entitysdk 0.5.0__tar.gz → 0.6.0__tar.gz

{entitysdk-0.5.0/src/entitysdk.egg-info → entitysdk-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.5.0
+Version: 0.6.0
 Summary: Python library for interacting with the entitycore service
 Author-email: Open Brain Institute <info@openbraininstitute.org>
 Maintainer-email: Open Brain Institute <info@openbraininstitute.org>

{entitysdk-0.5.0 → entitysdk-0.6.0}/examples/01_searching.ipynb

@@ -283,22 +283,8 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "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": "3.12.10"
+   "name": "python"
   }
  },
  "nbformat": 4,

entitysdk-0.6.0/examples/02_morphology.ipynb

@@ -0,0 +1,417 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "47471adc-9c79-4262-9fc4-66f5579f14a8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import io\n",
+    "import os\n",
+    "import tempfile\n",
+    "from pathlib import Path\n",
+    "\n",
+    "from rich import print as rprint\n",
+    "\n",
+    "from entitysdk.client import Client\n",
+    "from entitysdk.common import ProjectContext\n",
+    "from entitysdk.models import (\n",
+    "    BrainLocation,\n",
+    "    BrainRegion,\n",
+    "    Contribution,\n",
+    "    MTypeClass,\n",
+    "    MTypeClassification,\n",
+    "    Organization,\n",
+    "    ReconstructionMorphology,\n",
+    "    Role,\n",
+    "    Species,\n",
+    "    Strain,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cacdf95f-d545-417b-b1bd-c8a5181c162f",
+   "metadata": {},
+   "source": [
+    "### Initialize the entitycore client"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5e4f4ff2-3d5b-4f3a-90a9-ea43d587ebce",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "entitycore_api_url = \"http://127.0.0.1:8000\"\n",
+    "project_context = ProjectContext(\n",
+    "    virtual_lab_id=\"a98b7abc-fc46-4700-9e3d-37137812c730\",\n",
+    "    project_id=\"0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6\",\n",
+    ")\n",
+    "token = os.getenv(\"ACCESS_TOKEN\", \"XXX\")\n",
+    "client = Client(api_url=entitycore_api_url, project_context=project_context, token_manager=token)\n",
+    "\n",
+    "\n",
+    "# uncomment for staging\n",
+    "# from obi_auth import get_token\n",
+    "# token = get_token(environment=\"staging\")\n",
+    "# Replace this with your vlab project url in staging\n",
+    "# project_context = ProjectContext.from_vlab_url(\"https://staging.openbraininstitute.org/app/virtual-lab/lab/594fd60d-7a38-436f-939d-500feaa13bba/project/ff89ca07-6613-4922-9ab0-2637221db8b5/home\")\n",
+    "# client = Client(environment=\"staging\", project_context=project_context)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "15b1762d-11df-42be-bcff-5f42b03ab2cd",
+   "metadata": {},
+   "source": [
+    "## Search for entities"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "93d30bc5-c40c-4a5d-ad9e-9b0c4abc3ef4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "species = client.search_entity(entity_type=Species, query={\"name\": \"Mus musculus\"}, limit=10).one()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2a697b1d-2bdc-488d-8ce6-5f7547af87fe",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(species)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0ea7fd15-bf51-4039-a1fd-c580ce813ff3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "strain = client.search_entity(entity_type=Strain, query={\"name\": \"Cux2-CreERT2\"}).one()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e5dde536-0c58-4d42-a834-1b1a0ec17e9d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(strain)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5d42a174-9737-4477-830a-3dc908dea925",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "brain_region = client.search_entity(entity_type=BrainRegion, query={\"annotation_value\": 68}).one()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "282200cd-ad0c-4bb3-bc21-88de85289179",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(brain_region)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a0193055-3448-4d1c-99cc-4d953727ef4e",
+   "metadata": {},
+   "source": [
+    "### Create a morphology object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fdc328df-2cef-4e23-b240-2de061f0e640",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "brain_location = BrainLocation(\n",
+    "    x=4101.52490234375,\n",
+    "    y=1173.8499755859375,\n",
+    "    z=4744.60009765625,\n",
+    ")\n",
+    "morphology = ReconstructionMorphology(\n",
+    "    name=\"my-morph\",\n",
+    "    description=\"A morphology\",\n",
+    "    species=species,\n",
+    "    strain=strain,\n",
+    "    brain_region=brain_region,\n",
+    "    location=brain_location,\n",
+    "    legacy_id=None,\n",
+    "    authorized_public=True,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2568abc1-8b72-4f35-85d3-19f6935ea232",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(morphology)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "83fb7e5e-73b5-4227-aa22-90bb789b0907",
+   "metadata": {},
+   "source": [
+    "## Register morphology"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2e32a168",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "registered = client.register_entity(entity=morphology)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5a4482d8-d5d4-45b9-80cb-264c1a531216",
+   "metadata": {},
+   "source": [
+    "## Add mtype to morphology"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "540aec85-ed13-4224-99ce-a0628f3fa745",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mtype = client.search_entity(entity_type=MTypeClass, query={\"pref_label\": \"L5_PC\"}).one()\n",
+    "\n",
+    "mtype_classification = MTypeClassification(\n",
+    "    mtype_class_id=mtype.id, entity_id=registered.id, authorized_public=True\n",
+    ")\n",
+    "\n",
+    "mtype_classification = client.register_entity(mtype_classification)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9cd036c4-e722-42a9-bed9-b6985a663400",
+   "metadata": {},
+   "source": [
+    "## Add contribution to morphology"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c74eedae-6674-4695-b20b-177c25c8a59c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "agent = client.search_entity(entity_type=Organization, limit=1).one()\n",
+    "role = client.search_entity(entity_type=Role, limit=1).one()\n",
+    "contribution = Contribution(\n",
+    "    agent=agent,\n",
+    "    role=role,\n",
+    "    entity=registered,\n",
+    ")\n",
+    "contribution = client.register_entity(contribution)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5eea0777-2256-4c00-b387-3d8b9171ef63",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(contribution)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c0d500bd",
+   "metadata": {},
+   "source": [
+    "## Upload assets"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "51d0c5b4-6251-4ee4-99ef-b6449a4d5da8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with tempfile.TemporaryDirectory() as tdir:\n",
+    "    file1 = Path(tdir, \"morph.h5\")\n",
+    "    file1.write_text(\"h5\")\n",
+    "\n",
+    "    file2 = Path(tdir, \"morph.swc\")\n",
+    "    file2.write_text(\"swc\")\n",
+    "\n",
+    "    # use a filepath to register first asset\n",
+    "    asset1 = client.upload_file(\n",
+    "        entity_id=registered.id,\n",
+    "        entity_type=ReconstructionMorphology,\n",
+    "        file_path=file1,\n",
+    "        file_content_type=\"application/h5\",\n",
+    "    )\n",
+    "    rprint(asset1)\n",
+    "\n",
+    "    # use an in-memory buffer to upload second asset\n",
+    "    buffer = io.BytesIO(b\"morph bytes buffer\")\n",
+    "\n",
+    "    asset2 = client.upload_content(\n",
+    "        entity_id=registered.id,\n",
+    "        entity_type=ReconstructionMorphology,\n",
+    "        file_content=buffer,\n",
+    "        file_name=\"buffer.h5\",\n",
+    "        file_content_type=\"application/swc\",\n",
+    "    )\n",
+    "    rprint(asset2)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1b5e396e-bf57-436d-9b06-ce198afc15ca",
+   "metadata": {},
+   "source": [
+    "## Retrieve it"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3a0f9360-a805-4ccf-ad7c-95f7237d0819",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# with assets and mtypes\n",
+    "fetched = client.get_entity(entity_id=registered.id, entity_type=ReconstructionMorphology)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b00725dc-ba90-4ddf-b3ba-dea612cd7720",
+   "metadata": {},
+   "source": [
+    "## Download asset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c89e91f7-a9bb-4d09-b921-4659e338225c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "downloaded = client.download_assets(\n",
+    "    fetched,\n",
+    "    selection={\"content_type\": \"application/swc\"},\n",
+    "    output_path=\"./my-file.h5\",\n",
+    ").one()\n",
+    "\n",
+    "content = client.download_content(\n",
+    "    entity_id=fetched.id, entity_type=type(fetched), asset_id=downloaded.asset.id\n",
+    ")\n",
+    "\n",
+    "print(content)\n",
+    "print(Path(\"my-file.h5\").read_text())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6879c149-3f59-4ee6-b878-92bdc6038de9",
+   "metadata": {},
+   "source": [
+    "## Delete asset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9a211674-54d2-498f-983a-ab3f3675087d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for asset in fetched.assets:\n",
+    "    if asset.content_type == \"application/swc\":\n",
+    "        print(\"Deleting asset \", asset.id)\n",
+    "        deleted_asset = client.delete_asset(\n",
+    "            entity_id=fetched.id,\n",
+    "            entity_type=type(registered),\n",
+    "            asset_id=asset.id,\n",
+    "        )\n",
+    "        break\n",
+    "\n",
+    "rprint(deleted_asset)\n",
+    "\n",
+    "fetched = client.get_entity(entity_id=registered.id, entity_type=ReconstructionMorphology)\n",
+    "rprint(fetched.assets)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f15c808c-c454-4277-9ec4-587922ac74f3",
+   "metadata": {},
+   "source": [
+    "## Search it"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "956cc4d7-9ca8-4bb4-9911-648b4ca18a49",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "hits = client.search_entity(\n",
+    "    entity_type=ReconstructionMorphology,\n",
+    "    query={\"name__ilike\": \"my-morph\", \"page\": 1, \"page_size\": 2},\n",
+    "    limit=None,\n",
+    ").all()\n",
+    "\n",
+    "print(\"Number of results: \", len(hits))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4091c7a8-75b9-49d0-8c98-378b7fb5df6d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(hits[0])"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

entitysdk-0.5.0/examples/04_circuit.ipynb → entitysdk-0.6.0/examples/03_circuit.ipynb

@@ -145,22 +145,8 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "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": "3.12.10"
+   "name": "python"
   }
  },
  "nbformat": 4,