entitysdk 0.4.0__tar.gz → 0.5.1__tar.gz

{entitysdk-0.4.0/src/entitysdk.egg-info → entitysdk-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.4.0
+Version: 0.5.1
 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>
@@ -66,14 +66,14 @@ client = Client(
         project_id=UUID("your-project-id"),
         virtual_lab_id=UUID("your-lab-id")
     ),
-    environment="staging"
+    environment="staging",
+    token_manager=token
 )
 
 # Search for morphologies
 iterator = client.search_entity(
     entity_type=models.ReconstructionMorphology,
     query={"mtype__pref_label": "L5_TPC:A"},
-    token=token,
     limit=1,
 )
 morphology = next(iterator)
@@ -84,7 +84,6 @@ client.upload_file(
     entity_type=models.ReconstructionMorphology,
     file_path="path/to/file.swc",
     file_content_type="application/swc",
-    token="your-token"
 )
 ```
 

{entitysdk-0.4.0 → entitysdk-0.5.1}/README.md

@@ -45,14 +45,14 @@ client = Client(
         project_id=UUID("your-project-id"),
         virtual_lab_id=UUID("your-lab-id")
     ),
-    environment="staging"
+    environment="staging",
+    token_manager=token
 )
 
 # Search for morphologies
 iterator = client.search_entity(
     entity_type=models.ReconstructionMorphology,
     query={"mtype__pref_label": "L5_TPC:A"},
-    token=token,
     limit=1,
 )
 morphology = next(iterator)
@@ -63,7 +63,6 @@ client.upload_file(
     entity_type=models.ReconstructionMorphology,
     file_path="path/to/file.swc",
     file_content_type="application/swc",
-    token="your-token"
 )
 ```
 

entitysdk-0.5.1/examples/02_morphology.ipynb

@@ -0,0 +1,498 @@
+{
+ "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": "code",
+   "execution_count": null,
+   "id": "70271bac-cc92-49a1-9bdd-aa03bac92a73",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(fetched)"
+   ]
+  },
+  {
+   "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": "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",
+   "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": {
+  "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"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

entitysdk-0.4.0/examples/05_simulation_campaign.ipynb → entitysdk-0.5.1/examples/04_simulation_campaign.ipynb

@@ -22,27 +22,6 @@
     "client = Client(api_url=entitycore_api_url, project_context=project_context, token_manager=token)"
    ]
   },
-  {
-   "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 = models.SimulationCampaign(\n",
-    "    name=\"my-campaign\", description=\"my-campaign-description\", scan_parameters={\"foo\": \"bar\"}\n",
-    ")\n",
-    "campaign = client.register_entity(campaign)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "490dd2a8-e9a1-442e-abe2-cfda8b3c0c8f",
@@ -85,6 +64,30 @@
     "circuit = client.register_entity(circuit)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "47679bbe-5550-4332-b5a6-0b0a916a0acc",
+   "metadata": {},
+   "source": [
+    "## Register a SimulationCampaign"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "520976c2-4575-4455-9d64-ed666f661550",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "campaign = models.SimulationCampaign(\n",
+    "    name=\"my-campaign\",\n",
+    "    description=\"my-campaign-description\",\n",
+    "    scan_parameters={\"foo\": \"bar\"},\n",
+    "    entity_id=circuit.id,\n",
+    ")\n",
+    "campaign = client.register_entity(campaign)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "d5c5fd58-3c00-4452-90ac-54ca0269e165",
@@ -138,6 +141,14 @@
    "source": [
     "rprint(campaign.simulations)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b3260f79-5852-4e61-923f-4325e030fc71",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

entitysdk-0.5.1/src/entitysdk/downloaders/__init__.py

@@ -0,0 +1 @@
+"""Downloaders module."""

entitysdk-0.5.1/src/entitysdk/downloaders/emodel.py

@@ -0,0 +1,29 @@
+"""Download functions for EModel entities."""
+
+from pathlib import Path
+
+from entitysdk.client import Client
+from entitysdk.models.emodel import EModel
+from entitysdk.utils.filesystem import create_dir
+
+
+def download_hoc(
+    client: Client,
+    emodel: EModel,
+    output_dir: str | Path,
+) -> Path:
+    """Download hoc file.
+
+    Args:
+        client (Client): EntitySDK client
+        emodel (EModel): EModel entitysdk object
+        output_dir (str or Path): directory to save the hoc file
+    """
+    output_dir = create_dir(output_dir)
+    asset = client.download_assets(
+        emodel,
+        selection={"content_type": "application/x-neuron-hoc"},
+        output_path=output_dir,
+    ).one()
+
+    return asset.output_path

entitysdk-0.5.1/src/entitysdk/downloaders/ion_channel_model.py

@@ -0,0 +1,29 @@
+"""Download functions for IonChannelModel entities."""
+
+from pathlib import Path
+
+from entitysdk.client import Client
+from entitysdk.models.ion_channel_model import IonChannelModel
+from entitysdk.utils.filesystem import create_dir
+
+
+def download_ion_channel_mechanism(
+    client: Client,
+    ion_channel_model: IonChannelModel,
+    output_dir: str | Path,
+) -> Path:
+    """Download one mechanism file.
+
+    Args:
+        client (Client): EntitySDK client
+        ion_channel_model (IonChannelModel): IonChannelModel entitysdk object
+        output_dir (str or Pathlib.Path): directory to save the mechanism file
+    """
+    output_dir = create_dir(output_dir)
+    asset = client.download_assets(
+        ion_channel_model,
+        selection={"content_type": "application/neuron-mod"},
+        output_path=output_dir,
+    ).one()
+
+    return asset.output_path