obi-notebook 0.1.dev10__tar.gz → 0.2.dev1__tar.gz

{obi_notebook-0.1.dev10 → obi_notebook-0.2.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obi_notebook
-Version: 0.1.dev10
+Version: 0.2.dev1
 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.dev1/example.ipynb

@@ -0,0 +1,183 @@
+{
+ "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\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": null,
+   "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": null,
+   "id": "77c47560-1163-4466-83fc-43abc6e0801a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "project_context = get_projects.get_projects(token, env=\"staging\")"
+   ]
+  },
+  {
+   "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",
+    "    env=environment_str,\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",
+    "    env=environment_str,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2c9d28c4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "morph_ids"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "90757b52",
+   "metadata": {},
+   "outputs": [],
+   "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": null,
+   "id": "6964ebe2",
+   "metadata": {},
+   "outputs": [],
+   "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-0.1.dev10 → obi_notebook-0.2.dev1}/src/obi_notebook/get_entities.py

@@ -8,6 +8,12 @@ from entitysdk import Client, models, types
 from ipydatagrid import DataGrid, TextRenderer
 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):
     widths = {}
@@ -17,6 +23,65 @@ def _estimate_column_widths(df, char_width=8, padding=2, max_size=250):
     return widths
 
 
+def _resolve_list_to_first_element(obj):
+    if isinstance(obj, list):
+        if len(obj) > 0:
+            return obj[0]["pref_label"]
+        return STR_NO_MTYPE
+    return obj["pref_label"]
+
+
+_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):
+    global LST_MTYPES_
+    if LST_MTYPES_ is None:
+        response = requests.get(
+            f"{entity_core_url}/mtype",
+            headers={"authorization": f"Bearer {token}"},
+            params={"page_size": 1000},
+            timeout=30,
+        )
+        data = response.json()
+        df_mtype = pd.json_normalize(data["data"])
+        LST_MTYPES_ = list(df_mtype["pref_label"])
+    return LST_MTYPES_
+
+
+def _list_of_existing_species(entity_core_url, token):
+    global LST_SPECIES_
+    if LST_SPECIES_ is None:
+        response = requests.get(
+            f"{entity_core_url}/species",
+            headers={"authorization": f"Bearer {token}"},
+            params={"page_size": 1000},
+            timeout=30,
+        )
+        data = response.json()
+        df_species = pd.json_normalize(data["data"])
+        LST_SPECIES_ = list(df_species["name"])
+    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,
@@ -46,6 +111,9 @@ def get_entities(
     if exclude_scales is None:
         exclude_scales = []
 
+    subdomain = "www" if env == "production" else "staging"
+    entity_core_url = f"https://{subdomain}.openbraininstitute.org/api/entitycore"
+
     # Widgets
     filters_dict = {}
     if entity_type == "circuit":
@@ -60,8 +128,30 @@ def get_entities(
             description="Scale:",
         )
         filters_dict["scale"] = scale_filter
-
-    filters_dict["name"] = widgets.Text(description="Name:")
+        filters_dict["name__ilike"] = widgets.Text(description="Name:")
+    elif entity_type == "reconstruction-morphology":
+        lst_mtypes = _list_of_existing_mtypes(entity_core_url, token) + [""]
+        mtype_filter = widgets.Combobox(
+            placeholder="Select M-Type",
+            description="M-Type:",
+            options=lst_mtypes,
+            ensure_option=True,
+        )
+        filters_dict["mtype__pref_label"] = mtype_filter
+        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:")
+    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(
@@ -76,9 +166,6 @@ def get_entities(
     # Output area
     output = widgets.Output()
 
-    subdomain = "www" if env == "production" else "staging"
-    entity_core_url = f"https://{subdomain}.openbraininstitute.org/api/entitycore"
-
     # Fetch and display function
     def fetch_data(filter_values):
         if page_size is None:
@@ -86,15 +173,15 @@ def get_entities(
         else:
             params = {"page_size": page_size}
         for k, v in filter_values.items():
-            if k == "name":
-                params["name__ilike"] = v
-            else:
-                params[k] = v
+            if isinstance(v, str):
+                if len(v.strip()) == 0:
+                    continue
+            params[k] = v
 
         headers = {"authorization": f"Bearer {token}"}
         if project_context:
-            headers["virtual-lab-id"] = project_context.virtual_lab_id
-            headers["project-id"] = project_context.project_id
+            headers["virtual-lab-id"] = str(project_context.virtual_lab_id)
+            headers["project-id"] = str(project_context.project_id)
         response = requests.get(
             f"{entity_core_url}/{entity_type}",
             headers=headers,
@@ -128,6 +215,7 @@ def get_entities(
                 "description",
                 "brain_region.name",
                 "subject.species.name",
+                "species.name",  # For morphologies
             ] + add_columns
             if len(df) == 0:
                 if show_pages and filters_dict["page"].value != 1:
@@ -139,6 +227,10 @@ def get_entities(
             proper_columns = [_col for _col in proper_columns if _col in df.columns]
             df = df[proper_columns].reset_index(drop=True)
 
+            for colname, fun in _df_postprocess_funs.get(entity_type, {}).items():
+                if colname in df.columns:
+                    df[colname] = df[colname].apply(fun)
+
             if show_pages:
                 num_pages = np.maximum(
                     1, np.ceil(pagination["total_items"] / pagination["page_size"]).astype(int)
@@ -190,7 +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-0.1.dev10 → obi_notebook-0.2.dev1}/src/obi_notebook.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obi_notebook
-Version: 0.1.dev10
+Version: 0.2.dev1
 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-0.1.dev10/example.ipynb

@@ -1,194 +0,0 @@
-{
- "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"
-   ]
-  },
-  {
-   "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=\"production\")"
-   ]
-  },
-  {
-   "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": "281a37021ded4183b265b05213be6b56",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Dropdown(description='Select:', options=(('My first project', {'id': '7d22829c-edc6-4b1d-8ab9-99dd9e511e74', '…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "project_context = get_projects.get_projects(token)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "d538dcac-1bdc-496b-8840-a7b32ea842ed",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "ProjectContext(project_id=UUID('7d22829c-edc6-4b1d-8ab9-99dd9e511e74'), virtual_lab_id=UUID('5f8376bf-b84f-4188-8ef5-e1df3d7529b4'), environment=<DeploymentEnvironment.production: 'production'>)"
-      ]
-     },
-     "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": "62af910b9d8e4094853ad04fa4b62426",
-       "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": "d55601c877f54aaa8a0dc6a92a9440d4",
-       "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",
-    "    page_size=10,\n",
-    "    default_scale=\"small\",\n",
-    "    exclude_scales=[\"single\"],\n",
-    "    add_columns=[\"subject.name\"],\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "id": "da699ed4-39fd-4602-b54d-58a0b58c2539",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "['e9380365-7f37-4b8f-854b-7de929c59a48',\n",
-       " '51fd0040-7d0e-424f-b8d9-87cd28321081',\n",
-       " 'beb65adc-5d4d-42b2-b45e-dc6ae83e4236',\n",
-       " '1eb58db1-9dc9-4b9a-b842-543fb79754dc',\n",
-       " '05cfa4e6-a44e-44ce-9005-65f204a406a6',\n",
-       " '30a3a072-6e60-4042-8698-01bb0875be63']"
-      ]
-     },
-     "execution_count": 6,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "circuit_ids"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a5f5445d-a61a-4fbe-962f-51e701434771",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "obi-one",
-   "language": "python",
-   "name": "obi-one"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.9"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}