obi-notebook 0.1.dev9__tar.gz → 0.1.dev10__tar.gz

{obi_notebook-0.1.dev9 → obi_notebook-0.1.dev10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obi_notebook
-Version: 0.1.dev9
+Version: 0.1.dev10
 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.dev9 → obi_notebook-0.1.dev10}/example.ipynb

@@ -8,7 +8,8 @@
    "outputs": [],
    "source": [
     "import obi_auth\n",
-    "from obi_notebook import get_projects, get_entities"
+    "\n",
+    "from obi_notebook import get_entities, get_projects"
    ]
   },
   {
@@ -46,12 +47,12 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "cc2954a000034b5db323c3c5bb43a985",
+       "model_id": "281a37021ded4183b265b05213be6b56",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Dropdown(description='Select:', options=(('Understanding connectivity', {'id': 'fe443f04-2d56-4c51-8347-8ca5f3…"
+       "Dropdown(description='Select:', options=(('My first project', {'id': '7d22829c-edc6-4b1d-8ab9-99dd9e511e74', '…"
       ]
      },
      "metadata": {},
@@ -71,7 +72,7 @@
     {
      "data": {
       "text/plain": [
-       "ProjectContext(project_id=UUID('fe443f04-2d56-4c51-8347-8ca5f3a97ee6'), virtual_lab_id=UUID('cee1a37f-fe43-4589-9197-c46746aff976'), environment=<DeploymentEnvironment.production: 'production'>)"
+       "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,
@@ -85,19 +86,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 5,
    "id": "93029f77-d71f-40f4-8c4d-9f23d2b650bc",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "371c88af967a42a984fdf8fbf362660f",
+       "model_id": "62af910b9d8e4094853ad04fa4b62426",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "HBox(children=(Dropdown(description='Scale:', options=('single', 'pair', 'small', 'microcircuit', 'region', 's…"
+       "HBox(children=(Dropdown(description='Scale:', index=1, options=('pair', 'small', 'microcircuit', 'region', 'sy…"
       ]
      },
      "metadata": {},
@@ -106,7 +107,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "3d13a11549b84a3193044113977ba95b",
+       "model_id": "d55601c877f54aaa8a0dc6a92a9440d4",
        "version_major": 2,
        "version_minor": 0
       },
@@ -120,27 +121,38 @@
    ],
    "source": [
     "circuit_ids = []\n",
-    "circuit_ids = get_entities.get_entities(\"circuit\", token, circuit_ids,)"
+    "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": 9,
+   "execution_count": 6,
    "id": "da699ed4-39fd-4602-b54d-58a0b58c2539",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "['1be432a7-c7fa-422b-bb47-8b189ede363e',\n",
-       " 'bf3a620d-5a36-401b-97ac-d27cde014039',\n",
-       " 'b907f9a6-04e3-4a51-85f6-25ace2c816dc',\n",
-       " 'ba297b44-9340-4646-8684-01ce31ed33f5',\n",
-       " '8176966b-cce1-45ef-9642-e87c4436ee7d',\n",
-       " 'f5e228e7-1c2b-4fa9-89ae-97026c97f83e']"
+       "['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": 9,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -152,7 +164,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b6b9479f-60b8-4fa1-bd0d-8dbbda0909b8",
+   "id": "a5f5445d-a61a-4fbe-962f-51e701434771",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -160,9 +172,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python (myenv)",
+   "display_name": "obi-one",
    "language": "python",
-   "name": "obi-notebook"
+   "name": "obi-one"
   },
   "language_info": {
    "codemirror_mode": {
@@ -174,7 +186,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.12.9"
   }
  },
  "nbformat": 4,

{obi_notebook-0.1.dev9 → obi_notebook-0.1.dev10}/src/obi_notebook/get_entities.py

@@ -1,9 +1,10 @@
 """A table widget to select entities."""
 
 import ipywidgets as widgets
+import numpy as np
 import pandas as pd
 import requests
-from entitysdk import Client, models
+from entitysdk import Client, models, types
 from ipydatagrid import DataGrid, TextRenderer
 from IPython.display import clear_output, display
 
@@ -17,24 +18,61 @@ def _estimate_column_widths(df, char_width=8, padding=2, max_size=250):
 
 
 def get_entities(
-    entity_type, token, result, env="production", project_context=None, return_entities=False
+    entity_type,
+    token,
+    result,
+    env="production",
+    project_context=None,
+    return_entities=False,
+    multi_select=True,
+    page_size=10,
+    show_pages=True,
+    add_columns=None,
+    default_scale=None,
+    exclude_scales=None,
 ):
     """Select entities of type entity_type and add them to result.
 
     Note: The 'result' parameter is a mutable object (a list) that is modified in-place
       and also returned.
     """
+    if page_size is not None:
+        if page_size <= 0:
+            raise ValueError("ERROR: Page size must be larger than 0!")
+        # TODO: Could add an upper limit as well here
+
+    if add_columns is None:
+        add_columns = []
+    if exclude_scales is None:
+        exclude_scales = []
+
     # Widgets
     filters_dict = {}
     if entity_type == "circuit":
+        scale_options = [
+            _scale.value for _scale in types.CircuitScale if _scale.value not in exclude_scales
+        ]
+        if default_scale is None or default_scale not in scale_options:
+            default_scale = scale_options[0]
         scale_filter = widgets.Dropdown(
-            options=["single", "pair", "small", "microcircuit", "region", "system", "whole"],
+            options=scale_options,
+            value=default_scale,
             description="Scale:",
         )
         filters_dict["scale"] = scale_filter
 
     filters_dict["name"] = widgets.Text(description="Name:")
 
+    if show_pages:
+        filters_dict["page"] = widgets.Dropdown(
+            options=[1],
+            value=1,
+            description="Results page:",
+            disabled=False,
+            style={"description_width": "auto"},
+            layout=widgets.Layout(width="max-content"),
+        )
+
     # Output area
     output = widgets.Output()
 
@@ -43,7 +81,10 @@ def get_entities(
 
     # Fetch and display function
     def fetch_data(filter_values):
-        params = {"page_size": 10}
+        if page_size is None:
+            params = {}
+        else:
+            params = {"page_size": page_size}
         for k, v in filter_values.items():
             if k == "name":
                 params["name__ilike"] = v
@@ -64,10 +105,11 @@ def get_entities(
         try:
             data = response.json()
             df = pd.json_normalize(data["data"])
-            return df
+            pagination = data["pagination"]
+            return df, pagination
         except Exception as e:
             print("Error fetching or parsing data:", e)
-            return pd.DataFrame()
+            return pd.DataFrame(), None
 
     grid = None
 
@@ -78,7 +120,7 @@ def get_entities(
         with output:
             clear_output()
             filter_values = {k: v.value for k, v in filters_dict.items()}
-            df = fetch_data(filter_values)
+            df, pagination = fetch_data(filter_values)
 
             proper_columns = [
                 "id",
@@ -86,12 +128,24 @@ def get_entities(
                 "description",
                 "brain_region.name",
                 "subject.species.name",
-            ]
+            ] + add_columns
             if len(df) == 0:
-                print("no results")
+                if show_pages and filters_dict["page"].value != 1:
+                    filters_dict["page"].options = [1]  # Will update .value as well
+                else:
+                    print("no results")
                 return
 
+            proper_columns = [_col for _col in proper_columns if _col in df.columns]
             df = df[proper_columns].reset_index(drop=True)
+
+            if show_pages:
+                num_pages = np.maximum(
+                    1, np.ceil(pagination["total_items"] / pagination["page_size"]).astype(int)
+                )
+                filters_dict["page"].options = range(1, num_pages + 1)
+                df.index = df.index + (pagination["page"] - 1) * pagination["page_size"]
+
             column_widths = _estimate_column_widths(df)
             grid = DataGrid(
                 df,
@@ -99,7 +153,6 @@ def get_entities(
                 # auto_fit_columns=True,
                 auto_fit_params={"area": "all"},
                 selection_mode="row",  # Enable row selection
-                selection_behavior="multi",
                 column_widths=column_widths,
             )
             grid.default_renderer = TextRenderer()
@@ -107,6 +160,23 @@ def get_entities(
 
             def on_selection_change(event, grid=grid):
                 with output:
+                    if not multi_select and len(grid.selections) > 0:
+                        if (event["new"][-1]["r1"] != event["new"][-1]["r2"]) or len(
+                            grid.selections
+                        ) > 1:  # Multiple rows selected
+                            if event["new"][-1]["r1"] == event["old"][-1]["r1"]:  # r1 unchanged
+                                new_r = event["new"][-1]["r1"]
+                            else:  # r2 unchanged
+                                new_r = event["new"][-1]["r2"]
+                            # Enforce selection of a single row (last one that was selected)
+                            grid.selections = [
+                                {
+                                    "r1": new_r,
+                                    "r2": new_r,
+                                    "c1": grid.selections[-1]["c1"],
+                                    "c2": grid.selections[-1]["c2"],
+                                }
+                            ]
                     result.clear()
                     l_ids = set()
                     for selection in grid.selections:

{obi_notebook-0.1.dev9 → obi_notebook-0.1.dev10}/src/obi_notebook.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obi_notebook
-Version: 0.1.dev9
+Version: 0.1.dev10
 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>