obi-notebook 0.1.dev10__tar.gz → 0.2.dev0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/PKG-INFO +1 -1
- obi_notebook-0.2.dev0/example.ipynb +147 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/src/obi_notebook/get_entities.py +72 -10
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/src/obi_notebook.egg-info/PKG-INFO +1 -1
- obi_notebook-0.1.dev10/example.ipynb +0 -194
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/.github/workflows/sdist.yml +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/.github/workflows/tox.yml +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/.gitignore +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/CHANGELOG.rst +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/LICENSE.txt +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/README.md +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/demo.gif +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/pyproject.toml +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/setup.cfg +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/src/obi_notebook/__init__.py +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/src/obi_notebook/get_projects.py +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/src/obi_notebook.egg-info/SOURCES.txt +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/src/obi_notebook.egg-info/dependency_links.txt +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/src/obi_notebook.egg-info/requires.txt +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/src/obi_notebook.egg-info/top_level.txt +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/tox.ini +0 -0
- {obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/uv.lock +0 -0
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Metadata-Version: 2.4
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Name: obi_notebook
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Version: 0.
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Version: 0.2.dev0
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Summary: convenience functions for OBI notebooks
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Author-email: Open Brain Institute <jean-denis.courcol@epfl.ch>
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Maintainer-email: Open Brain Institute <jean-denis.courcol@epfl.ch>
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@@ -0,0 +1,147 @@
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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "7eb47475-67c6-499a-a2b4-19f8a64974d0",
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"metadata": {},
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"outputs": [],
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"source": [
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"import obi_auth\n",
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"\n",
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"from obi_notebook import get_entities, get_projects"
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]
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},
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{
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"cell_type": "markdown",
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"id": "4d984b92-cadd-4b07-9813-b2333272610f",
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"metadata": {},
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"source": [
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"get authentication token for production"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "323cb45c-91e3-451f-8a80-374e61433d31",
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"metadata": {},
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"outputs": [],
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"source": [
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"token = obi_auth.get_token(environment=\"production\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "b60e8643-3ad5-4619-a052-5bd8b64713fd",
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"metadata": {},
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"source": [
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"a widget to select project to use"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "77c47560-1163-4466-83fc-43abc6e0801a",
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"metadata": {},
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"outputs": [],
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"source": [
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"project_context = get_projects.get_projects(token)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d538dcac-1bdc-496b-8840-a7b32ea842ed",
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"metadata": {},
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"outputs": [],
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"source": [
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"project_context"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "93029f77-d71f-40f4-8c4d-9f23d2b650bc",
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"metadata": {},
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"outputs": [],
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"source": [
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"circuit_ids = []\n",
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"circuit_ids = get_entities.get_entities(\n",
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" \"circuit\",\n",
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" token,\n",
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" circuit_ids,\n",
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" return_entities=False,\n",
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" multi_select=True,\n",
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" show_pages=True,\n",
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" project_context=project_context,\n",
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" page_size=10,\n",
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" default_scale=\"small\",\n",
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" exclude_scales=[\"single\"],\n",
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" add_columns=[\"subject.name\"],\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "da699ed4-39fd-4602-b54d-58a0b58c2539",
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"metadata": {},
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"outputs": [],
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"source": [
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"circuit_ids"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "a5f5445d-a61a-4fbe-962f-51e701434771",
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"metadata": {},
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"outputs": [],
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"source": [
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"morph_ids = []\n",
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"morph_ids = get_entities.get_entities(\n",
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" \"reconstruction-morphology\",\n",
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" token,\n",
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" morph_ids,\n",
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" return_entities=False,\n",
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" multi_select=True,\n",
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" show_pages=True,\n",
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" project_context=project_context,\n",
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" page_size=100,\n",
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" add_columns=[\"mtypes\"],\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ab24b139",
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"metadata": {},
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"outputs": [],
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"source": [
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"morph_ids"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": ".venv (3.13.1)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.13.1"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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from ipydatagrid import DataGrid, TextRenderer
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from IPython.display import clear_output, display
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LST_MTYPES_ = None
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LST_SPECIES_ = None
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STR_NO_MTYPE = "NONE"
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def _estimate_column_widths(df, char_width=8, padding=2, max_size=250):
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widths = {}
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return widths
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def _resolve_list_to_first_element(obj):
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if isinstance(obj, list):
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if len(obj) > 0:
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return obj[0]["pref_label"]
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return STR_NO_MTYPE
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return obj["pref_label"]
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_df_postprocess_funs = {"reconstruction-morphology": {"mtypes": _resolve_list_to_first_element}}
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def _list_of_existing_mtypes(entity_core_url, token):
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global LST_MTYPES_
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if LST_MTYPES_ is None:
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response = requests.get(
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f"{entity_core_url}/mtype",
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headers={"authorization": f"Bearer {token}"},
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params={"page_size": 1000},
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timeout=30,
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)
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data = response.json()
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df_mtype = pd.json_normalize(data["data"])
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LST_MTYPES_ = list(df_mtype["pref_label"])
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return LST_MTYPES_
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def _list_of_existing_species(entity_core_url, token):
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global LST_SPECIES_
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if LST_SPECIES_ is None:
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response = requests.get(
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f"{entity_core_url}/species",
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headers={"authorization": f"Bearer {token}"},
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params={"page_size": 1000},
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timeout=30,
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)
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data = response.json()
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df_species = pd.json_normalize(data["data"])
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LST_SPECIES_ = list(df_species["name"])
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return LST_SPECIES_
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def get_entities(
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entity_type,
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token,
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if exclude_scales is None:
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exclude_scales = []
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subdomain = "www" if env == "production" else "staging"
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entity_core_url = f"https://{subdomain}.openbraininstitute.org/api/entitycore"
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# Widgets
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filters_dict = {}
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if entity_type == "circuit":
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description="Scale:",
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filters_dict["scale"] = scale_filter
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elif entity_type == "reconstruction-morphology":
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lst_mtypes = _list_of_existing_mtypes(entity_core_url, token) + [""]
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mtype_filter = widgets.Combobox(
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placeholder="Select M-Type",
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description="M-Type:",
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options=lst_mtypes,
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ensure_option=True,
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)
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filters_dict["mtype__pref_label"] = mtype_filter
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lst_species = _list_of_existing_species(entity_core_url, token) + [""]
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species_filter = widgets.Dropdown(options=lst_species, value="", description="Species:")
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filters_dict["species__name"] = species_filter
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filters_dict["
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filters_dict["name__ilike"] = widgets.Text(description="Name:")
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filters_dict["page"] = widgets.Dropdown(
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# Output area
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output = widgets.Output()
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entity_core_url = f"https://{subdomain}.openbraininstitute.org/api/entitycore"
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# Fetch and display function
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def fetch_data(filter_values):
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else:
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params = {"page_size": page_size}
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for k, v in filter_values.items():
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if len(v.strip()) == 0:
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continue
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params[k] = v
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headers = {"authorization": f"Bearer {token}"}
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if project_context:
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headers["virtual-lab-id"] = project_context.virtual_lab_id
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headers["project-id"] = project_context.project_id
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headers["virtual-lab-id"] = str(project_context.virtual_lab_id)
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headers["project-id"] = str(project_context.project_id)
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response = requests.get(
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f"{entity_core_url}/{entity_type}",
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"description",
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"brain_region.name",
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"subject.species.name",
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"species.name", # For morphologies
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] + add_columns
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if show_pages and filters_dict["page"].value != 1:
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for colname, fun in _df_postprocess_funs.get(entity_type, {}).items():
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Metadata-Version: 2.4
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Name: obi_notebook
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Version: 0.
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Version: 0.2.dev0
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Summary: convenience functions for OBI notebooks
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Author-email: Open Brain Institute <jean-denis.courcol@epfl.ch>
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Maintainer-email: Open Brain Institute <jean-denis.courcol@epfl.ch>
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{obi_notebook-0.1.dev10 → obi_notebook-0.2.dev0}/src/obi_notebook.egg-info/dependency_links.txt
RENAMED
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