obi-notebook 0.2.dev0__tar.gz → 0.2.dev1__tar.gz

{obi_notebook-0.2.dev0 → obi_notebook-0.2.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obi_notebook
-Version: 0.2.dev0
+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.dev0 → obi_notebook-0.2.dev1}/example.ipynb

@@ -9,7 +9,9 @@
    "source": [
     "import obi_auth\n",
     "\n",
-    "from obi_notebook import get_entities, get_projects"
+    "from obi_notebook import get_entities, get_projects\n",
+    "\n",
+    "environment_str = \"staging\""
    ]
   },
   {
@@ -27,7 +29,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "token = obi_auth.get_token(environment=\"production\")"
+    "token = obi_auth.get_token(environment=environment_str)"
    ]
   },
   {
@@ -45,7 +47,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "project_context = get_projects.get_projects(token)"
+    "project_context = get_projects.get_projects(token, env=\"staging\")"
    ]
   },
   {
@@ -78,6 +80,7 @@
     "    default_scale=\"small\",\n",
     "    exclude_scales=[\"single\"],\n",
     "    add_columns=[\"subject.name\"],\n",
+    "    env=environment_str,\n",
     ")"
    ]
   },
@@ -109,18 +112,51 @@
     "    project_context=project_context,\n",
     "    page_size=100,\n",
     "    add_columns=[\"mtypes\"],\n",
+    "    env=environment_str,\n",
     ")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ab24b139",
+   "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": {

{obi_notebook-0.2.dev0 → obi_notebook-0.2.dev1}/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,
@@ -108,6 +128,7 @@ def get_entities(
             description="Scale:",
         )
         filters_dict["scale"] = scale_filter
+        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(
@@ -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.dev1}/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.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>