obi-notebook 0.2.dev0__tar.gz → 0.2.dev2__tar.gz

{obi_notebook-0.2.dev0 → obi_notebook-0.2.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obi_notebook
-Version: 0.2.dev0
+Version: 0.2.dev2
 Summary: convenience functions for OBI notebooks
 Author-email: Open Brain Institute <jean-denis.courcol@epfl.ch>
 Maintainer-email: Open Brain Institute <jean-denis.courcol@epfl.ch>

obi_notebook-0.2.dev2/example.ipynb

@@ -0,0 +1,333 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "7eb47475-67c6-499a-a2b4-19f8a64974d0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import obi_auth\n",
+    "\n",
+    "from obi_notebook import get_entities, get_projects\n",
+    "\n",
+    "environment_str = \"staging\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4d984b92-cadd-4b07-9813-b2333272610f",
+   "metadata": {},
+   "source": [
+    "get authentication token for production"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "323cb45c-91e3-451f-8a80-374e61433d31",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "token = obi_auth.get_token(environment=environment_str)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b60e8643-3ad5-4619-a052-5bd8b64713fd",
+   "metadata": {},
+   "source": [
+    "a widget to select project to use"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "77c47560-1163-4466-83fc-43abc6e0801a",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "639a72897c7045f78bb7aea5afbec767",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Dropdown(description='Select:', options=(('Proximal vs. distal inhibition', {'id': '32008ab5-76cf-47cd-b98b-a5…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "project_context = get_projects.get_projects(token, env=\"staging\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "d538dcac-1bdc-496b-8840-a7b32ea842ed",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "ProjectContext(project_id=UUID('32008ab5-76cf-47cd-b98b-a5013b30b533'), virtual_lab_id=UUID('1d8cccc0-f992-46aa-aac6-88e63c914314'), environment=<DeploymentEnvironment.staging: 'staging'>)"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "project_context"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "93029f77-d71f-40f4-8c4d-9f23d2b650bc",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "e4b6463129a546d394d57efc46d07d7c",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "HBox(children=(Dropdown(description='Scale:', index=1, options=('pair', 'small', 'microcircuit', 'region', 'sy…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "9201fb70a891499cadada69780277194",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Output()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "circuit_ids = []\n",
+    "circuit_ids = get_entities.get_entities(\n",
+    "    \"circuit\",\n",
+    "    token,\n",
+    "    circuit_ids,\n",
+    "    return_entities=False,\n",
+    "    multi_select=True,\n",
+    "    show_pages=True,\n",
+    "    project_context=project_context,\n",
+    "    page_size=10,\n",
+    "    default_scale=\"small\",\n",
+    "    exclude_scales=[\"single\"],\n",
+    "    add_columns=[\"subject.name\"],\n",
+    "    env=environment_str,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "da699ed4-39fd-4602-b54d-58a0b58c2539",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['b86271b6-c56f-4c26-b502-05ef5bb514b6',\n",
+       " '3877500c-126d-410c-aa09-e44831464e80',\n",
+       " 'd66cea8b-5c9d-4bfb-bbfd-ca3d5fb5f12c']"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "circuit_ids"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "a5f5445d-a61a-4fbe-962f-51e701434771",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "5fb0a08d2ce94d58a039c47fdd2f217f",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "HBox(children=(Combobox(value='', description='M-Type:', ensure_option=True, options=('A_BC', 'A_BFP', 'ACB_CT…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "a0c7ca20d54946f2af3e181c3adb3d70",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Output()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "morph_ids = []\n",
+    "morph_ids = get_entities.get_entities(\n",
+    "    \"cell-morphology\",\n",
+    "    token,\n",
+    "    morph_ids,\n",
+    "    return_entities=False,\n",
+    "    multi_select=True,\n",
+    "    show_pages=True,\n",
+    "    project_context=project_context,\n",
+    "    page_size=100,\n",
+    "    add_columns=[\"mtypes\"],\n",
+    "    env=environment_str,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "2c9d28c4",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['50248fe3-83bd-4c88-917b-63bcf0e01385',\n",
+       " '1c8ce2b1-3da1-4953-9b1b-bee8656000c4',\n",
+       " '15d02969-1e40-40ba-9081-d475d05897fd']"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "morph_ids"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "90757b52",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "c2a91b53873b4e1fa54c161a59830f6b",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "HBox(children=(Combobox(value='', description='EM-Dataset:', ensure_option=True, options=('Portion 65 of the I…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "a08fd579c61b4377a0dd01478a5951be",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Output()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "cell_mesh_ids = []\n",
+    "circuit_ids = get_entities.get_entities(\n",
+    "    \"em-cell-mesh\",\n",
+    "    token,\n",
+    "    cell_mesh_ids,\n",
+    "    return_entities=False,\n",
+    "    multi_select=True,\n",
+    "    show_pages=True,\n",
+    "    project_context=project_context,\n",
+    "    page_size=10,\n",
+    "    env=environment_str,\n",
+    "    add_columns=[\"dense_reconstruction_cell_id\", \"subject.name\"],\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "6964ebe2",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['2205be1a-a6db-4523-9a7b-0af309996583']"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cell_mesh_ids"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv (3.13.1)",
+   "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": "3.13.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{obi_notebook-0.2.dev0 → obi_notebook-0.2.dev2}/src/obi_notebook/get_entities.py

@@ -10,7 +10,9 @@ from IPython.display import clear_output, display
 
 LST_MTYPES_ = None
 LST_SPECIES_ = None
+LST_EMDATASETS_ = None
 STR_NO_MTYPE = "NONE"
+ENTITY_CLASS_DICT = {"em-cell-mesh": "EMCellMesh"}
 
 
 def _estimate_column_widths(df, char_width=8, padding=2, max_size=250):
@@ -29,7 +31,10 @@ def _resolve_list_to_first_element(obj):
     return obj["pref_label"]
 
 
-_df_postprocess_funs = {"reconstruction-morphology": {"mtypes": _resolve_list_to_first_element}}
+_df_postprocess_funs = {
+    "reconstruction-morphology": {"mtypes": _resolve_list_to_first_element},
+    "em-cell-mesh": {"dense_reconstruction_cell_id": str},
+}
 
 
 def _list_of_existing_mtypes(entity_core_url, token):
@@ -62,6 +67,21 @@ def _list_of_existing_species(entity_core_url, token):
     return LST_SPECIES_
 
 
+def _list_of_existing_em_dense_datasets(entity_core_url, token):
+    global LST_EMDATASETS_
+    if LST_EMDATASETS_ is None:
+        response = requests.get(
+            f"{entity_core_url}/em-dense-reconstruction-dataset",
+            headers={"authorization": f"Bearer {token}"},
+            params={"page_size": 1000},
+            timeout=30,
+        )
+        data = response.json()
+        df_species = pd.json_normalize(data["data"])
+        LST_EMDATASETS_ = list(df_species["name"])
+    return LST_EMDATASETS_
+
+
 def get_entities(
     entity_type,
     token,
@@ -108,7 +128,8 @@ def get_entities(
             description="Scale:",
         )
         filters_dict["scale"] = scale_filter
-    elif entity_type == "reconstruction-morphology":
+        filters_dict["name__ilike"] = widgets.Text(description="Name:")
+    elif entity_type == "reconstruction-morphology" or entity_type == "cell-morphology":
         lst_mtypes = _list_of_existing_mtypes(entity_core_url, token) + [""]
         mtype_filter = widgets.Combobox(
             placeholder="Select M-Type",
@@ -120,8 +141,17 @@ def get_entities(
         lst_species = _list_of_existing_species(entity_core_url, token) + [""]
         species_filter = widgets.Dropdown(options=lst_species, value="", description="Species:")
         filters_dict["species__name"] = species_filter
-
-    filters_dict["name__ilike"] = widgets.Text(description="Name:")
+        filters_dict["name__ilike"] = widgets.Text(description="Name:")
+    elif entity_type == "em-cell-mesh":
+        lst_em_datasets = _list_of_existing_em_dense_datasets(entity_core_url, token) + [""]
+        em_dataset_filter = widgets.Combobox(
+            placeholder="Select EM Dataset",
+            description="EM-Dataset:",
+            options=lst_em_datasets,
+            ensure_option=True,
+        )
+        filters_dict["em_dense_reconstruction_dataset__name__ilike"] = em_dataset_filter
+        filters_dict["dense_reconstruction_cell_id"] = widgets.Text(description="Cell ID:")
 
     if show_pages:
         filters_dict["page"] = widgets.Dropdown(
@@ -252,7 +282,11 @@ def get_entities(
                             token_manager=token,
                         )
 
-                        model_class = getattr(models, entity_type.capitalize())
+                        entity_class_default = "".join(
+                            [_token.capitalize() for _token in entity_type.split("-")]
+                        )
+                        entity_class_name = ENTITY_CLASS_DICT.get(entity_type, entity_class_default)
+                        model_class = getattr(models, entity_class_name)
                         retrieved_entities = client.search_entity(
                             entity_type=model_class, query={"id__in": list(l_ids)}
                         )

{obi_notebook-0.2.dev0 → obi_notebook-0.2.dev2}/src/obi_notebook.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obi_notebook
-Version: 0.2.dev0
+Version: 0.2.dev2
 Summary: convenience functions for OBI notebooks
 Author-email: Open Brain Institute <jean-denis.courcol@epfl.ch>
 Maintainer-email: Open Brain Institute <jean-denis.courcol@epfl.ch>

obi_notebook-0.2.dev0/example.ipynb

@@ -1,147 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7eb47475-67c6-499a-a2b4-19f8a64974d0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import obi_auth\n",
-    "\n",
-    "from obi_notebook import get_entities, get_projects"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "4d984b92-cadd-4b07-9813-b2333272610f",
-   "metadata": {},
-   "source": [
-    "get authentication token for production"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "323cb45c-91e3-451f-8a80-374e61433d31",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "token = obi_auth.get_token(environment=\"production\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "b60e8643-3ad5-4619-a052-5bd8b64713fd",
-   "metadata": {},
-   "source": [
-    "a widget to select project to use"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "77c47560-1163-4466-83fc-43abc6e0801a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "project_context = get_projects.get_projects(token)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "d538dcac-1bdc-496b-8840-a7b32ea842ed",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "project_context"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "93029f77-d71f-40f4-8c4d-9f23d2b650bc",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "circuit_ids = []\n",
-    "circuit_ids = get_entities.get_entities(\n",
-    "    \"circuit\",\n",
-    "    token,\n",
-    "    circuit_ids,\n",
-    "    return_entities=False,\n",
-    "    multi_select=True,\n",
-    "    show_pages=True,\n",
-    "    project_context=project_context,\n",
-    "    page_size=10,\n",
-    "    default_scale=\"small\",\n",
-    "    exclude_scales=[\"single\"],\n",
-    "    add_columns=[\"subject.name\"],\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "da699ed4-39fd-4602-b54d-58a0b58c2539",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "circuit_ids"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a5f5445d-a61a-4fbe-962f-51e701434771",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "morph_ids = []\n",
-    "morph_ids = get_entities.get_entities(\n",
-    "    \"reconstruction-morphology\",\n",
-    "    token,\n",
-    "    morph_ids,\n",
-    "    return_entities=False,\n",
-    "    multi_select=True,\n",
-    "    show_pages=True,\n",
-    "    project_context=project_context,\n",
-    "    page_size=100,\n",
-    "    add_columns=[\"mtypes\"],\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ab24b139",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "morph_ids"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": ".venv (3.13.1)",
-   "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": "3.13.1"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}