entitysdk 0.5.1__tar.gz → 0.6.1__tar.gz

{entitysdk-0.5.1/src/entitysdk.egg-info → entitysdk-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.5.1
+Version: 0.6.1
 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-0.5.1 → entitysdk-0.6.1}/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-0.5.1 → entitysdk-0.6.1}/examples/02_morphology.ipynb

@@ -312,16 +312,6 @@
     "fetched = client.get_entity(entity_id=registered.id, entity_type=ReconstructionMorphology)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "70271bac-cc92-49a1-9bdd-aa03bac92a73",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "rprint(fetched)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "b00725dc-ba90-4ddf-b3ba-dea612cd7720",
@@ -382,63 +372,6 @@
     "rprint(fetched.assets)"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "34b39d9d-2b08-4933-b3cb-3f9a9c08004b",
-   "metadata": {},
-   "source": [
-    "## Update asset"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "69d44c3c-b07c-46d2-978f-98b1b80b5212",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# update h5 asset with another file\n",
-    "with tempfile.TemporaryDirectory() as tdir:\n",
-    "    file1 = Path(tdir, \"updated.h5\")\n",
-    "    file1.write_text(\"updated h5\")\n",
-    "    file1.touch()\n",
-    "\n",
-    "    for asset in fetched.assets:\n",
-    "        if asset.content_type == \"application/h5\":\n",
-    "            updated_asset = client.update_asset_file(\n",
-    "                entity_id=fetched.id,\n",
-    "                entity_type=type(registered),\n",
-    "                asset_id=asset.id,\n",
-    "                file_name=asset1.path,\n",
-    "                file_path=file1,\n",
-    "                file_content_type=asset.content_type,\n",
-    "            )\n",
-    "            break\n",
-    "\n",
-    "\n",
-    "# synchronize morphology with new server data\n",
-    "fetched = client.get_entity(\n",
-    "    entity_id=registered.id, entity_type=ReconstructionMorphology, token=token\n",
-    ")\n",
-    "rprint(fetched.assets)\n",
-    "\n",
-    "\n",
-    "# download updated file and check it was successfully updated\n",
-    "for asset in fetched.assets:\n",
-    "    if asset.content_type == \"application/h5\":\n",
-    "        client.download_file(\n",
-    "            entity_id=fetched.id,\n",
-    "            entity_type=type(fetched),\n",
-    "            asset_id=updated_asset.id,\n",
-    "            output_path=\"./my-file.h5\",\n",
-    "        )\n",
-    "        content = client.download_content(\n",
-    "            entity_id=fetched.id, entity_type=type(fetched), asset_id=asset.id\n",
-    "        )\n",
-    "        break\n",
-    "print(content)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "f15c808c-c454-4277-9ec4-587922ac74f3",
@@ -475,22 +408,8 @@
   }
  ],
  "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-0.5.1 → entitysdk-0.6.1}/examples/03_circuit.ipynb

@@ -8,8 +8,11 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "import tempfile\n",
+    "from pathlib import Path\n",
     "\n",
     "from rich import print as rprint\n",
+    "from utils import create_mock_circuit_dir\n",
     "\n",
     "from entitysdk import Client, ProjectContext, models\n",
     "\n",
@@ -109,39 +112,116 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8bf620b4-fafc-4476-a719-bbe6e7a821bf",
+   "id": "c3ff25a9-fc61-4c19-8949-140c1dd33af7",
    "metadata": {},
    "source": [
-    "## Fetch Circuit"
+    "## Upload directory"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bed0af2c-ae46-41b0-ba77-485daef0a87b",
+   "id": "3dccd413-f91b-42b1-8efe-56d01f68ddd0",
    "metadata": {},
    "outputs": [],
    "source": [
-    "fetched = client.get_entity(entity_id=registered_circuit.id, entity_type=models.Circuit)"
+    "with tempfile.TemporaryDirectory() as tdir:\n",
+    "    # create a hierarchy of files to upload\n",
+    "    create_mock_circuit_dir(tdir)\n",
+    "\n",
+    "    files = {str(path.relative_to(tdir)): path for path in Path(tdir).rglob(\"*\") if path.is_file()}\n",
+    "\n",
+    "    directory_asset = client.upload_directory(\n",
+    "        entity_id=registered_circuit.id,\n",
+    "        entity_type=models.Circuit,\n",
+    "        name=\"circuit\",\n",
+    "        paths=files,\n",
+    "    )"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6ad6ce94-ad74-4710-b274-1883fdeb41f5",
+   "metadata": {},
+   "source": [
+    "## List directory"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ee27c8b5-dfa5-4fa5-ac2f-6cf158057bcf",
+   "id": "3b0d302e-46fe-4d97-b221-99833975eede",
    "metadata": {},
    "outputs": [],
    "source": [
-    "rprint(fetched)"
+    "files = client.list_directory(\n",
+    "    entity_id=registered_circuit.id, entity_type=models.Circuit, asset_id=directory_asset.id\n",
+    ")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f359b797-02ad-4358-bef7-ad3f3008d323",
+   "id": "749b85d2-dbce-455b-9ade-fec7e17f7208",
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "rprint(files)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "aad97379-3010-42c9-9fc5-f30101163f1c",
+   "metadata": {},
+   "source": [
+    "## Download directory"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ace27230-6dfa-4bc6-8b2c-33998a22a111",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with tempfile.TemporaryDirectory() as tdir:\n",
+    "    client.download_directory(\n",
+    "        entity_id=registered_circuit.id,\n",
+    "        entity_type=models.Circuit,\n",
+    "        asset_id=directory_asset.id,\n",
+    "        output_path=Path(tdir),\n",
+    "    )\n",
+    "    files = {str(path.relative_to(tdir)): path for path in Path(tdir).rglob(\"*\") if path.is_file()}\n",
+    "    rprint(files)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8bf620b4-fafc-4476-a719-bbe6e7a821bf",
+   "metadata": {},
+   "source": [
+    "## Fetch Circuit"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bed0af2c-ae46-41b0-ba77-485daef0a87b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fetched = client.get_entity(entity_id=registered_circuit.id, entity_type=models.Circuit)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ee27c8b5-dfa5-4fa5-ac2f-6cf158057bcf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(fetched)"
+   ]
   }
  ],
  "metadata": {

entitysdk-0.6.1/examples/04_simulation_campaign.ipynb

@@ -0,0 +1,389 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9bc20f94-86d5-494d-b2c7-079ea731c162",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "from datetime import UTC, datetime\n",
+    "\n",
+    "from rich import print as rprint\n",
+    "\n",
+    "from entitysdk import Client, ProjectContext, models\n",
+    "\n",
+    "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)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2e29f4cb-28ae-447a-8ac2-bc319f2d33b8",
+   "metadata": {},
+   "source": [
+    "## Register a Circuit"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5d5d04b1-59be-44a9-a283-2856783768f0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "species = client.search_entity(\n",
+    "    entity_type=models.Species, query={\"name__ilike\": \"Homo sapiens\"}\n",
+    ").one()\n",
+    "\n",
+    "subject = models.Subject(\n",
+    "    name=\"my-subject\", description=\"my-subject-description\", sex=\"male\", species=species\n",
+    ")\n",
+    "subject = client.register_entity(subject)\n",
+    "\n",
+    "brain_region = client.search_entity(entity_type=models.BrainRegion, query={\"acronym\": \"CB\"}).first()\n",
+    "\n",
+    "\n",
+    "circuit = models.Circuit(\n",
+    "    name=\"my-circuit\",\n",
+    "    description=\"my-circuit\",\n",
+    "    subject=subject,\n",
+    "    brain_region=brain_region,\n",
+    "    number_synapses=2,\n",
+    "    number_neurons=5,\n",
+    "    number_connections=10,\n",
+    "    scale=\"microcircuit\",\n",
+    "    build_category=\"em_reconstruction\",\n",
+    ")\n",
+    "\n",
+    "circuit = client.register_entity(circuit)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "08520e6d-1b5d-4d89-afeb-1f77feeeff6d",
+   "metadata": {},
+   "source": [
+    "# 1. Register the entire provenance at once\n",
+    "When all entities are available up front the entire provenance can be generated using the creation endpoints without any updating taking place."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bb0984e9-b382-435c-b114-69b76403dcda",
+   "metadata": {},
+   "source": [
+    "## Register all entities"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1e7eb667-d6cf-46db-9f7c-b69ab1838cf5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "campaign = client.register_entity(\n",
+    "    models.SimulationCampaign(\n",
+    "        name=\"my-campaign\",\n",
+    "        description=\"my-campaign-description\",\n",
+    "        entity_id=circuit.id,\n",
+    "        scan_parameters={\"foo\": \"bar\"},\n",
+    "    )\n",
+    ")\n",
+    "\n",
+    "simulations = [\n",
+    "    client.register_entity(\n",
+    "        models.Simulation(\n",
+    "            name=f\"sim-{i}\",\n",
+    "            description=f\"sim-{i}\",\n",
+    "            scan_parameters={\"foo\": \"bar\"},\n",
+    "            entity_id=circuit.id,\n",
+    "            simulation_campaign_id=campaign.id,\n",
+    "        )\n",
+    "    )\n",
+    "    for i in range(5)\n",
+    "]\n",
+    "simulation_results = [\n",
+    "    client.register_entity(models.SimulationResult(name=f\"result-{i}\", description=f\"result-{i}\"))\n",
+    "    for i in range(5)\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6c8b7d39-2858-4d39-8a87-01f8fd71c2af",
+   "metadata": {},
+   "source": [
+    "## Register activities"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4a13c71f-84ae-4bcf-bfbd-637b124963db",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "simulation_generation = client.register_entity(\n",
+    "    models.SimulationGeneration(\n",
+    "        start_time=datetime.now(UTC),\n",
+    "        used=[campaign],\n",
+    "        generated=simulations,\n",
+    "    )\n",
+    ")\n",
+    "\n",
+    "simulation_executions = [\n",
+    "    client.register_entity(\n",
+    "        models.SimulationExecution(\n",
+    "            used=[simulations[i]],\n",
+    "            generated=[simulation_results[i]],\n",
+    "            start_time=datetime.now(UTC),\n",
+    "            status=\"done\",\n",
+    "        )\n",
+    "    )\n",
+    "    for i in range(5)\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "085c2ae7-ca05-49d9-92a7-a14db5b52616",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(simulation_generation)\n",
+    "rprint(simulation_executions)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "34d071a7-47d5-4f46-ba42-269082cfc71e",
+   "metadata": {},
+   "source": [
+    "# 2. Register provenance gradually"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "eb0132f6-88e4-4700-a2b7-799bb0ee77e6",
+   "metadata": {},
+   "source": [
+    "## Register a SimulationCampaign"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ed03bf00-51da-43eb-b887-8d0502c404c6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "campaign = client.register_entity(\n",
+    "    models.SimulationCampaign(\n",
+    "        name=\"my-campaign\",\n",
+    "        description=\"my-campaign-description\",\n",
+    "        entity_id=circuit.id,\n",
+    "        scan_parameters={\"foo\": \"bar\"},\n",
+    "    )\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "379201b4-39fd-4c0c-ac51-bc6bc2a976cb",
+   "metadata": {},
+   "source": [
+    "## Register SimulationGeneration"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "279f388c-968d-4a4f-bdf5-34612bce6440",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sim_generation = client.register_entity(\n",
+    "    models.SimulationGeneration(\n",
+    "        start_time=datetime.now(UTC),\n",
+    "        used=[campaign],\n",
+    "    )\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d5c5fd58-3c00-4452-90ac-54ca0269e165",
+   "metadata": {},
+   "source": [
+    "## Register Simulations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "75430feb-1bf2-4152-8204-75619fe8d51e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "simulations = [\n",
+    "    client.register_entity(\n",
+    "        models.Simulation(\n",
+    "            name=f\"sim-{i}\",\n",
+    "            description=f\"sim-{i}\",\n",
+    "            scan_parameters={\"foo\": \"bar\"},\n",
+    "            entity_id=circuit.id,\n",
+    "            simulation_campaign_id=campaign.id,\n",
+    "        )\n",
+    "    )\n",
+    "    for i in range(5)\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "847511de-60a7-4c37-aeae-9eba5ee50f8a",
+   "metadata": {},
+   "source": [
+    "## Update SimulationGeneration with simulations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6f113473-4af1-4824-9102-f64e6ddc779d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data_to_update = {\n",
+    "    \"generated_ids\": [s.id for s in simulations],\n",
+    "    \"end_time\": datetime.now(UTC),\n",
+    "}\n",
+    "\n",
+    "updated_sim_generation = client.update_entity(\n",
+    "    entity_id=sim_generation.id, entity_type=type(sim_generation), attrs_or_entity=data_to_update\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "29ee7fc8-da7a-4a05-af19-5032865e7246",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(updated_sim_generation)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "027b5f7a-5191-4785-9e45-616a8c1a93da",
+   "metadata": {},
+   "source": [
+    "## Create simulation executions"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5622a11d-205d-458c-b3a9-6002cc6f9ae0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "executions = [\n",
+    "    client.register_entity(\n",
+    "        models.SimulationExecution(\n",
+    "            used=[simulations[i]],\n",
+    "            start_time=datetime.now(UTC),\n",
+    "            status=\"created\",\n",
+    "        )\n",
+    "    )\n",
+    "    for i in range(5)\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9ffccf17-1429-4538-bec0-21e9cc444a95",
+   "metadata": {},
+   "source": [
+    "## Create simulation results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b74fab6e-be66-4c0a-bd0d-da4ecdcabed3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results = [\n",
+    "    client.register_entity(models.SimulationResult(name=f\"result-{i}\", description=f\"result-{i}\"))\n",
+    "    for i in range(5)\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "77819c3b-a111-4c62-bf07-a66a1801b69f",
+   "metadata": {},
+   "source": [
+    "## Update simulation executions with results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6ee592a1-06a5-4593-bb00-84ea40e956e0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "updated_executions = [\n",
+    "    client.update_entity(\n",
+    "        entity_id=executions[i].id,\n",
+    "        entity_type=models.SimulationExecution,\n",
+    "        attrs_or_entity={\n",
+    "            \"generated_ids\": [results[i].id],\n",
+    "            \"end_time\": datetime.now(UTC),\n",
+    "            \"status\": \"done\",\n",
+    "        },\n",
+    "    )\n",
+    "    for i in range(5)\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "98d1320a-fdcb-4d4a-ae25-faac8d7676b3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(updated_executions)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b3260f79-5852-4e61-923f-4325e030fc71",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

entitysdk-0.6.1/examples/utils.py

@@ -0,0 +1,13 @@
+"""Helpers."""
+
+from pathlib import Path
+
+
+def create_mock_circuit_dir(output_dir: Path):
+    """Create a mock hierarchy that looks like a circuit."""
+    output_dir = Path(output_dir)
+    output_dir.mkdir(exist_ok=True)
+    (output_dir / "circuit_config.json").touch()
+    (output_dir / "sonata").mkdir()
+    (output_dir / "sonata" / "nodes.h5").touch()
+    (output_dir / "sonata" / "edges.h5").touch()

{entitysdk-0.5.1 → entitysdk-0.6.1}/pyproject.toml

@@ -59,6 +59,7 @@ select = [
     "UP", # pyupgrade
 ]
 ignore = [
+    "S101", # allow `assert`
 ]
 
 [tool.ruff.lint.pydocstyle]