/gen3/tools/indexing/validate_manifest_format.py
index 5e86cb117..3dd07da72 100644
--- a/gen3/tools/indexing/validate_manifest_format.py
+++ b/gen3/tools/indexing/validate_manifest_format.py
@@ -1,6 +1,7 @@
 """
 Module to implement is_valid_manifest_format
 """
+
 import warnings
 import csv
 
diff --git a/gen3/tools/indexing/verify_manifest.py b/gen3/tools/indexing/verify_manifest.py
index 2f4d5f274..6df711af8 100644
--- a/gen3/tools/indexing/verify_manifest.py
+++ b/gen3/tools/indexing/verify_manifest.py
@@ -39,6 +39,7 @@ def _get_authz_from_row(row):
     MAX_CONCURRENT_REQUESTS (int): maximum number of desired concurrent requests across
         processes/threads
 """
+
 import aiohttp
 import asyncio
 import csv
@@ -48,7 +49,8 @@ def _get_authz_from_row(row):
 import time
 
 from gen3.index import Gen3Index
-from gen3.utils import get_or_create_event_loop_for_thread
+from gen3.tools.utils import AUTHZ_STANDARD_KEY
+from gen3.utils import get_or_create_event_loop_for_thread, standardize_str
 
 MAX_CONCURRENT_REQUESTS = 24
 CURRENT_DIR = os.path.dirname(os.path.realpath(__file__))
@@ -136,7 +138,21 @@ def _get_authz_from_row(row):
     Returns:
         List[str]: authz resources for the indexd record
     """
-    return [item for item in row.get("authz", "").strip().split(" ") if item]
+    authz = (
+        [
+            element.strip().replace("'", "").replace('"', "").replace("%20", " ")
+            for element in standardize_str(row[AUTHZ_STANDARD_KEY])
+            .strip()
+            .lstrip("[")
+            .rstrip("]")
+            .split(" ")
+        ]
+        if AUTHZ_STANDARD_KEY in row
+        and row[AUTHZ_STANDARD_KEY] != "[]"
+        and row[AUTHZ_STANDARD_KEY]
+        else []
+    )
+    return authz
 
 
 def _get_urls_from_row(row):
diff --git a/gen3/tools/metadata/crosswalk.py b/gen3/tools/metadata/crosswalk.py
index de4ff97a3..ed3b8df11 100644
--- a/gen3/tools/metadata/crosswalk.py
+++ b/gen3/tools/metadata/crosswalk.py
@@ -139,9 +139,9 @@ async def read_crosswalk_metadata(
                             )
                             crosswalk_columns.add(column_name)
 
-                            crosswalk_info[
-                                commons_url + "|" + identifier_name
-                            ] = indentifer_info.get("description")
+                            crosswalk_info[commons_url + "|" + identifier_name] = (
+                                indentifer_info.get("description")
+                            )
 
                     json.dump(guid_crosswalk_metadata, cached_guid_file)
 
diff --git a/gen3/tools/metadata/discovery.py b/gen3/tools/metadata/discovery.py
index 8ba8ce31b..6ccb32af8 100644
--- a/gen3/tools/metadata/discovery.py
+++ b/gen3/tools/metadata/discovery.py
@@ -286,17 +286,17 @@ def combine_discovery_metadata(
     custom_manifests_mapping_config["row_column_name"] = (
         metadata_prefix + metadata_column_to_map
     )
-    custom_manifests_mapping_config[
-        "indexing_manifest_column_name"
-    ] = discovery_column_to_map_on
+    custom_manifests_mapping_config["indexing_manifest_column_name"] = (
+        discovery_column_to_map_on
+    )
 
     # by default, the functions for parsing the manifests and rows assumes a 1:1
     # mapping. There is an additional function provided for partial string matching
     # which we can use here.
     if not exact_match:
-        custom_manifest_row_parsers[
-            "guids_for_manifest_row"
-        ] = get_guids_for_manifest_row_partial_match
+        custom_manifest_row_parsers["guids_for_manifest_row"] = (
+            get_guids_for_manifest_row_partial_match
+        )
 
     temporary_output_filename = (
         CURRENT_DIR.rstrip("/") + "/temp_" + os.path.basename(output_filename)
diff --git a/gen3/tools/metadata/ingest_manifest.py b/gen3/tools/metadata/ingest_manifest.py
index 9a3ae14ff..dfa87af8a 100644
--- a/gen3/tools/metadata/ingest_manifest.py
+++ b/gen3/tools/metadata/ingest_manifest.py
@@ -19,6 +19,7 @@
 
     MAX_CONCURRENT_REQUESTS (int): Maximum concurrent requests to mds for ingestion
 """
+
 import aiohttp
 import asyncio
 import csv
diff --git a/gen3/tools/metadata/verify_manifest.py b/gen3/tools/metadata/verify_manifest.py
index 9c843b027..f3b7235ac 100644
--- a/gen3/tools/metadata/verify_manifest.py
+++ b/gen3/tools/metadata/verify_manifest.py
@@ -22,6 +22,7 @@
     MAX_CONCURRENT_REQUESTS (int): maximum number of desired concurrent requests across
         processes/threads
 """
+
 import asyncio
 import aiohttp
 import csv
diff --git a/gen3/tools/utils.py b/gen3/tools/utils.py
index 578097789..0f4ec7016 100644
--- a/gen3/tools/utils.py
+++ b/gen3/tools/utils.py
@@ -132,17 +132,17 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                     current_column_name
                     and current_column_name.lower() in GUID_COLUMN_NAMES
                 ):
-                    fieldnames[
-                        fieldnames.index(current_column_name)
-                    ] = GUID_STANDARD_KEY
+                    fieldnames[fieldnames.index(current_column_name)] = (
+                        GUID_STANDARD_KEY
+                    )
                     output_column_name = GUID_STANDARD_KEY
                 elif (
                     current_column_name
                     and current_column_name.lower() in FILENAME_COLUMN_NAMES
                 ):
-                    fieldnames[
-                        fieldnames.index(current_column_name)
-                    ] = FILENAME_STANDARD_KEY
+                    fieldnames[fieldnames.index(current_column_name)] = (
+                        FILENAME_STANDARD_KEY
+                    )
                     output_column_name = FILENAME_STANDARD_KEY
                 elif (
                     current_column_name
@@ -170,9 +170,9 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                     current_column_name
                     and current_column_name.lower() in URLS_COLUMN_NAMES
                 ):
-                    fieldnames[
-                        fieldnames.index(current_column_name)
-                    ] = URLS_STANDARD_KEY
+                    fieldnames[fieldnames.index(current_column_name)] = (
+                        URLS_STANDARD_KEY
+                    )
                     output_column_name = URLS_STANDARD_KEY
                     if not _verify_format(row[current_column_name], URL_FORMAT):
                         logging.error(
@@ -183,9 +183,9 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                     current_column_name
                     and current_column_name.lower() in AUTHZ_COLUMN_NAMES
                 ):
-                    fieldnames[
-                        fieldnames.index(current_column_name)
-                    ] = AUTHZ_STANDARD_KEY
+                    fieldnames[fieldnames.index(current_column_name)] = (
+                        AUTHZ_STANDARD_KEY
+                    )
                     output_column_name = AUTHZ_STANDARD_KEY
                     if not _verify_format(row[current_column_name], AUTHZ_FORMAT):
                         logging.error(
@@ -196,9 +196,9 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                     current_column_name
                     and current_column_name.lower() in SIZE_COLUMN_NAMES
                 ):
-                    fieldnames[
-                        fieldnames.index(current_column_name)
-                    ] = SIZE_STANDARD_KEY
+                    fieldnames[fieldnames.index(current_column_name)] = (
+                        SIZE_STANDARD_KEY
+                    )
                     output_column_name = SIZE_STANDARD_KEY
                     if not _verify_format(row[current_column_name], SIZE_FORMAT):
                         logging.error(
@@ -209,9 +209,9 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                     current_column_name
                     and current_column_name.lower() in PREV_GUID_COLUMN_NAMES
                 ):
-                    fieldnames[
-                        fieldnames.index(current_column_name)
-                    ] = PREV_GUID_STANDARD_KEY
+                    fieldnames[fieldnames.index(current_column_name)] = (
+                        PREV_GUID_STANDARD_KEY
+                    )
                     output_column_name = PREV_GUID_STANDARD_KEY
                     # only validate format if value is provided (since this is optional)
                     if row[current_column_name] and not _verify_format(
@@ -239,9 +239,11 @@ def get_and_verify_fileinfos_from_tsv_manifest(
                         output_row[output_column_name] = (
                             int(row[current_column_name])
                             if output_column_name == SIZE_STANDARD_KEY
-                            else row[current_column_name].strip()
-                            if type(row[current_column_name]) == str
-                            else row[current_column_name]
+                            else (
+                                row[current_column_name].strip()
+                                if type(row[current_column_name]) == str
+                                else row[current_column_name]
+                            )
                         )
                     except ValueError:
                         # don't break
diff --git a/gen3/utils.py b/gen3/utils.py
index a501d1e5c..76060cc76 100644
--- a/gen3/utils.py
+++ b/gen3/utils.py
@@ -270,7 +270,7 @@ def _verify_schema(data, schema):
     return True
 
 
-def _standardize_str(s):
+def standardize_str(s):
     """
     Remove unnecessary spaces
 
@@ -304,7 +304,7 @@ def get_urls(raw_urls_string):
         .replace('"', "")
         .replace("%20", " ")
         .rstrip(",")
-        for element in _standardize_str(raw_urls_string)
+        for element in standardize_str(raw_urls_string)
         .strip()
         .lstrip("[")
         .rstrip("]")
diff --git a/poetry.lock b/poetry.lock
index 6fd949415..42ea28785 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand.
 
 [[package]]
 name = "aiofiles"
@@ -157,7 +157,6 @@ files = [
 [package.dependencies]
 aiohappyeyeballs = ">=2.5.0"
 aiosignal = ">=1.4.0"
-async-timeout = {version = ">=4.0,<6.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
 frozenlist = ">=1.1.1"
 multidict = ">=4.5,<7.0"
@@ -203,6 +202,31 @@ typing-extensions = ">=4"
 [package.extras]
 tz = ["backports.zoneinfo ; python_version < \"3.9\"", "tzdata"]
 
+[[package]]
+name = "annotated-doc"
+version = "0.0.4"
+description = "Document parameters, class attributes, return types, and variables inline, with Annotated."
+optional = true
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "extra == \"ai\""
+files = [
+    {file = "annotated_doc-0.0.4-py3-none-any.whl", hash = "sha256:571ac1dc6991c450b25a9c2d84a3705e2ae7a53467b5d111c24fa8baabbed320"},
+    {file = "annotated_doc-0.0.4.tar.gz", hash = "sha256:fbcda96e87e9c92ad167c2e53839e57503ecfda18804ea28102353485033faa4"},
+]
+
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+groups = ["main"]
+files = [
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
 [[package]]
 name = "anyio"
 version = "4.11.0"
@@ -216,7 +240,6 @@ files = [
 ]
 
 [package.dependencies]
-exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""}
 idna = ">=2.8"
 sniffio = ">=1.1"
 typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""}
@@ -225,18 +248,91 @@ typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""}
 trio = ["trio (>=0.31.0)"]
 
 [[package]]
-name = "async-timeout"
-version = "5.0.1"
-description = "Timeout context manager for asyncio programs"
+name = "appnope"
+version = "0.1.4"
+description = "Disable App Nap on macOS >= 10.9"
+optional = false
+python-versions = ">=3.6"
+groups = ["dev"]
+markers = "platform_system == \"Darwin\""
+files = [
+    {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"},
+    {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
+]
+
+[[package]]
+name = "argon2-cffi"
+version = "25.1.0"
+description = "Argon2 for Python"
 optional = false
 python-versions = ">=3.8"
-groups = ["main"]
-markers = "python_version < \"3.11\""
+groups = ["dev"]
+files = [
+    {file = "argon2_cffi-25.1.0-py3-none-any.whl", hash = "sha256:fdc8b074db390fccb6eb4a3604ae7231f219aa669a2652e0f20e16ba513d5741"},
+    {file = "argon2_cffi-25.1.0.tar.gz", hash = "sha256:694ae5cc8a42f4c4e2bf2ca0e64e51e23a040c6a517a85074683d3959e1346c1"},
+]
+
+[package.dependencies]
+argon2-cffi-bindings = "*"
+
+[[package]]
+name = "argon2-cffi-bindings"
+version = "25.1.0"
+description = "Low-level CFFI bindings for Argon2"
+optional = false
+python-versions = ">=3.9"
+groups = ["dev"]
+files = [
+    {file = "argon2_cffi_bindings-25.1.0-cp314-cp314t-macosx_10_13_universal2.whl", hash = "sha256:3d3f05610594151994ca9ccb3c771115bdb4daef161976a266f0dd8aa9996b8f"},
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+[package.dependencies]
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+    {version = ">=2.0.0b1", markers = "python_version >= \"3.14\""},
+]
+
+[[package]]
+name = "asttokens"
+version = "3.0.1"
+description = "Annotate AST trees with source code positions"
+optional = false
+python-versions = ">=3.8"
+groups = ["main", "dev"]
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+astroid = ["astroid (>=2,<5)"]
+test = ["astroid (>=2,<5)", "pytest (<9.0)", "pytest-cov", "pytest-xdist"]
+
 [[package]]
 name = "asyncio"
 version = "3.4.3"
@@ -277,45 +373,19 @@ files = [
 
 [[package]]
 name = "authlib"
-version = "1.6.5"
+version = "1.6.12"
 description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
 files = [
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 [package.dependencies]
 cryptography = "*"
 
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-name = "authutils"
-version = "6.2.6"
-description = "Gen3 auth utility functions"
-optional = false
-python-versions = "<4.0,>=3.9"
-groups = ["dev"]
-markers = "python_version < \"3.11\""
-files = [
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-xmltodict = ">=0.9,<1.0"
-
-[package.extras]
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-flask = ["Flask (<=2.3.3)"]
-
 [[package]]
 name = "authutils"
 version = "6.2.7"
@@ -323,7 +393,6 @@ description = "Gen3 auth utility functions"
 optional = false
 python-versions = "<4.0,>=3.9.2"
 groups = ["dev"]
-markers = "python_version >= \"3.11\""
 files = [
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@@ -354,6 +423,48 @@ files = [
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 ]
 
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+description = "Screen-scraping library"
+optional = false
+python-versions = ">=3.7.0"
+groups = ["dev"]
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+]
+
+[package.dependencies]
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+typing-extensions = ">=4.0.0"
+
+[package.extras]
+cchardet = ["cchardet"]
+chardet = ["chardet"]
+charset-normalizer = ["charset-normalizer"]
+html5lib = ["html5lib"]
+lxml = ["lxml"]
+
+[[package]]
+name = "bleach"
+version = "6.4.0"
+description = "An easy safelist-based HTML-sanitizing tool."
+optional = false
+python-versions = ">=3.10"
+groups = ["dev"]
+files = [
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+
+[package.dependencies]
+tinycss2 = {version = ">=1.1.0", optional = true, markers = "extra == \"css\""}
+webencodings = "*"
+
+[package.extras]
+css = ["tinycss2 (>=1.1.0)"]
+
 [[package]]
 name = "blinker"
 version = "1.9.0"
@@ -442,7 +553,6 @@ description = "Foreign Function Interface for Python calling C code."
 optional = false
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-markers = "platform_python_implementation != \"PyPy\""
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@@ -658,31 +768,14 @@ files = [
 
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-
-[package.dependencies]
-colorama = {version = "*", markers = "platform_system == \"Windows\""}
-
-[[package]]
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-version = "8.3.0"
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-markers = "python_version >= \"3.11\""
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 [package.dependencies]
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 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 groups = ["main", "dev"]
+markers = "platform_system == \"Windows\" or sys_platform == \"win32\""
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 [[package]]
-name = "coverage"
-version = "7.10.7"
-description = "Code coverage measurement for Python"
+name = "comm"
+version = "0.2.3"
+description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
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-groups = ["dev"]
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-
-[package.dependencies]
-tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
+python-versions = ">=3.8"
+groups = ["main", "dev"]
+files = [
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+]
 
 [package.extras]
-toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
+test = ["pytest"]
 
 [[package]]
 name = "coverage"
@@ -829,7 +816,6 @@ description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.10"
 groups = ["dev"]
-markers = "python_version >= \"3.11\""
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 [package.extras]
 toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
 
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-[package.extras]
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-nox = ["nox"]
-pep8test = ["check-sdist", "click", "mypy", "ruff"]
-sdist = ["build"]
-ssh = ["bcrypt (>=3.1.5)"]
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-test-randomorder = ["pytest-randomly"]
-
 [[package]]
 name = "cryptography"
 version = "44.0.3"
@@ -986,7 +921,6 @@ description = "cryptography is a package which provides cryptographic recipes an
 optional = false
 python-versions = "!=3.9.0,!=3.9.1,>=3.7"
 groups = ["dev"]
-markers = "python_version >= \"3.11\""
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@@ -1040,6 +974,106 @@ ssh = ["bcrypt (>=3.1.5)"]
 test = ["certifi (>=2024)", "cryptography-vectors (==44.0.3)", "pretend (>=0.7)", "pytest (>=7.4.0)", "pytest-benchmark (>=4.0)", "pytest-cov (>=2.10.1)", "pytest-xdist (>=3.5.0)"]
 test-randomorder = ["pytest-randomly"]
 
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+groups = ["main"]
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+
 [[package]]
 name = "dataclasses-json"
 version = "0.5.9"
@@ -1060,6 +1094,70 @@ typing-inspect = ">=0.4.0"
 [package.extras]
 dev = ["flake8", "hypothesis", "ipython", "mypy (>=0.710)", "portray", "pytest (>=7.2.0)", "setuptools", "simplejson", "twine", "types-dataclasses ; python_version == \"3.6\"", "wheel"]
 
+[[package]]
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+description = "An implementation of the Debug Adapter Protocol for Python"
+optional = false
+python-versions = ">=3.8"
+groups = ["dev"]
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+]
+
+[[package]]
+name = "decorator"
+version = "5.3.1"
+description = "Decorators for Humans"
+optional = false
+python-versions = ">=3.8"
+groups = ["main", "dev"]
+files = [
+    {file = "decorator-5.3.1-py3-none-any.whl", hash = "sha256:f47fe6fdbd2edd623ecfe36875d37aba411624e2670dd395dddae1358689bb3c"},
+    {file = "decorator-5.3.1.tar.gz", hash = "sha256:4cbcdd55a6efadb9dbea26b858f4fb3264567b52d69ca0d25b721b553f60ea82"},
+]
+
+[[package]]
+name = "defusedxml"
+version = "0.7.1"
+description = "XML bomb protection for Python stdlib modules"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+groups = ["dev"]
+files = [
+    {file = "defusedxml-0.7.1-py2.py3-none-any.whl", hash = "sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61"},
+    {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"},
+]
+
 [[package]]
 name = "deptry"
 version = "0.23.1"
@@ -1091,7 +1189,6 @@ click = ">=8.0.0,<9"
 colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\""}
 packaging = ">=23.2"
 requirements-parser = ">=0.11.0,<1"
-tomli = {version = ">=2.0.1", markers = "python_full_version < \"3.11.0\""}
 
 [[package]]
 name = "dictionaryutils"
@@ -1169,23 +1266,19 @@ httpx = ">=0.28.1,<1.0.0"
 requests = ">=2.23.0,<3.0.0"
 
 [[package]]
-name = "exceptiongroup"
-version = "1.3.0"
-description = "Backport of PEP 654 (exception groups)"
+name = "executing"
+version = "2.2.1"
+description = "Get the currently executing AST node of a frame, and other information"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 groups = ["main", "dev"]
-markers = "python_version < \"3.11\""
 files = [
-    {file = "exceptiongroup-1.3.0-py3-none-any.whl", hash = "sha256:4d111e6e0c13d0644cad6ddaa7ed0261a0b36971f6d23e7ec9b4b9097da78a10"},
-    {file = "exceptiongroup-1.3.0.tar.gz", hash = "sha256:b241f5885f560bc56a59ee63ca4c6a8bfa46ae4ad651af316d4e81817bb9fd88"},
+    {file = "executing-2.2.1-py2.py3-none-any.whl", hash = "sha256:760643d3452b4d777d295bb167ccc74c64a81df23fb5e08eff250c425a4b2017"},
+    {file = "executing-2.2.1.tar.gz", hash = "sha256:3632cc370565f6648cc328b32435bd120a1e4ebb20c77e3fdde9a13cd1e533c4"},
 ]
 
-[package.dependencies]
-typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.13\""}
-
 [package.extras]
-test = ["pytest (>=6)"]
+tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich ; python_version >= \"3.11\""]
 
 [[package]]
 name = "fastavro"
@@ -1249,6 +1342,21 @@ lz4 = ["lz4"]
 snappy = ["cramjam"]
 zstandard = ["zstandard"]
 
+[[package]]
+name = "fastjsonschema"
+version = "2.21.2"
+description = "Fastest Python implementation of JSON schema"
+optional = false
+python-versions = "*"
+groups = ["dev"]
+files = [
+    {file = "fastjsonschema-2.21.2-py3-none-any.whl", hash = "sha256:1c797122d0a86c5cace2e54bf4e819c36223b552017172f32c5c024a6b77e463"},
+    {file = "fastjsonschema-2.21.2.tar.gz", hash = "sha256:b1eb43748041c880796cd077f1a07c3d94e93ae84bba5ed36800a33554ae05de"},
+]
+
+[package.extras]
+devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
+
 [[package]]
 name = "fhirclient"
 version = "4.3.2"
@@ -1268,6 +1376,18 @@ requests = ">=2.4"
 [package.extras]
 tests = ["pytest (>=2.5)", "pytest-cov", "responses"]
 
+[[package]]
+name = "filelock"
+version = "3.29.0"
+description = "A platform independent file lock."
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+files = [
+    {file = "filelock-3.29.0-py3-none-any.whl", hash = "sha256:96f5f6344709aa1572bbf631c640e4ebeeb519e08da902c39a001882f30ac258"},
+    {file = "filelock-3.29.0.tar.gz", hash = "sha256:69974355e960702e789734cb4871f884ea6fe50bd8404051a3530bc07809cf90"},
+]
+
 [[package]]
 name = "flask"
 version = "2.3.3"
@@ -1283,7 +1403,6 @@ files = [
 [package.dependencies]
 blinker = ">=1.6.2"
 click = ">=8.1.3"
-importlib-metadata = {version = ">=3.6.0", markers = "python_version < \"3.10\""}
 itsdangerous = ">=2.1.2"
 Jinja2 = ">=3.1.2"
 Werkzeug = ">=2.3.7"
@@ -1432,6 +1551,46 @@ files = [
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 ]
 
+[[package]]
+name = "fsspec"
+version = "2026.3.0"
+description = "File-system specification"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+files = [
+    {file = "fsspec-2026.3.0-py3-none-any.whl", hash = "sha256:d2ceafaad1b3457968ed14efa28798162f1638dbb5d2a6868a2db002a5ee39a4"},
+    {file = "fsspec-2026.3.0.tar.gz", hash = "sha256:1ee6a0e28677557f8c2f994e3eea77db6392b4de9cd1f5d7a9e87a0ae9d01b41"},
+]
+
+[package.extras]
+abfs = ["adlfs"]
+adl = ["adlfs"]
+arrow = ["pyarrow (>=1)"]
+dask = ["dask", "distributed"]
+dev = ["pre-commit", "ruff (>=0.5)"]
+doc = ["numpydoc", "sphinx", "sphinx-design", "sphinx-rtd-theme", "yarl"]
+dropbox = ["dropbox", "dropboxdrivefs", "requests"]
+full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs (>2024.2.0)", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs (>2024.2.0)", "smbprotocol", "tqdm"]
+fuse = ["fusepy"]
+gcs = ["gcsfs (>2024.2.0)"]
+git = ["pygit2"]
+github = ["requests"]
+gs = ["gcsfs"]
+gui = ["panel"]
+hdfs = ["pyarrow (>=1)"]
+http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)"]
+libarchive = ["libarchive-c"]
+oci = ["ocifs"]
+s3 = ["s3fs (>2024.2.0)"]
+sftp = ["paramiko"]
+smb = ["smbprotocol"]
+ssh = ["paramiko"]
+test = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "numpy", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "requests"]
+test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask[dataframe,test]", "moto[server] (>4,<5)", "pytest-timeout", "xarray"]
+test-full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "backports-zstd ; python_version < \"3.14\"", "cloudpickle", "dask", "distributed", "dropbox", "dropboxdrivefs", "fastparquet", "fusepy", "gcsfs", "jinja2", "kerchunk", "libarchive-c", "lz4", "notebook", "numpy", "ocifs", "pandas (<3.0.0)", "panel", "paramiko", "pyarrow", "pyarrow (>=1)", "pyftpdlib", "pygit2", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "python-snappy", "requests", "smbprotocol", "tqdm", "urllib3", "zarr", "zstandard ; python_version < \"3.14\""]
+tqdm = ["tqdm"]
+
 [[package]]
 name = "gen3authz"
 version = "1.5.1"
@@ -1496,6 +1655,45 @@ files = [
     {file = "h11-0.16.0.tar.gz", hash = "sha256:4e35b956cf45792e4caa5885e69fba00bdbc6ffafbfa020300e549b208ee5ff1"},
 ]
 
+[[package]]
+name = "hf-xet"
+version = "1.4.3"
+description = "Fast transfer of large files with the Hugging Face Hub."
+optional = true
+python-versions = ">=3.8"
+groups = ["main"]
+markers = "extra == \"ai\" and (platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"arm64\" or platform_machine == \"aarch64\")"
+files = [
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+]
+
+[package.extras]
+tests = ["pytest"]
+
 [[package]]
 name = "hsclient"
 version = "0.1"
@@ -1562,6 +1760,43 @@ http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
 zstd = ["zstandard (>=0.18.0)"]
 
+[[package]]
+name = "huggingface-hub"
+version = "1.12.0"
+description = "Client library to download and publish models, datasets and other repos on the huggingface.co hub"
+optional = true
+python-versions = ">=3.10.0"
+groups = ["main"]
+markers = "extra == \"ai\""
+files = [
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+    {file = "huggingface_hub-1.12.0.tar.gz", hash = "sha256:7c3fe85e24b652334e5d456d7a812cd9a071e75630fac4365d9165ab5e4a34b6"},
+]
+
+[package.dependencies]
+filelock = ">=3.10.0"
+fsspec = ">=2023.5.0"
+hf-xet = {version = ">=1.4.3,<2.0.0", markers = "platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"arm64\" or platform_machine == \"aarch64\""}
+httpx = ">=0.23.0,<1"
+packaging = ">=20.9"
+pyyaml = ">=5.1"
+tqdm = ">=4.42.1"
+typer = "*"
+typing-extensions = ">=4.1.0"
+
+[package.extras]
+all = ["Jinja2", "Pillow", "authlib (>=1.3.2)", "duckdb", "fastapi", "fastapi", "httpx", "itsdangerous", "jedi", "libcst (>=1.4.0)", "mypy (==1.15.0)", "numpy", "pytest (>=8.4.2)", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-mock", "pytest-rerunfailures (<16.0)", "pytest-vcr", "pytest-xdist", "ruff (>=0.9.0)", "soundfile", "ty", "types-PyYAML", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)", "urllib3 (<2.0)"]
+dev = ["Jinja2", "Pillow", "authlib (>=1.3.2)", "duckdb", "fastapi", "fastapi", "httpx", "itsdangerous", "jedi", "libcst (>=1.4.0)", "mypy (==1.15.0)", "numpy", "pytest (>=8.4.2)", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-mock", "pytest-rerunfailures (<16.0)", "pytest-vcr", "pytest-xdist", "ruff (>=0.9.0)", "soundfile", "ty", "types-PyYAML", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)", "urllib3 (<2.0)"]
+fastai = ["fastai (>=2.4)", "fastcore (>=1.3.27)", "toml"]
+gradio = ["gradio (>=5.0.0)", "requests"]
+hf-xet = ["hf-xet (>=1.4.3,<2.0.0)"]
+mcp = ["mcp (>=1.8.0)"]
+oauth = ["authlib (>=1.3.2)", "fastapi", "httpx", "itsdangerous"]
+quality = ["libcst (>=1.4.0)", "mypy (==1.15.0)", "ruff (>=0.9.0)", "ty"]
+testing = ["Jinja2", "Pillow", "authlib (>=1.3.2)", "duckdb", "fastapi", "fastapi", "httpx", "itsdangerous", "jedi", "numpy", "pytest (>=8.4.2)", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-mock", "pytest-rerunfailures (<16.0)", "pytest-vcr", "pytest-xdist", "soundfile", "urllib3 (<2.0)"]
+torch = ["safetensors[torch]", "torch"]
+typing = ["types-PyYAML", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)"]
+
 [[package]]
 name = "humanfriendly"
 version = "10.0"
@@ -1598,12 +1833,11 @@ version = "8.7.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.9"
-groups = ["main", "dev"]
+groups = ["main"]
 files = [
     {file = "importlib_metadata-8.7.0-py3-none-any.whl", hash = "sha256:e5dd1551894c77868a30651cef00984d50e1002d06942a7101d34870c5f02afd"},
     {file = "importlib_metadata-8.7.0.tar.gz", hash = "sha256:d13b81ad223b890aa16c5471f2ac3056cf76c5f10f82d6f9292f0b415f389000"},
 ]
-markers = {dev = "python_version < \"3.11\""}
 
 [package.dependencies]
 zipp = ">=3.20"
@@ -1664,19 +1898,6 @@ url = "https://github.com/uc-cdis/indexd.git"
 reference = "5.0.4"
 resolved_reference = "5d3e54c31edba946f92d6d9ddccb016a7520e668"
 
-[[package]]
-name = "iniconfig"
-version = "2.1.0"
-description = "brain-dead simple config-ini parsing"
-optional = false
-python-versions = ">=3.8"
-groups = ["dev"]
-markers = "python_version < \"3.11\""
-files = [
-    {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"},
-    {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"},
-]
-
 [[package]]
 name = "iniconfig"
 version = "2.3.0"
@@ -1684,33 +1905,168 @@ description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.10"
 groups = ["dev"]
-markers = "python_version >= \"3.11\""
 files = [
     {file = "iniconfig-2.3.0-py3-none-any.whl", hash = "sha256:f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12"},
     {file = "iniconfig-2.3.0.tar.gz", hash = "sha256:c76315c77db068650d49c5b56314774a7804df16fee4402c1f19d6d15d8c4730"},
 ]
 
 [[package]]
-name = "itsdangerous"
-version = "2.2.0"
-description = "Safely pass data to untrusted environments and back."
+name = "ipykernel"
+version = "7.2.0"
+description = "IPython Kernel for Jupyter"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.10"
 groups = ["dev"]
 files = [
-    {file = "itsdangerous-2.2.0-py3-none-any.whl", hash = "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef"},
-    {file = "itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173"},
+    {file = "ipykernel-7.2.0-py3-none-any.whl", hash = "sha256:3bbd4420d2b3cc105cbdf3756bfc04500b1e52f090a90716851f3916c62e1661"},
+    {file = "ipykernel-7.2.0.tar.gz", hash = "sha256:18ed160b6dee2cbb16e5f3575858bc19d8f1fe6046a9a680c708494ce31d909e"},
 ]
 
+[package.dependencies]
+appnope = {version = ">=0.1.2", markers = "platform_system == \"Darwin\""}
+comm = ">=0.1.1"
+debugpy = ">=1.6.5"
+ipython = ">=7.23.1"
+jupyter-client = ">=8.8.0"
+jupyter-core = ">=5.1,<6.0.dev0 || >=6.1.dev0"
+matplotlib-inline = ">=0.1"
+nest-asyncio = ">=1.4"
+packaging = ">=22"
+psutil = ">=5.7"
+pyzmq = ">=25"
+tornado = ">=6.4.1"
+traitlets = ">=5.4.0"
+
+[package.extras]
+cov = ["coverage[toml]", "matplotlib", "pytest-cov", "trio"]
+docs = ["intersphinx-registry", "myst-parser", "pydata-sphinx-theme", "sphinx (<8.2.0)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
+pyqt5 = ["pyqt5"]
+pyside6 = ["pyside6"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0,<10)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
+
 [[package]]
-name = "jinja2"
-version = "3.1.6"
-description = "A very fast and expressive template engine."
+name = "ipython"
+version = "9.14.0"
+description = "IPython: Productive Interactive Computing"
 optional = false
-python-versions = ">=3.7"
-groups = ["dev"]
+python-versions = ">=3.11"
+groups = ["main", "dev"]
 files = [
-    {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"},
+    {file = "ipython-9.14.0-py3-none-any.whl", hash = "sha256:8fd984a3372c14b12790b084ba6b5cff5678c0cb063244a0034f06a51f20d6c2"},
+    {file = "ipython-9.14.0.tar.gz", hash = "sha256:6f27ff0f1d9ea050e0551f71568bc4b34d8aba579e8f111c5b4175f44ac6b4aa"},
+]
+
+[package.dependencies]
+colorama = {version = ">=0.4.4", markers = "sys_platform == \"win32\""}
+decorator = ">=5.1.0"
+ipython-pygments-lexers = ">=1.0.0"
+jedi = ">=0.18.2"
+matplotlib-inline = ">=0.1.6"
+pexpect = {version = ">4.6", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
+prompt_toolkit = ">=3.0.41,<3.1.0"
+psutil = {version = ">=7", markers = "sys_platform != \"emscripten\""}
+pygments = ">=2.14.0"
+stack_data = ">=0.6.0"
+traitlets = ">=5.13.0"
+typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
+
+[package.extras]
+all = ["argcomplete (>=3.0)", "ipython[doc,matplotlib,terminal,test,test-extra]", "types-decorator"]
+black = ["black"]
+doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[matplotlib,test]", "setuptools (>=80.0)", "sphinx (>=8.0)", "sphinx-rtd-theme (>=0.1.8)", "sphinx_toml (==0.0.4)", "typing_extensions"]
+matplotlib = ["matplotlib (>3.9)"]
+test = ["packaging (>=23.0.0)", "pytest (>=7.0.0)", "pytest-asyncio (>=1.0.0)", "setuptools (>=80.0)", "testpath (>=0.2)"]
+test-extra = ["curio", "ipykernel (>6.30)", "ipython[matplotlib]", "ipython[test]", "jupyter_ai", "nbclient", "nbformat", "numpy (>=2.0)", "pandas (>2.1)", "trio (>=0.22.0)"]
+
+[[package]]
+name = "ipython-genutils"
+version = "0.2.0"
+description = "Vestigial utilities from IPython"
+optional = false
+python-versions = "*"
+groups = ["dev"]
+files = [
+    {file = "ipython_genutils-0.2.0-py2.py3-none-any.whl", hash = "sha256:72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8"},
+    {file = "ipython_genutils-0.2.0.tar.gz", hash = "sha256:eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"},
+]
+
+[[package]]
+name = "ipython-pygments-lexers"
+version = "1.1.1"
+description = "Defines a variety of Pygments lexers for highlighting IPython code."
+optional = false
+python-versions = ">=3.8"
+groups = ["main", "dev"]
+files = [
+    {file = "ipython_pygments_lexers-1.1.1-py3-none-any.whl", hash = "sha256:a9462224a505ade19a605f71f8fa63c2048833ce50abc86768a0d81d876dc81c"},
+    {file = "ipython_pygments_lexers-1.1.1.tar.gz", hash = "sha256:09c0138009e56b6854f9535736f4171d855c8c08a563a0dcd8022f78355c7e81"},
+]
+
+[package.dependencies]
+pygments = "*"
+
+[[package]]
+name = "ipywidgets"
+version = "8.1.8"
+description = "Jupyter interactive widgets"
+optional = false
+python-versions = ">=3.7"
+groups = ["main"]
+files = [
+    {file = "ipywidgets-8.1.8-py3-none-any.whl", hash = "sha256:ecaca67aed704a338f88f67b1181b58f821ab5dc89c1f0f5ef99db43c1c2921e"},
+    {file = "ipywidgets-8.1.8.tar.gz", hash = "sha256:61f969306b95f85fba6b6986b7fe45d73124d1d9e3023a8068710d47a22ea668"},
+]
+
+[package.dependencies]
+comm = ">=0.1.3"
+ipython = ">=6.1.0"
+jupyterlab_widgets = ">=3.0.15,<3.1.0"
+traitlets = ">=4.3.1"
+widgetsnbextension = ">=4.0.14,<4.1.0"
+
+[package.extras]
+test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
+
+[[package]]
+name = "itsdangerous"
+version = "2.2.0"
+description = "Safely pass data to untrusted environments and back."
+optional = false
+python-versions = ">=3.8"
+groups = ["dev"]
+files = [
+    {file = "itsdangerous-2.2.0-py3-none-any.whl", hash = "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef"},
+    {file = "itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173"},
+]
+
+[[package]]
+name = "jedi"
+version = "0.20.0"
+description = "An autocompletion tool for Python that can be used for text editors."
+optional = false
+python-versions = ">=3.10"
+groups = ["main", "dev"]
+files = [
+    {file = "jedi-0.20.0-py2.py3-none-any.whl", hash = "sha256:7bdd9c2634f56713299976f4cbd59cb3fa92165cc5e05ea811fb253480728b67"},
+    {file = "jedi-0.20.0.tar.gz", hash = "sha256:c3f4ccbd276696f4b19c54618d4fb18f9fc24b0aef02acf704b23f487daa1011"},
+]
+
+[package.dependencies]
+parso = ">=0.8.6,<0.9.0"
+
+[package.extras]
+dev = ["Django", "attrs", "colorama", "docopt", "flake8 (==7.1.2)", "pytest (<9.0.0)", "types-setuptools (==80.9.0.20250529)", "typing-extensions", "zuban (==0.7.0)"]
+docs = ["Jinja2 (==3.1.6)", "MarkupSafe (==3.0.3)", "Pygments (==2.20.0)", "Sphinx (==9.1.0)", "alabaster (==1.0.0)", "babel (==2.18.0)", "certifi (==2026.4.22)", "charset-normalizer (==3.4.7)", "docutils (==0.22.4)", "idna (==3.13)", "imagesize (==2.0.0)", "iniconfig (==2.3.0)", "packaging (==26.2)", "pluggy (==1.6.0)", "pytest (==9.0.3)", "requests (==2.33.1)", "roman-numerals (==4.1.0)", "snowballstemmer (==3.0.1)", "sphinx-rtd-theme (==3.1.0)", "sphinxcontrib-applehelp (==2.0.0)", "sphinxcontrib-devhelp (==2.0.0)", "sphinxcontrib-htmlhelp (==2.1.0)", "sphinxcontrib-jquery (==4.1)", "sphinxcontrib-jsmath (==1.0.1)", "sphinxcontrib-qthelp (==2.0.0)", "sphinxcontrib-serializinghtml (==2.0.0)", "urllib3 (==2.6.3)"]
+
+[[package]]
+name = "jinja2"
+version = "3.1.6"
+description = "A very fast and expressive template engine."
+optional = false
+python-versions = ">=3.7"
+groups = ["main", "dev"]
+files = [
+    {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"},
     {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"},
 ]
 
@@ -1720,6 +2076,31 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "joblib"
+version = "1.5.3"
+description = "Lightweight pipelining with Python functions"
+optional = true
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "extra == \"ai\""
+files = [
+    {file = "joblib-1.5.3-py3-none-any.whl", hash = "sha256:5fc3c5039fc5ca8c0276333a188bbd59d6b7ab37fe6632daa76bc7f9ec18e713"},
+    {file = "joblib-1.5.3.tar.gz", hash = "sha256:8561a3269e6801106863fd0d6d84bb737be9e7631e33aaed3fb9ce5953688da3"},
+]
+
+[[package]]
+name = "jsonpointer"
+version = "3.1.1"
+description = "Identify specific nodes in a JSON document (RFC 6901) "
+optional = false
+python-versions = ">=3.10"
+groups = ["dev"]
+files = [
+    {file = "jsonpointer-3.1.1-py3-none-any.whl", hash = "sha256:8ff8b95779d071ba472cf5bc913028df06031797532f08a7d5b602d8b2a488ca"},
+    {file = "jsonpointer-3.1.1.tar.gz", hash = "sha256:0b801c7db33a904024f6004d526dcc53bbb8a4a0f4e32bfd10beadf60adf1900"},
+]
+
 [[package]]
 name = "jsonschema"
 version = "3.2.0"
@@ -1734,24 +2115,179 @@ files = [
 
 [package.dependencies]
 attrs = ">=17.4.0"
+idna = {version = "*", optional = true, markers = "extra == \"format_nongpl\""}
+jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format_nongpl\""}
 pyrsistent = ">=0.14.0"
+rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format_nongpl\""}
+rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format_nongpl\""}
 setuptools = "*"
 six = ">=1.11.0"
+webcolors = {version = "*", optional = true, markers = "extra == \"format_nongpl\""}
 
 [package.extras]
 format = ["idna", "jsonpointer (>1.13)", "rfc3987", "strict-rfc3339", "webcolors"]
 format-nongpl = ["idna", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "webcolors"]
 
+[[package]]
+name = "jupyter-client"
+version = "8.8.0"
+description = "Jupyter protocol implementation and client libraries"
+optional = false
+python-versions = ">=3.10"
+groups = ["dev"]
+files = [
+    {file = "jupyter_client-8.8.0-py3-none-any.whl", hash = "sha256:f93a5b99c5e23a507b773d3a1136bd6e16c67883ccdbd9a829b0bbdb98cd7d7a"},
+    {file = "jupyter_client-8.8.0.tar.gz", hash = "sha256:d556811419a4f2d96c869af34e854e3f059b7cc2d6d01a9cd9c85c267691be3e"},
+]
+
+[package.dependencies]
+jupyter-core = ">=5.1"
+python-dateutil = ">=2.8.2"
+pyzmq = ">=25.0"
+tornado = ">=6.4.1"
+traitlets = ">=5.3"
+
+[package.extras]
+docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+orjson = ["orjson"]
+test = ["anyio", "coverage", "ipykernel (>=6.14)", "msgpack", "mypy ; platform_python_implementation != \"PyPy\"", "paramiko ; sys_platform == \"win32\"", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.6.2)", "pytest-timeout"]
+
+[[package]]
+name = "jupyter-core"
+version = "5.9.1"
+description = "Jupyter core package. A base package on which Jupyter projects rely."
+optional = false
+python-versions = ">=3.10"
+groups = ["dev"]
+files = [
+    {file = "jupyter_core-5.9.1-py3-none-any.whl", hash = "sha256:ebf87fdc6073d142e114c72c9e29a9d7ca03fad818c5d300ce2adc1fb0743407"},
+    {file = "jupyter_core-5.9.1.tar.gz", hash = "sha256:4d09aaff303b9566c3ce657f580bd089ff5c91f5f89cf7d8846c3cdf465b5508"},
+]
+
+[package.dependencies]
+platformdirs = ">=2.5"
+traitlets = ">=5.3"
+
+[package.extras]
+docs = ["intersphinx-registry", "myst-parser", "pydata-sphinx-theme", "sphinx-autodoc-typehints", "sphinxcontrib-spelling", "traitlets"]
+test = ["ipykernel", "pre-commit", "pytest (<9)", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "jupyter-events"
+version = "0.6.3"
+description = "Jupyter Event System library"
+optional = false
+python-versions = ">=3.7"
+groups = ["dev"]
+files = [
+    {file = "jupyter_events-0.6.3-py3-none-any.whl", hash = "sha256:57a2749f87ba387cd1bfd9b22a0875b889237dbf2edc2121ebb22bde47036c17"},
+    {file = "jupyter_events-0.6.3.tar.gz", hash = "sha256:9a6e9995f75d1b7146b436ea24d696ce3a35bfa8bfe45e0c33c334c79464d0b3"},
+]
+
+[package.dependencies]
+jsonschema = {version = ">=3.2.0", extras = ["format-nongpl"]}
+python-json-logger = ">=2.0.4"
+pyyaml = ">=5.3"
+rfc3339-validator = "*"
+rfc3986-validator = ">=0.1.1"
+traitlets = ">=5.3"
+
+[package.extras]
+cli = ["click", "rich"]
+docs = ["jupyterlite-sphinx", "myst-parser", "pydata-sphinx-theme", "sphinxcontrib-spelling"]
+test = ["click", "coverage", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "pytest-console-scripts", "pytest-cov", "rich"]
+
+[[package]]
+name = "jupyter-server"
+version = "2.10.0"
+description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
+optional = false
+python-versions = ">=3.8"
+groups = ["dev"]
+files = [
+    {file = "jupyter_server-2.10.0-py3-none-any.whl", hash = "sha256:dde56c9bc3cb52d7b72cc0f696d15d7163603526f1a758eb4a27405b73eab2a5"},
+    {file = "jupyter_server-2.10.0.tar.gz", hash = "sha256:47b8f5e63440125cb1bb8957bf12b18453ee5ed9efe42d2f7b2ca66a7019a278"},
+]
+
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@@ -1762,13 +2298,38 @@ babel = ["Babel"]
 lingua = ["lingua"]
 testing = ["pytest"]
 
+[[package]]
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+version = "4.0.0"
+description = "Python port of markdown-it. Markdown parsing, done right!"
+optional = true
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "extra == \"ai\""
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+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions", "requests"]
+
 [[package]]
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 python-versions = ">=3.9"
-groups = ["dev"]
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@@ -1896,6 +2457,67 @@ files = [
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+
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+
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+python-versions = ">=3.7"
+groups = ["main"]
+markers = "extra == \"ai\""
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+description = "A sane and fast Markdown parser with useful plugins and renderers"
+optional = false
+python-versions = ">=3.8"
+groups = ["dev"]
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+groups = ["main"]
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+tests = ["pytest (>=4.6)"]
+
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@@ -2052,160 +2674,550 @@ files = [
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+json-logging = ["json-logging"]
+test = ["coverage", "nbval", "pytest", "pytest-cov", "pytest-jupyter", "pytest-playwright", "pytest-tornasync", "requests", "requests-unixsocket ; sys_platform != \"win32\"", "testpath"]
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@@ -2336,6 +3403,38 @@ files = [
 dev = ["pre-commit", "tox"]
 testing = ["coverage", "pytest", "pytest-benchmark"]
 
+[[package]]
+name = "prometheus-client"
+version = "0.25.0"
+description = "Python client for the Prometheus monitoring system."
+optional = false
+python-versions = ">=3.9"
+groups = ["dev"]
+files = [
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+]
+
+[package.extras]
+aiohttp = ["aiohttp"]
+django = ["django"]
+twisted = ["twisted"]
+
+[[package]]
+name = "prompt-toolkit"
+version = "3.0.52"
+description = "Library for building powerful interactive command lines in Python"
+optional = false
+python-versions = ">=3.8"
+groups = ["main", "dev"]
+files = [
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+]
+
+[package.dependencies]
+wcwidth = "*"
+
 [[package]]
 name = "propcache"
 version = "0.4.1"
@@ -2468,23 +3567,87 @@ files = [
     {file = "propcache-0.4.1.tar.gz", hash = "sha256:f48107a8c637e80362555f37ecf49abe20370e557cc4ab374f04ec4423c97c3d"},
 ]
 
+[[package]]
+name = "psutil"
+version = "7.2.2"
+description = "Cross-platform lib for process and system monitoring."
+optional = false
+python-versions = ">=3.6"
+groups = ["main", "dev"]
+files = [
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+]
+markers = {main = "sys_platform != \"emscripten\""}
+
+[package.extras]
+dev = ["abi3audit", "black", "check-manifest", "colorama ; os_name == \"nt\"", "coverage", "packaging", "psleak", "pylint", "pyperf", "pypinfo", "pyreadline3 ; os_name == \"nt\"", "pytest", "pytest-cov", "pytest-instafail", "pytest-xdist", "pywin32 ; os_name == \"nt\" and implementation_name != \"pypy\"", "requests", "rstcheck", "ruff", "setuptools", "sphinx", "sphinx_rtd_theme", "toml-sort", "twine", "validate-pyproject[all]", "virtualenv", "vulture", "wheel", "wheel ; os_name == \"nt\" and implementation_name != \"pypy\"", "wmi ; os_name == \"nt\" and implementation_name != \"pypy\""]
+test = ["psleak", "pytest", "pytest-instafail", "pytest-xdist", "pywin32 ; os_name == \"nt\" and implementation_name != \"pypy\"", "setuptools", "wheel ; os_name == \"nt\" and implementation_name != \"pypy\"", "wmi ; os_name == \"nt\" and implementation_name != \"pypy\""]
+
 [[package]]
 name = "psycopg2"
-version = "2.9.11"
+version = "2.9.12"
 description = "psycopg2 - Python-PostgreSQL Database Adapter"
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
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+]
+
+[[package]]
+name = "ptyprocess"
+version = "0.7.0"
+description = "Run a subprocess in a pseudo terminal"
+optional = false
+python-versions = "*"
+groups = ["main", "dev"]
+files = [
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+]
+markers = {main = "sys_platform != \"win32\" and sys_platform != \"emscripten\"", dev = "sys_platform != \"win32\" and sys_platform != \"emscripten\" or os_name != \"nt\""}
+
+[[package]]
+name = "pure-eval"
+version = "0.2.3"
+description = "Safely evaluate AST nodes without side effects"
+optional = false
+python-versions = "*"
+groups = ["main", "dev"]
+files = [
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 ]
 
+[package.extras]
+tests = ["pytest"]
+
 [[package]]
 name = "py"
 version = "1.11.0"
@@ -2504,22 +3667,192 @@ description = "C parser in Python"
 optional = false
 python-versions = ">=3.8"
 groups = ["dev"]
-markers = "platform_python_implementation != \"PyPy\" and implementation_name != \"PyPy\""
+markers = "implementation_name != \"PyPy\""
 files = [
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 ]
 
+[[package]]
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+version = "2.13.4"
+description = "Data validation using Python type hints"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
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+pydantic-core = "2.46.4"
+typing-extensions = ">=4.14.1"
+typing-inspection = ">=0.4.2"
+
+[package.extras]
+email = ["email-validator (>=2.0.0)"]
+timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""]
+
+[[package]]
+name = "pydantic-core"
+version = "2.46.4"
+description = "Core functionality for Pydantic validation and serialization"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
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+version = "2.13.0"
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 [package.dependencies]
@@ -2527,9 +3860,6 @@ cryptography = {version = ">=3.4.0", optional = true, markers = "extra == \"cryp
 
 [package.extras]
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 python-json-logger = ">=2.0.0"
 PyYAML = ">=6.0.1"
 
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 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
-groups = ["main"]
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 python-versions = ">=3.8"
-groups = ["main"]
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 [package.dependencies]
-requests = ">=2.22,<3"
+numpy = ">=1.26.4,<2.7"
 
 [package.extras]
-fixture = ["fixtures"]
+dev = ["click (<8.3.0)", "cython-lint (>=0.12.2)", "mypy (==1.10.0)", "pycodestyle", "ruff (>=0.12.0)", "spin", "types-psutil", "typing_extensions"]
+doc = ["intersphinx_registry", "jupyterlite-pyodide-kernel", "jupyterlite-sphinx (>=0.19.1)", "jupytext", "linkify-it-py", "matplotlib (>=3.5)", "myst-nb (>=1.2.0)", "numpydoc", "pooch", "pydata-sphinx-theme (>=0.15.2)", "sphinx (>=5.0.0,<8.2.0)", "sphinx-copybutton", "sphinx-design (>=0.4.0)", "tabulate"]
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 [[package]]
-name = "requirements-parser"
-version = "0.13.0"
-description = "This is a small Python module for parsing Pip requirement files."
+name = "send2trash"
+version = "2.1.0"
+description = "Send file to trash natively under Mac OS X, Windows and Linux"
 optional = false
-python-versions = "<4.0,>=3.8"
+python-versions = ">=3.8"
 groups = ["dev"]
 files = [
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+]
+
+[package.extras]
+nativelib = ["pyobjc (>=9.0) ; sys_platform == \"darwin\"", "pywin32 (>=305) ; sys_platform == \"win32\""]
+test = ["pytest (>=8)"]
+
+[[package]]
+name = "sentence-transformers"
+version = "5.5.0"
+description = "Embeddings, Retrieval, and Reranking"
+optional = true
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "extra == \"ai\""
+files = [
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 ]
 
 [package.dependencies]
-packaging = ">=23.2"
+huggingface-hub = ">=0.23.0"
+numpy = ">=1.20.0"
+scikit-learn = ">=0.22.0"
+scipy = ">=1.0.0"
+torch = ">=1.11.0"
+tqdm = ">=4.0.0"
+transformers = ">=4.41.0,<6.0.0"
+typing_extensions = ">=4.5.0"
+
+[package.extras]
+audio = ["transformers[audio]"]
+dev = ["accelerate (>=0.20.3)", "datasets (>=2.0.0)", "peft", "pre-commit", "pytest", "pytest-cov", "pytest-env", "pytest-subtests", "pytest-xdist", "transformers[audio,video,vision]"]
+image = ["transformers[vision]"]
+onnx = ["optimum-onnx[onnxruntime]"]
+onnx-gpu = ["optimum-onnx[onnxruntime-gpu]"]
+openvino = ["optimum-intel[openvino]"]
+train = ["accelerate (>=0.20.3)", "datasets (>=2.0.0)"]
+video = ["transformers[video]"]
 
 [[package]]
 name = "setuptools"
@@ -2861,6 +4731,19 @@ enabler = ["pytest-enabler (>=2.2)"]
 test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21) ; python_version >= \"3.9\" and sys_platform != \"cygwin\"", "jaraco.envs (>=2.2)", "jaraco.path (>=3.7.2)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf ; sys_platform != \"cygwin\"", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
 type = ["importlib_metadata (>=7.0.2) ; python_version < \"3.10\"", "jaraco.develop (>=7.21) ; sys_platform != \"cygwin\"", "mypy (==1.14.*)", "pytest-mypy"]
 
+[[package]]
+name = "shellingham"
+version = "1.5.4"
+description = "Tool to Detect Surrounding Shell"
+optional = true
+python-versions = ">=3.7"
+groups = ["main"]
+markers = "extra == \"ai\""
+files = [
+    {file = "shellingham-1.5.4-py2.py3-none-any.whl", hash = "sha256:7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686"},
+    {file = "shellingham-1.5.4.tar.gz", hash = "sha256:8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de"},
+]
+
 [[package]]
 name = "six"
 version = "1.17.0"
@@ -2885,6 +4768,18 @@ files = [
     {file = "sniffio-1.3.1.tar.gz", hash = "sha256:f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc"},
 ]
 
+[[package]]
+name = "soupsieve"
+version = "2.8.4"
+description = "A modern CSS selector implementation for Beautiful Soup."
+optional = false
+python-versions = ">=3.9"
+groups = ["dev"]
+files = [
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+    {file = "soupsieve-2.8.4.tar.gz", hash = "sha256:e121fd02e975c695e4e9e8774a5ee35d74714b59307868dcc5319ad2d9e3328e"},
+]
+
 [[package]]
 name = "sqlalchemy"
 version = "1.3.24"
@@ -2971,6 +4866,141 @@ test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3
 timezone = ["python-dateutil"]
 url = ["furl (>=0.4.1)"]
 
+[[package]]
+name = "stack-data"
+version = "0.6.3"
+description = "Extract data from python stack frames and tracebacks for informative displays"
+optional = false
+python-versions = "*"
+groups = ["main", "dev"]
+files = [
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+    {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"},
+]
+
+[package.dependencies]
+asttokens = ">=2.1.0"
+executing = ">=1.2.0"
+pure-eval = "*"
+
+[package.extras]
+tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
+
+[[package]]
+name = "sympy"
+version = "1.14.0"
+description = "Computer algebra system (CAS) in Python"
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "sympy-1.14.0-py3-none-any.whl", hash = "sha256:e091cc3e99d2141a0ba2847328f5479b05d94a6635cb96148ccb3f34671bd8f5"},
+    {file = "sympy-1.14.0.tar.gz", hash = "sha256:d3d3fe8df1e5a0b42f0e7bdf50541697dbe7d23746e894990c030e2b05e72517"},
+]
+
+[package.dependencies]
+mpmath = ">=1.1.0,<1.4"
+
+[package.extras]
+dev = ["hypothesis (>=6.70.0)", "pytest (>=7.1.0)"]
+
+[[package]]
+name = "terminado"
+version = "0.18.1"
+description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
+optional = false
+python-versions = ">=3.8"
+groups = ["dev"]
+files = [
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+    {file = "terminado-0.18.1.tar.gz", hash = "sha256:de09f2c4b85de4765f7714688fff57d3e75bad1f909b589fde880460c753fd2e"},
+]
+
+[package.dependencies]
+ptyprocess = {version = "*", markers = "os_name != \"nt\""}
+pywinpty = {version = ">=1.1.0", markers = "os_name == \"nt\""}
+tornado = ">=6.1.0"
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
+test = ["pre-commit", "pytest (>=7.0)", "pytest-timeout"]
+typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
+
+[[package]]
+name = "threadpoolctl"
+version = "3.6.0"
+description = "threadpoolctl"
+optional = true
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "extra == \"ai\""
+files = [
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+]
+
+[[package]]
+name = "tinycss2"
+version = "1.5.1"
+description = "A tiny CSS parser"
+optional = false
+python-versions = ">=3.10"
+groups = ["dev"]
+files = [
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+]
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+[package.dependencies]
+webencodings = ">=0.4"
+
+[package.extras]
+doc = ["furo", "sphinx"]
+test = ["pytest", "ruff"]
+
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 slack = ["slack-sdk"]
 telegram = ["requests"]
 
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 version = "4.15.0"
@@ -3086,6 +5263,21 @@ files = [
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 typing-extensions = ">=3.7.4"
 
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@@ -3116,24 +5308,89 @@ h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
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+files = [
+    {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"},
+    {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"},
+]
+
+[[package]]
+name = "websocket-client"
+version = "1.9.0"
+description = "WebSocket client for Python with low level API options"
+optional = false
+python-versions = ">=3.9"
+groups = ["dev"]
+files = [
+    {file = "websocket_client-1.9.0-py3-none-any.whl", hash = "sha256:af248a825037ef591efbf6ed20cc5faa03d3b47b9e5a2230a529eeee1c1fc3ef"},
+    {file = "websocket_client-1.9.0.tar.gz", hash = "sha256:9e813624b6eb619999a97dc7958469217c3176312b3a16a4bd1bc7e08a46ec98"},
+]
+
+[package.extras]
+docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx_rtd_theme (>=1.1.0)"]
+optional = ["python-socks", "wsaccel"]
+test = ["pytest", "websockets"]
+
 [[package]]
 name = "werkzeug"
-version = "3.1.3"
+version = "3.1.8"
 description = "The comprehensive WSGI web application library."
 optional = false
 python-versions = ">=3.9"
 groups = ["dev"]
 files = [
-    {file = "werkzeug-3.1.3-py3-none-any.whl", hash = "sha256:54b78bf3716d19a65be4fceccc0d1d7b89e608834989dfae50ea87564639213e"},
-    {file = "werkzeug-3.1.3.tar.gz", hash = "sha256:60723ce945c19328679790e3282cc758aa4a6040e4bb330f53d30fa546d44746"},
+    {file = "werkzeug-3.1.8-py3-none-any.whl", hash = "sha256:63a77fb8892bf28ebc3178683445222aa500e48ebad5ec77b0ad80f8726b1f50"},
+    {file = "werkzeug-3.1.8.tar.gz", hash = "sha256:9bad61a4268dac112f1c5cd4630a56ede601b6ed420300677a869083d70a4c44"},
 ]
 
 [package.dependencies]
-MarkupSafe = ">=2.1.1"
+markupsafe = ">=2.1.1"
 
 [package.extras]
 watchdog = ["watchdog (>=2.3)"]
 
+[[package]]
+name = "widgetsnbextension"
+version = "4.0.15"
+description = "Jupyter interactive widgets for Jupyter Notebook"
+optional = false
+python-versions = ">=3.7"
+groups = ["main"]
+files = [
+    {file = "widgetsnbextension-4.0.15-py3-none-any.whl", hash = "sha256:8156704e4346a571d9ce73b84bee86a29906c9abfd7223b7228a28899ccf3366"},
+    {file = "widgetsnbextension-4.0.15.tar.gz", hash = "sha256:de8610639996f1567952d763a5a41af8af37f2575a41f9852a38f947eb82a3b9"},
+]
+
 [[package]]
 name = "xmltodict"
 version = "0.13.0"
@@ -3297,12 +5554,11 @@ version = "3.23.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.9"
-groups = ["main", "dev"]
+groups = ["main"]
 files = [
     {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"},
     {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"},
 ]
-markers = {dev = "python_version < \"3.11\""}
 
 [package.extras]
 check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1) ; sys_platform != \"cygwin\""]
@@ -3313,9 +5569,10 @@ test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more_it
 type = ["pytest-mypy"]
 
 [extras]
+ai = ["httpx", "sentence-transformers"]
 fhir = ["fhirclient"]
 
 [metadata]
 lock-version = "2.1"
-python-versions = ">=3.9, <4"
-content-hash = "0ef223739ee0f4e9faf3bf60aa2c6ca6ea2757f7b84023e93c838109379a6915"
+python-versions = ">=3.11, <3.15"
+content-hash = "720b45712ed28a1414a3f10b5d25ca314ac57219fbcd3927963e6b807aaa07d6"
diff --git a/pyproject.toml b/pyproject.toml
index 8d82e591d..505af2495 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "gen3"
 homepage = "https://gen3.org/"
-version = "4.27.8"
+version = "4.29.0"
 description = "Gen3 CLI and Python SDK"
 authors = ["Center for Translational Data Science at the University of Chicago "]
 license = "Apache-2.0"
@@ -13,38 +13,52 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Intended Audience :: Developers",
     "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering",
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.9, <4"
+python = ">=3.11, <3.15"
 requests = "*"
 indexclient = "^2.3.0"
 drsclient = ">=0.3.0"
 aiohttp = "*"
 backoff = "*"
 cdislogging = "^1.1.0"
-click = "*"
+click = ">=8.3.3"
 importlib_metadata = ">=8,<9"
 jsonschema = "*"
 # FIXME updating to >=0.6.0 breaks a few tests
 dataclasses-json = "<=0.5.9"
 pypfb = ">=0.6.2"
-tqdm = "^4.61.2"
+tqdm = ">=4.61.2"
 humanfriendly ="*"
 python-dateutil = "*"
 aiofiles = "*"
 pandas = ">=1.4.2"
-xmltodict = "^0.13.0"
+xmltodict = ">=0.13.0"
 gen3users = "*"
+numpy = ">=2.4.6"
+pydantic = ">=2.13.4"
+ipywidgets = ">=8.1.8"
 
 # A list of all of the optional dependencies, some of which are included in the
 # below `extras`. They can be opted into by apps.
+# fhir
 fhirclient = { version = "*", optional = true }
 
+# ai
+sentence-transformers = { version = ">5.4.1", optional = true }
+httpx = { version = "*", optional = true }
+# TODO: Trying removing the following sub-dep when sentence-transformers updates beyond 5.5.0
+torch = ">=2.10.0"
+
 [tool.poetry.extras]
 fhir = ["fhirclient"]
+ai = [
+    "sentence-transformers",
+    "httpx",
+]
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^6.0.0"
@@ -52,7 +66,9 @@ pytest-cov = "*"
 requests-mock = "*"
 cdisutilstest = { git = "https://github.com/uc-cdis/cdisutils-test.git", tag = "2.0.0" }
 indexd = { git = "https://github.com/uc-cdis/indexd.git", tag = "5.0.4" }
-deptry = "^0.23.1"
+deptry = ">=0.23.1"
+ipykernel = "*"
+notebook = "*"
 
 [tool.poetry.scripts]
 gen3 = "gen3.cli.__main__:main"
diff --git a/tests/conftest.py b/tests/conftest.py
index f118fe9f5..d99f7157c 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,10 +1,12 @@
 """
 Conf Test for Gen3 test suite
 """
+
 from multiprocessing import Process
 import multiprocessing
-from unittest.mock import patch
+from unittest.mock import MagicMock, patch
 import os
+from click.testing import CliRunner
 import pytest
 import requests
 
@@ -25,7 +27,6 @@
 from gen3.auth import Gen3Auth
 from gen3.object import Gen3Object
 
-
 os.makedirs("tests/outputs", exist_ok=True)
 
 
@@ -236,3 +237,30 @@ def drsclient(drs_client):
     Mock drsclient
     """
     return drs_client
+
+
+@pytest.fixture
+def runner():
+    """Returns a click runner instance."""
+    return CliRunner()
+
+
+@pytest.fixture
+def mock_ctx_obj():
+    """Returns a mock context object for click commands.
+
+    The context contains an ``auth_factory`` that returns an auth object with
+    an ``endpoint`` attribute, and the ``endpoint`` and ``ai_api_prefix``
+    values used by the command group.
+    """
+    mock_auth = MagicMock()
+    mock_auth.endpoint = "http://localhost:4142"
+
+    mock_auth_factory = MagicMock()
+    mock_auth_factory.get.return_value = mock_auth
+
+    return {
+        "auth_factory": mock_auth_factory,
+        "endpoint": "http://localhost:4142",
+        "ai_api_prefix": "",
+    }
diff --git a/tests/download_tests/test_async_download.py b/tests/download_tests/test_async_download.py
index f42442b3b..f559e0dec 100644
--- a/tests/download_tests/test_async_download.py
+++ b/tests/download_tests/test_async_download.py
@@ -9,7 +9,6 @@
 from gen3.file import Gen3File
 from gen3.utils import get_or_create_event_loop_for_thread
 
-
 DIR = Path(__file__).resolve().parent
 NO_DOWNLOAD_ACCESS_MESSAGE = """
 You do not have access to download data.
@@ -18,7 +17,6 @@
 
 
 def _load_manifest(manifest_file_path):
-
     """
     Function to convert manifest to python objects, stored in a list.
 
@@ -166,7 +164,6 @@ def test_download_single(
 
     @patch("gen3.file.requests")
     def test_download_single_no_auth(self, mock_get, download_dir, mock_gen3_auth):
-
         """
         Testing how download_single function reacts when it is given no authorisation details
         Request(url) should return status_code = 403 and download function should return False
@@ -196,7 +193,6 @@ def test_download_single_no_auth(self, mock_get, download_dir, mock_gen3_auth):
 
     @patch("gen3.file.requests")
     def test_download_single_wrong_auth(self, mock_get, download_dir, mock_gen3_auth):
-
         """
         Testing how download_single function reacts when it is given wrong authorisation details
         Request(url) should return status_code = 403 and download function should return False
@@ -226,7 +222,6 @@ def test_download_single_wrong_auth(self, mock_get, download_dir, mock_gen3_auth
 
     @patch("gen3.file.requests")
     def test_download_single_bad_id(self, mock_get, download_dir, mock_gen3_auth):
-
         """
         Testing how download_single function reacts when it is given a manifest with bad id
         Request(url) should return status_code = 404 (File not found) and download function should return False
@@ -256,7 +251,6 @@ def test_download_single_bad_id(self, mock_get, download_dir, mock_gen3_auth):
         assert result == False
 
     def test_load_manifest_bad_format(self):
-
         """
         Testing how load_manifest function reacts when it is given a manifest with bad format as input
         Function should not load the manifest and should return an empty manifest_list
diff --git a/tests/download_tests/test_download.py b/tests/download_tests/test_download.py
index b94cb0b03..e0d1e62b6 100644
--- a/tests/download_tests/test_download.py
+++ b/tests/download_tests/test_download.py
@@ -246,7 +246,7 @@ def test_get_drs_object_type(drs_objects, index, expected):
     assert get_drs_object_type(drs_objects[index]) == expected
 
 
-@pytest.mark.parametrize("hostname", [("test.datacommons.io")])
+@pytest.mark.parametrize("hostname", ["test.datacommons.io"])
 def test_get_external_wts_oidc(wts_oidc, hostname):
     with requests_mock.Mocker() as m:
         m.get(f"https://{hostname}/wts/external_oidc/", json=wts_oidc[hostname])
diff --git a/tests/embeddings_tests/README.md b/tests/embeddings_tests/README.md
new file mode 100644
index 000000000..26d3089d4
--- /dev/null
+++ b/tests/embeddings_tests/README.md
@@ -0,0 +1,5 @@
+The .tsv's in here contain snippets of previously generated embeddings of fully public data. The .tsvs have columns with the format expected for Gen3 AI Embeddings bulk import. For example, for using with `gen3 ai embeddings publish...` CLI commands.
+
+The embeddings represent "real" data to be used in testing in the future.
+
+Note: These were generated by transforming internal .h5 format files used in previous proof of concepts.
\ No newline at end of file
diff --git a/tests/embeddings_tests/test_expr.tsv b/tests/embeddings_tests/test_expr.tsv
new file mode 100644
index 000000000..7615ff033
--- /dev/null
+++ b/tests/embeddings_tests/test_expr.tsv
@@ -0,0 +1,4 @@
+embedding	authz	collection_name	collection_id	case_id	file_id	model
+"[-0.2024536281824112, 0.8700736165046692, 0.6367368102073669, 1.0295965671539307, 1.3029881715774536, 0.6979042291641235, 0.09141989797353745, -0.7052130103111267, 0.05628640949726105, -0.6558999419212341, -0.698043704032898, -8.845816612243652, -0.10774289071559906, -0.8967481255531311, 0.30785858631134033, -0.218824565410614, -0.1945626139640808, -0.6851598024368286, -0.2565596103668213, -0.1704675555229187, 0.17284531891345978, -0.6091238260269165, -0.13866744935512543, 0.21102923154830933, -0.2252902388572693, -0.6781346201896667, -0.34671345353126526, 0.4128320515155792, -0.8277935981750488, 1.1078327894210815, 0.6355611085891724, -0.5727114081382751, 1.2589396238327026, 0.4476923644542694, 0.34200647473335266, -0.1336929202079773, 0.1772320717573166, 1.1591079235076904, -1.5068682432174683, 0.02006017416715622, -0.6712247133255005, -0.5338364839553833, 5.475770473480225, -0.3881995379924774, 1.026019811630249, -0.117962546646595, -0.2552171051502228, -0.43384769558906555, -1.4432331323623657, -0.09555564075708389, 0.037277694791555405, -0.8553200960159302, -0.06689377129077911, -0.22948388755321503, -0.6298796534538269, 0.5966225266456604, -0.13349662721157074, -0.16505523025989532, -0.9155815243721008, -0.03902330994606018, 0.48878201842308044, 0.9861955642700195, -0.8381974697113037, -0.5137110352516174, -0.9829555749893188, 0.07967071980237961, 0.3077264726161957, 0.06789758056402206, 0.941411554813385, -0.42186906933784485, 0.5567692518234253, 0.38038623332977295, 0.46958717703819275, -0.3595823645591736, -0.5077025890350342, 0.13748227059841156, 0.11002576351165771, -0.16163720190525055, -0.18104378879070282, 1.0819607973098755, 0.8306452631950378, -0.44499292969703674, 0.5418969988822937, -1.1315350532531738, 0.3580150306224823, -0.07379359751939774, -0.6808024644851685, 0.3528731167316437, 0.04792550206184387, 0.12353166937828064, 0.8670023679733276, 0.08373359590768814, -0.41165003180503845, 0.727061927318573, 0.06704757362604141, 4.503935813903809, -0.8532129526138306, -0.594979465007782, 0.919654130935669, -0.23700065910816193, 0.5048814415931702, -0.4086969196796417, -0.4986532926559448, -0.06626451015472412, 1.1717911958694458, -0.07520367950201035, 0.06578060984611511, 0.3701489567756653, -0.9265334010124207, -0.3234957158565521, -0.05426352471113205, -0.3846246004104614, 1.1056557893753052, -1.1724191904067993, 1.147159218788147, 1.1236810684204102, -0.46618154644966125, -0.9549393057823181, -0.204567089676857, 1.1774815320968628, -0.6236163973808289, -0.5526822805404663, -0.6998738646507263, -0.5858327746391296, -0.2566048204898834, 0.8487930297851562, -0.37117043137550354, -1.3030366897583008, -8.013142585754395, -0.09955956786870956, -0.7133530378341675, 0.21573762595653534, 0.02987380139529705, 0.169014573097229, 0.858149528503418, -0.9776293039321899, -0.6704788208007812, -0.7800702452659607, -0.11321384459733963, -0.4539415240287781, 0.6066994071006775, -0.501072108745575, -0.04097514599561691, 0.44614145159721375, -0.07055798172950745, -0.4469953179359436, 0.25786444544792175, 0.3830481767654419, 0.2865692675113678, 0.5758309364318848, -0.7816569209098816, -0.16137219965457916, 0.07098924368619919, 1.0406609773635864, -0.25058403611183167, 0.2329045534133911, 0.3159070611000061, 0.011400481685996056, 1.1727708578109741, -0.6722333431243896, 0.0047455462627112865, 0.7064188122749329, 0.19687819480895996, -0.7298651337623596, -0.6731472611427307, -0.29894983768463135, -0.5114670395851135, 1.2121055126190186, 0.27098193764686584, -1.1139729022979736, -0.34051188826560974, 0.47438573837280273, -0.5396663546562195, -0.45061254501342773, -0.5249454379081726, -0.12127259373664856, -0.13513071835041046, -0.32455986738204956, 0.8758406043052673, -0.6840516924858093, -1.1088807582855225, -0.48474231362342834, 0.6212708950042725, 0.2537653148174286, 0.2028423398733139, -0.16007283329963684, -1.0832301378250122, -0.6427255272865295, 0.5219706892967224, -0.10779555141925812, 0.14352789521217346, 0.916231095790863, 0.6226103901863098, 0.3076702952384949, 1.5312645435333252, -0.33734557032585144, 0.41539466381073, 2.244152545928955, -0.13458096981048584, 0.3584960401058197, -0.20201975107192993, -0.8333280086517334, -0.6809530854225159, 0.14703354239463806, -0.4365242123603821, -0.33620592951774597, -0.18233400583267212, -0.22426031529903412, -0.5442564487457275, 0.4168570935726166, -0.5127552151679993, 3.5123233795166016, -0.3374885618686676, 0.7329320907592773, -0.09450151026248932, 0.14233481884002686, -0.8451797366142273, 0.4592364430427551, 0.462772011756897, 0.35650205612182617, -0.24574220180511475, 1.1549229621887207, 0.6380702257156372, 0.06404341012239456, 0.15603697299957275, -0.3920949101448059, 0.053627148270606995, -0.5836009383201599, 0.09549576044082642, 0.22595234215259552, 0.13617555797100067, 0.7152342796325684, 0.6793820261955261, 0.17555320262908936, 0.6218454837799072, 0.49658674001693726, -0.40870344638824463, -0.7512102127075195, -23.303945541381836, 0.405129611492157, 0.3400692045688629, 1.0545461177825928, 0.6485701203346252, -0.1535542607307434, 0.3560626208782196, 0.9628076553344727, -0.511151909828186, -0.6748654842376709, -0.6606578826904297, 0.11375259608030319, -0.9489352107048035, 0.017717955633997917, 0.5313513278961182, 0.08885449171066284, -0.20959705114364624, -0.5676986575126648]"	/programs/dev/projects/testproject1	test_expr		TCGA-05-4244	e0e055b6-6800-40e7-bde5-718823408f0c	expr
+"[-0.21098750829696655, 0.8999685049057007, 0.6318586468696594, 0.9548228979110718, 1.1571954488754272, 0.5339417457580566, 0.015891127288341522, -0.7026917338371277, 0.04075244814157486, -0.501552939414978, -0.6925984621047974, -8.84329605102539, -0.17547869682312012, -0.8503749966621399, 0.35973337292671204, -0.18932057917118073, -0.1361524760723114, -0.6625967621803284, -0.17621438205242157, -0.09718206524848938, 0.19409120082855225, -0.6379923224449158, -0.11429573595523834, 0.11196231096982956, -0.3210512101650238, -0.5825065970420837, -0.3804585933685303, 0.28380119800567627, -0.7360841035842896, 1.0406644344329834, 0.5594694018363953, -0.7057065963745117, 0.9364557862281799, 0.4513166546821594, 0.3793163299560547, -0.052856091409921646, 0.12097060680389404, 0.9977852702140808, -1.5820757150650024, -0.015619124285876751, -0.7463712692260742, -0.5128862261772156, 5.627805233001709, -0.21938584744930267, 0.8136599063873291, -0.12776827812194824, -0.25363442301750183, 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\ No newline at end of file
diff --git a/tests/embeddings_tests/test_hist.tsv b/tests/embeddings_tests/test_hist.tsv
new file mode 100644
index 000000000..d89a0d173
--- /dev/null
+++ b/tests/embeddings_tests/test_hist.tsv
@@ -0,0 +1,4 @@
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\ No newline at end of file
diff --git a/tests/embeddings_tests/test_summ.tsv b/tests/embeddings_tests/test_summ.tsv
new file mode 100644
index 000000000..666a399ed
--- /dev/null
+++ b/tests/embeddings_tests/test_summ.tsv
@@ -0,0 +1,4 @@
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\ No newline at end of file
diff --git a/tests/test_cli_ai_collections.py b/tests/test_cli_ai_collections.py
new file mode 100644
index 000000000..218747783
--- /dev/null
+++ b/tests/test_cli_ai_collections.py
@@ -0,0 +1,102 @@
+"""
+Tests for the embeddings collections CRUD commands for:
+`gen3 ai embeddings collections`.
+
+Note: These are pretty minimal, they basically just make sure the
+      Embeddings client gets passed the right info from the command line.
+"""
+
+from unittest.mock import AsyncMock, patch
+
+from gen3.cli.ai.main import ai
+
+
+@patch("gen3.cli.ai.main.EmbeddingsClient")
+def test_create_collection_success(patched_embeddings_client, runner, mock_ctx_obj):
+    """Test successful creation of an embeddings collection."""
+    mocked_client = AsyncMock()
+    mocked_client.create_collection.return_value = {
+        "name": "ctds-github-md",
+        "dimensions": 384,
+    }
+    patched_embeddings_client.return_value = mocked_client
+
+    result = runner.invoke(
+        ai,
+        [
+            "embeddings",
+            "collections",
+            "create",
+            "ctds-github-md",
+            "--dimensions",
+            "384",
+            "--description",
+            "All markdown from CTDS Github",
+        ],
+        obj=mock_ctx_obj,
+    )
+    assert result.exit_code == 0
+    mocked_client.create_collection.assert_called_once_with(
+        "ctds-github-md", 384, "All markdown from CTDS Github"
+    )
+
+
+@patch("gen3.cli.ai.main.EmbeddingsClient")
+def test_read_collections_all_success(patched_embeddings_client, runner, mock_ctx_obj):
+    """Test reading all collections."""
+    mocked_client = AsyncMock()
+    mocked_client.list_collections.return_value = {
+        "collections": [
+            {"name": "ctds-github-md", "dimensions": 384},
+            {"name": "other", "dimensions": 256},
+        ]
+    }
+    patched_embeddings_client.return_value = mocked_client
+
+    result = runner.invoke(ai, ["embeddings", "collections", "read"], obj=mock_ctx_obj)
+    assert result.exit_code == 0
+    mocked_client.list_collections.assert_called_once_with()
+    assert "ctds-github-md" in result.output
+    assert "other" in result.output
+    assert "384" in result.output
+    assert "256" in result.output
+
+
+@patch("gen3.cli.ai.main.EmbeddingsClient")
+def test_read_collection_specific_success(
+    patched_embeddings_client, runner, mock_ctx_obj
+):
+    """Test reading a specific collection."""
+    mocked_client = AsyncMock()
+    mocked_client.list_collections.return_value = {
+        "name": "ctds-github-md",
+        "dimensions": 384,
+    }
+    patched_embeddings_client.return_value = mocked_client
+
+    result = runner.invoke(
+        ai,
+        ["embeddings", "collections", "read", "ctds-github-md"],
+        obj=mock_ctx_obj,
+    )
+    assert result.exit_code == 0
+    mocked_client.list_collections.assert_called_once_with(
+        collection_name="ctds-github-md"
+    )
+    assert "ctds-github-md" in result.output
+    assert "384" in result.output
+
+
+@patch("gen3.cli.ai.main.EmbeddingsClient")
+def test_delete_collection_success(patched_embeddings_client, runner, mock_ctx_obj):
+    """Test successful deletion of a collection."""
+    mocked_client = AsyncMock()
+    patched_embeddings_client.return_value = mocked_client
+
+    result = runner.invoke(
+        ai,
+        ["embeddings", "collections", "delete", "ctds-github-md"],
+        obj=mock_ctx_obj,
+    )
+    assert result.exit_code == 0
+    mocked_client.delete_collection.assert_called_once_with("ctds-github-md")
diff --git a/tests/test_cli_ai_embeddings.py b/tests/test_cli_ai_embeddings.py
new file mode 100644
index 000000000..c1c1aaa89
--- /dev/null
+++ b/tests/test_cli_ai_embeddings.py
@@ -0,0 +1,152 @@
+"""
+Tests for the embeddings commands for:
+`gen3 ai embeddings ...`.
+"""
+
+import csv
+import json
+from unittest.mock import AsyncMock, MagicMock, patch
+
+from gen3.cli.ai.main import ai
+
+
+@patch("gen3.cli.ai.embeddings._get_collection_id_and_name")
+@patch("gen3.cli.ai.main.EmbeddingsClient")
+def test_publish_embeddings_success(
+    patched_embeddings_client, patched_get_collection_id, runner, tmp_path, mock_ctx_obj
+):
+    """
+    Tests successful publication of embeddings from a manifest file.
+
+    Note: tmp_path is a pytest built-in fixture
+    """
+    mocked_embeddings_client = AsyncMock()
+    patched_embeddings_client.return_value = mocked_embeddings_client
+    patched_get_collection_id.return_value = "test_collection_id", "test_collection"
+
+    manifest_file = tmp_path / "embeddings.tsv"
+    mock_json_metadata = json.dumps({"key": "value"})
+    with open(manifest_file, "w") as file:
+        writer = csv.writer(file, delimiter="\t")
+        writer.writerow(
+            ["embedding", "collection_name", "other_data", "mock_json_metadata"]
+        )
+        writer.writerow(
+            [
+                json.dumps([0.1, 0.2, 0.3]),
+                "test_collection",
+                "foobar",
+                mock_json_metadata,
+            ]
+        )
+
+    result = runner.invoke(
+        ai,
+        [
+            "embeddings",
+            "publish",
+            str(manifest_file),
+            "--default-collection",
+            "test_collection",
+        ],
+        obj=mock_ctx_obj,
+    )
+    assert result.exit_code == 0
+
+    mocked_embeddings_client.create_embeddings.assert_called()
+    args, kwargs = mocked_embeddings_client.create_embeddings.call_args
+    assert (
+        kwargs["embeddings_with_metadata"][0]["metadata"].get("other_data") == "foobar"
+    )
+    assert (
+        kwargs["embeddings_with_metadata"][0]["metadata"].get("mock_json_metadata")
+        == mock_json_metadata
+    )
+    assert kwargs["collection_name"] == "test_collection"
+    assert kwargs["collection_id"] == "test_collection_id"
+
+
+@patch("gen3.cli.ai.embeddings._get_collection_id_and_name")
+@patch("gen3.cli.ai.main.EmbeddingsClient")
+def test_publish_embeddings_invalid_json(
+    patched_embeddings_client, patched_get_collection_id, runner, tmp_path, mock_ctx_obj
+):
+    """
+    Tests handling of invalid JSON in the embedding column of the manifest.
+
+    Note: tmp_path is a pytest built-in fixture
+    """
+    # patched_embeddings_client.return_value = mock_ctx_obj["client"]
+    patched_get_collection_id.return_value = "test_collection_id", "test_collection"
+
+    manifest_file = tmp_path / "embeddings.tsv"
+    with open(manifest_file, "w") as file:
+        writer = csv.writer(file, delimiter="\t")
+        writer.writerow(["embedding", "collection_name", "guid"])
+        writer.writerow(["not-a-json", "test_collection", "test_guid"])
+
+    result = runner.invoke(
+        ai,
+        [
+            "embeddings",
+            "publish",
+            str(manifest_file),
+            "--default-collection",
+            "test_collection",
+        ],
+        obj=mock_ctx_obj,
+    )
+    assert result.exit_code == 0
+
+    patched_embeddings_client.create_embeddings.assert_not_called()
+
+
+@patch("gen3.cli.ai.embeddings.LocalEmbeddingClient")
+def test_chunk_and_embed_text_success(
+    patched_local_emb_client, runner, tmp_path, mock_ctx_obj
+):
+    """
+    Tests successful chunking and embedding of text files.
+
+    Note: tmp_path is a pytest built-in fixture
+    """
+    test_file = tmp_path / "test.txt"
+    test_file.write_text("This is a test content for embedding.")
+
+    mock_local_client = MagicMock()
+    mock_local_client.embed.return_value = [
+        {
+            "embedding": [0.1, 0.2],
+            "metadata": {"file": str(test_file)},
+            "authz": "/foo/bar",
+        }
+    ]
+    patched_local_emb_client.return_value = mock_local_client
+
+    out_manifest = tmp_path / "output.tsv"
+
+    result = runner.invoke(
+        ai,
+        [
+            "embeddings",
+            "embed-files",
+            str(test_file),
+            "--collection-name",
+            "test_collection",
+            "--out-manifest-file",
+            str(out_manifest),
+            "--strategy",
+            "text",
+        ],
+        obj=mock_ctx_obj,
+    )
+    assert result.exit_code == 0
+
+    with open(out_manifest, "r") as file:
+        reader = csv.DictReader(file, delimiter="\t")
+        rows = list(reader)
+        assert len(rows) == 1
+        assert rows[0]["collection_name"] == "test_collection"
+        assert rows[0]["authz"] == "/foo/bar"
+        assert rows[0]["file"] == str(test_file)
+        assert json.loads(rows[0]["embedding"]) == [0.1, 0.2]
diff --git a/tests/test_crosswalk.py b/tests/test_crosswalk.py
index d23e0ac33..e883b0be3 100644
--- a/tests/test_crosswalk.py
+++ b/tests/test_crosswalk.py
@@ -2,6 +2,7 @@
 These tests are heavily based off the docs/crosswalk.md example.
 See the test data in /tests/test_data/crosswalk
 """
+
 import asyncio
 import os
 from unittest.mock import MagicMock, patch
diff --git a/tests/test_dbgap_fhir.py b/tests/test_dbgap_fhir.py
index fb75e40c9..11c908454 100644
--- a/tests/test_dbgap_fhir.py
+++ b/tests/test_dbgap_fhir.py
@@ -1,6 +1,7 @@
 """
 Tests gen3.nih
 """
+
 import json
 import os
 import pytest
diff --git a/tests/test_discovery_objects.py b/tests/test_discovery_objects.py
index bf762962c..060d344da 100644
--- a/tests/test_discovery_objects.py
+++ b/tests/test_discovery_objects.py
@@ -12,7 +12,6 @@
     OPTIONAL_OBJECT_FIELDS,
 )
 
-
 MOCK_METADATA_1 = {
     "str_key": "str_val \n \t \\",
     "listval": ["v1", "v2"],
diff --git a/tests/test_doi.py b/tests/test_doi.py
index 5c4c84577..9dae84875 100644
--- a/tests/test_doi.py
+++ b/tests/test_doi.py
@@ -1,6 +1,7 @@
 """
 Tests gen3.doi
 """
+
 import json
 import os
 import pytest
diff --git a/tests/test_file.py b/tests/test_file.py
index a02a80eb8..f7c8e26bf 100644
--- a/tests/test_file.py
+++ b/tests/test_file.py
@@ -1,12 +1,12 @@
 """
 Tests gen3.file.Gen3File for calls
 """
+
 from unittest.mock import patch
 import json
 import pytest
 from requests import HTTPError
 
-
 NO_UPLOAD_ACCESS_MESSAGE = """
     You do not have access to upload data. 
     You either need general file uploader permissions or 
diff --git a/tests/test_index.py b/tests/test_index.py
index 7653cb1d2..a2c830eb3 100644
--- a/tests/test_index.py
+++ b/tests/test_index.py
@@ -279,18 +279,17 @@ def test_desc_and_content_dates(gen3_index):
     assert version_record["content_created_date"] == new_version["content_created_date"]
     assert version_record["content_updated_date"] == new_version["content_updated_date"]
 
+
 def test_create_record_response(gen3_index):
     """
     Verifies the return value for create_record echoes back the parameters for the record that was created.
     """
     to_create = {
-        "hashes": {
-            "md5": "374c12456782738abcfe387492837483"
-        },
+        "hashes": {"md5": "374c12456782738abcfe387492837483"},
         "size": 10,
-        "urls": ['s3://foo/bar'],
-        "file_name": 'new_file',
-        "acl": ['*']
+        "urls": ["s3://foo/bar"],
+        "file_name": "new_file",
+        "acl": ["*"],
     }
     record = gen3_index.create_record(**to_create)
     for field, expected_value in to_create.items():
diff --git a/tests/test_object.py b/tests/test_object.py
index 0a2cca746..0ae937239 100644
--- a/tests/test_object.py
+++ b/tests/test_object.py
@@ -1,6 +1,7 @@
 """
 Tests gen3.object.Gen3Object for calls
 """
+
 from unittest.mock import MagicMock, patch
 import requests
 from httpx import delete
diff --git a/tests/test_utils.py b/tests/test_utils.py
index cea5a94f7..20694a409 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -3,103 +3,106 @@
 from gen3.external.nih.utils import get_dbgap_accession_as_parts
 
 
-@pytest.mark.parametrize("test_input, expected", [
-    (
-        'phs000123',
-        {
-            'phsid': 'phs000123',
-            'phsid_number': '000123',
-            'version': '',
-            'version_number': '',
-            'participant_set': '',
-            'participant_set_number': '',
-            'consent': '',
-            'consent_number': ''
-        }
-    ),
-    (
-        'phs000123.p1.c3',
-        {
-            'phsid': 'phs000123',
-            'phsid_number': '000123',
-            'version': '',
-            'version_number': '',
-            'participant_set': 'p1',
-            'participant_set_number': '1',
-            'consent': 'c3',
-            'consent_number': '3'
-        }
-    ),
-    (
-        'phs000123.v3.c3',
-        {
-            'phsid': 'phs000123',
-            'phsid_number': '000123',
-            'version': 'v3',
-            'version_number': '3',
-            'participant_set': '',
-            'participant_set_number': '',
-            'consent': 'c3',
-            'consent_number': '3'
-        }
-    ),
-    (
-        'phs000123.v3.p1.c3',
-        {
-            'phsid': 'phs000123',
-            'phsid_number': '000123',
-            'version': 'v3',
-            'version_number': '3',
-            'participant_set': 'p1',
-            'participant_set_number': '1',
-            'consent': 'c3',
-            'consent_number': '3'
-        }
-    ),
-    # Unexpected order of v, p, and c
-    (
-        'phs000123.p3.v1.c3',
-        {
-            'phsid': 'phs000123',
-            'phsid_number': '000123',
-            'version': '',
-            'version_number': '',
-            'participant_set': 'p3',
-            'participant_set_number': '3',
-            'consent': '',
-            'consent_number': ''
-        }
-    ),
-    (
-        'phs000123.v3.c1.p3',
-        {
-            'phsid': 'phs000123',
-            'phsid_number': '000123',
-            'version': 'v3',
-            'version_number': '3',
-            'participant_set': '',
-            'participant_set_number': '',
-            'consent': 'c1',
-            'consent_number': '1'
-        }
-    ),
-    (
-        'phs000123.p3.v1',
-        {
-            'phsid': 'phs000123',
-            'phsid_number': '000123',
-            'version': '',
-            'version_number': '',
-            'participant_set': 'p3',
-            'participant_set_number': '3',
-            'consent': '',
-            'consent_number': ''
-        }
-    ),
-])
+@pytest.mark.parametrize(
+    "test_input, expected",
+    [
+        (
+            "phs000123",
+            {
+                "phsid": "phs000123",
+                "phsid_number": "000123",
+                "version": "",
+                "version_number": "",
+                "participant_set": "",
+                "participant_set_number": "",
+                "consent": "",
+                "consent_number": "",
+            },
+        ),
+        (
+            "phs000123.p1.c3",
+            {
+                "phsid": "phs000123",
+                "phsid_number": "000123",
+                "version": "",
+                "version_number": "",
+                "participant_set": "p1",
+                "participant_set_number": "1",
+                "consent": "c3",
+                "consent_number": "3",
+            },
+        ),
+        (
+            "phs000123.v3.c3",
+            {
+                "phsid": "phs000123",
+                "phsid_number": "000123",
+                "version": "v3",
+                "version_number": "3",
+                "participant_set": "",
+                "participant_set_number": "",
+                "consent": "c3",
+                "consent_number": "3",
+            },
+        ),
+        (
+            "phs000123.v3.p1.c3",
+            {
+                "phsid": "phs000123",
+                "phsid_number": "000123",
+                "version": "v3",
+                "version_number": "3",
+                "participant_set": "p1",
+                "participant_set_number": "1",
+                "consent": "c3",
+                "consent_number": "3",
+            },
+        ),
+        # Unexpected order of v, p, and c
+        (
+            "phs000123.p3.v1.c3",
+            {
+                "phsid": "phs000123",
+                "phsid_number": "000123",
+                "version": "",
+                "version_number": "",
+                "participant_set": "p3",
+                "participant_set_number": "3",
+                "consent": "",
+                "consent_number": "",
+            },
+        ),
+        (
+            "phs000123.v3.c1.p3",
+            {
+                "phsid": "phs000123",
+                "phsid_number": "000123",
+                "version": "v3",
+                "version_number": "3",
+                "participant_set": "",
+                "participant_set_number": "",
+                "consent": "c1",
+                "consent_number": "1",
+            },
+        ),
+        (
+            "phs000123.p3.v1",
+            {
+                "phsid": "phs000123",
+                "phsid_number": "000123",
+                "version": "",
+                "version_number": "",
+                "participant_set": "p3",
+                "participant_set_number": "3",
+                "consent": "",
+                "consent_number": "",
+            },
+        ),
+    ],
+)
 def test_get_dbgap_accession_as_parts(test_input, expected):
     """
     Test dbgap accession parsing works and outputs expected fields and values.
     """
 
-    assert get_dbgap_accession_as_parts(test_input) == expected
\ No newline at end of file
+    assert get_dbgap_accession_as_parts(test_input) == expected
diff --git a/tests/utils_mock_dbgap_study_registration_response.py b/tests/utils_mock_dbgap_study_registration_response.py
index 163913e5f..ebea3b2e5 100644
--- a/tests/utils_mock_dbgap_study_registration_response.py
+++ b/tests/utils_mock_dbgap_study_registration_response.py
@@ -112,9 +112,7 @@
         
     
 
-""".replace(
-    "\n", ""
-)
+""".replace("\n", "")
 
 """
 Does not have child studies 
@@ -227,9 +225,7 @@
         
     
 
-""".replace(
-    "\n", ""
-)
+""".replace("\n", "")
 
 MOCK_PHS000089 = """
 
@@ -643,9 +639,7 @@
     
 
 
-""".replace(
-    "\n", ""
-)
+""".replace("\n", "")
 
 """
 Has multiple studies
@@ -862,14 +856,10 @@
         
     
 
-""".replace(
-    "\n", ""
-)
+""".replace("\n", "")
 
 MOCK_BAD_RESPONSE = """
 {
     "
 }
-""".replace(
-    "\n", ""
-)
+""".replace("\n", "")