diff --git a/.gitignore b/.gitignore
index 7811cf1082c5ed754b89c51f7a87879ad462a29f..4161f66797c227fbf3c06fd16b56166e51c4112e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,3 +19,4 @@ scratch/
*.egg-info/
scripts*
.pdm-python
+*.prof
\ No newline at end of file
diff --git a/UsingONE.ipynb b/UsingONE.ipynb
index 170179c5a76061ed55cf240589bfb7e636b114f8..84d254a0544172503148974583c0faaa192fa60b 100644
--- a/UsingONE.ipynb
+++ b/UsingONE.ipynb
@@ -20,6 +20,11281 @@
"connector = Connector(url=\"127.0.0.1\")"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "id": "ec96c21a",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "[Parameter(name='atlas_acronym', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='atlas_id', location=<ParameterLocation.QUERY: 'query'>, schema=Number(type=<DataType.NUMBER: 'number'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, multiple_of=None, maximum=None, exclusive_maximum=None, minimum=None, exclusive_minimum=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='atlas_name', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='attribute', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='auto_datetime', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=<StringFormat.DATETIME: 'date-time'>), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='data_repository', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='dataset_types', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='date_range', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='default_data_repository', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='django', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='end_time', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=<StringFormat.DATETIME: 'date-time'>), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='exclude_procedures', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='extended_qc', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='histology', location=<ParameterLocation.QUERY: 'query'>, schema=Boolean(type=<DataType.BOOLEAN: 'boolean'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='id', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=<StringFormat.UUID: 'uuid'>), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='json', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='lab', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='limit', location=<ParameterLocation.QUERY: 'query'>, schema=Integer(type=<DataType.INTEGER: 'integer'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, multiple_of=None, maximum=None, exclusive_maximum=None, minimum=None, exclusive_minimum=None, format=None), content=None, required=False, description='Number of results to return per page.', deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='location', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='n_correct_trials', location=<ParameterLocation.QUERY: 'query'>, schema=Integer(type=<DataType.INTEGER: 'integer'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, multiple_of=None, maximum=None, exclusive_maximum=None, minimum=None, exclusive_minimum=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='n_trials', location=<ParameterLocation.QUERY: 'query'>, schema=Integer(type=<DataType.INTEGER: 'integer'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, multiple_of=None, maximum=None, exclusive_maximum=None, minimum=None, exclusive_minimum=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='name', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='narrative', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='number', location=<ParameterLocation.QUERY: 'query'>, schema=Integer(type=<DataType.INTEGER: 'integer'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, multiple_of=None, maximum=None, exclusive_maximum=None, minimum=None, exclusive_minimum=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='object', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='offset', location=<ParameterLocation.QUERY: 'query'>, schema=Integer(type=<DataType.INTEGER: 'integer'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, multiple_of=None, maximum=None, exclusive_maximum=None, minimum=None, exclusive_minimum=None, format=None), content=None, required=False, description='The initial index from which to return the results.', deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='parent_session', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=<StringFormat.UUID: 'uuid'>), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='performance_gte', location=<ParameterLocation.QUERY: 'query'>, schema=Number(type=<DataType.NUMBER: 'number'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, multiple_of=None, maximum=None, exclusive_maximum=None, minimum=None, exclusive_minimum=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='performance_lte', location=<ParameterLocation.QUERY: 'query'>, schema=Number(type=<DataType.NUMBER: 'number'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, multiple_of=None, maximum=None, exclusive_maximum=None, minimum=None, exclusive_minimum=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='procedures', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='project', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='projects', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='qc', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='start_time', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=<StringFormat.DATETIME: 'date-time'>), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='subject', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='tag', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='task_protocol', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='type', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={}),\n",
+ " Parameter(name='users', location=<ParameterLocation.QUERY: 'query'>, schema=String(type=<DataType.STRING: 'string'>, title=None, enum=[], example=None, description=None, default=None, nullable=False, read_only=False, write_only=False, deprecated=False, extensions={}, max_length=None, min_length=None, pattern=None, format=None), content=None, required=False, description=None, deprecated=False, style=<QueryParameterStyle.FORM: 'form'>, explode=True, extensions={})]"
+ ]
+ },
+ "execution_count": 2,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "connector.web_client.endpoint(\"sessions\").actions[\"list\"].operation.parameters"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "id": "5000341f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "sessions = connector.search(subject = \"ea04\", start_time = \"2025-11-01\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "id": "b0f0d952",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Loading sessions details: 100%|██████████| 30/30 [00:03<00:00, 8.11it/s]\n"
+ ]
+ }
+ ],
+ "source": [
+ "sessions = connector.search(subject = \"ea04\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "id": "cc3adaa7",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{'id': 'b7ae0fae-6831-4018-9455-2d72181bb77f',\n",
+ " 'subject': 'ea04',\n",
+ " 'users': ['wilsonmena'],\n",
+ " 'location': None,\n",
+ " 'procedures': [],\n",
+ " 'lab': 'HaissLab',\n",
+ " 'projects': [],\n",
+ " 'type': None,\n",
+ " 'task_protocol': '',\n",
+ " 'number': 1,\n",
+ " 'start_time': '2025-11-01T00:00:00+01:00',\n",
+ " 'end_time': None,\n",
+ " 'narrative': '',\n",
+ " 'parent_session': None,\n",
+ " 'n_correct_trials': None,\n",
+ " 'n_trials': None,\n",
+ " 'url': 'http://127.0.0.1/sessions/b7ae0fae-6831-4018-9455-2d72181bb77f',\n",
+ " 'extended_qc': None,\n",
+ " 'qc': 'NOT_SET',\n",
+ " 'wateradmin_session_related': [],\n",
+ " 'data_dataset_session_related': [],\n",
+ " 'auto_datetime': '2025-04-28T08:36:04.693721+02:00',\n",
+ " 'alias': 'ea04/2025-11-01/001',\n",
+ " 'u_alias': 'ea04_2025-11-01_001',\n",
+ " 'path': '//157.99.138.167/cajal_data2/ONE/MotorSense/ea04/2025-11-01/001',\n",
+ " 'json': None,\n",
+ " 'probe_insertion': [],\n",
+ " 'notes': [],\n",
+ " 'default_data_repository_path': '//157.99.138.167/cajal_data2/ONE/MotorSense',\n",
+ " 'default_data_repository_name': 'Cajal2MotorSense',\n",
+ " 'default_data_repository_pk': '70a43e0f-09b3-4c0f-996c-12edbdaff06d',\n",
+ " 'rel_path': 'ea04/2025-11-01/001',\n",
+ " 'admin_url': '/admin/actions/session/b7ae0fae-6831-4018-9455-2d72181bb77f/change/'}"
+ ]
+ },
+ "execution_count": 16,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "connector.web_client.create(endpoint=\"sessions\", data={\"users\":[\"wilsonmena\"], \"subject\":\"ea04\", \"start_time\":\"2025-11-01\",\"number\":1})"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "id": "8c0e5a20",
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "HTTPError",
+ "evalue": "[Errno 500] http://127.0.0.1:80/sessions?date_range=%5B%272025-11-01%27%2C+%272025-11-02%27%5D&subject=ea04: '[\"“[\\'2025-11-01\\'” value has an invalid date format. It must be in YYYY-MM-DD format.\"]'",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+ "\u001b[31mHTTPError\u001b[39m Traceback (most recent call last)",
+ "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[3]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m session = \u001b[43mconnector\u001b[49m\u001b[43m.\u001b[49m\u001b[43msearch\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdate_range\u001b[49m\u001b[43m \u001b[49m\u001b[43m=\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43m2025-11-01\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43m2025-11-02\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msubject\u001b[49m\u001b[43m \u001b[49m\u001b[43m=\u001b[49m\u001b[43m \u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mea04\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n",
+ "\u001b[36mFile \u001b[39m\u001b[32m~\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\connector\\core.py:70\u001b[39m, in \u001b[36mConnector.search\u001b[39m\u001b[34m(self, endpoint, details, raises, **kwargs)\u001b[39m\n\u001b[32m 69\u001b[39m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34msearch\u001b[39m(\u001b[38;5;28mself\u001b[39m, endpoint=\u001b[33m\"\u001b[39m\u001b[33msessions\u001b[39m\u001b[33m\"\u001b[39m, details=\u001b[38;5;28;01mTrue\u001b[39;00m, raises=\u001b[38;5;28;01mTrue\u001b[39;00m, **kwargs):\n\u001b[32m---> \u001b[39m\u001b[32m70\u001b[39m search_result = \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mweb_client\u001b[49m\u001b[43m.\u001b[49m\u001b[43msearch\u001b[49m\u001b[43m(\u001b[49m\u001b[43mendpoint\u001b[49m\u001b[43m=\u001b[49m\u001b[43mendpoint\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdetails\u001b[49m\u001b[43m=\u001b[49m\u001b[43mdetails\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 71\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m raises:\n\u001b[32m 72\u001b[39m search_result = \u001b[38;5;28mself\u001b[39m.raise_if_search_empty(search_result)\n",
+ "\u001b[36mFile \u001b[39m\u001b[32m~\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\web\\clients.py:145\u001b[39m, in \u001b[36mClient.search\u001b[39m\u001b[34m(self, endpoint, details, **kwargs)\u001b[39m\n\u001b[32m 138\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[33m\"\u001b[39m\u001b[33mid\u001b[39m\u001b[33m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m kwargs.keys() \u001b[38;5;129;01mor\u001b[39;00m \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m \u001b[38;5;129;01min\u001b[39;00m kwargs.keys():\n\u001b[32m 139\u001b[39m \u001b[38;5;66;03m# just in case, we warn the user if she/he supplied id or name, and the endpoint doesn't implement retrieve\u001b[39;00m\n\u001b[32m 140\u001b[39m logger.warning(\n\u001b[32m 141\u001b[39m \u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[33mEndpoint \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mendpoint\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m does not implement retrieve. \u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m 142\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mYou specified id or name but it will not work to select a specific item. Listing instead\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m 143\u001b[39m )\n\u001b[32m--> \u001b[39m\u001b[32m145\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mlist\u001b[49m\u001b[43m(\u001b[49m\u001b[43mendpoint\u001b[49m\u001b[43m=\u001b[49m\u001b[43mendpoint\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdetails\u001b[49m\u001b[43m=\u001b[49m\u001b[43mdetails\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
+ "\u001b[36mFile \u001b[39m\u001b[32m~\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\web\\clients.py:176\u001b[39m, in \u001b[36mClient.list\u001b[39m\u001b[34m(self, endpoint, details, **kwargs)\u001b[39m\n\u001b[32m 175\u001b[39m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34mlist\u001b[39m(\u001b[38;5;28mself\u001b[39m, *, endpoint: \u001b[38;5;28mstr\u001b[39m, details=\u001b[38;5;28;01mTrue\u001b[39;00m, **kwargs):\n\u001b[32m--> \u001b[39m\u001b[32m176\u001b[39m results = \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mrest\u001b[49m\u001b[43m(\u001b[49m\u001b[43mendpoint\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mlist\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 177\u001b[39m results = [] \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m results \u001b[38;5;28;01melse\u001b[39;00m results\n\u001b[32m 178\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m.details_aggregation(results, endpoint) \u001b[38;5;28;01mif\u001b[39;00m details \u001b[38;5;28;01melse\u001b[39;00m results\n",
+ "\u001b[36mFile \u001b[39m\u001b[32m~\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\web\\clients.py:99\u001b[39m, in \u001b[36mClient.rest\u001b[39m\u001b[34m(self, endpoint_name, action, timeout, **kwargs)\u001b[39m\n\u001b[32m 91\u001b[39m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34mrest\u001b[39m(\n\u001b[32m 92\u001b[39m \u001b[38;5;28mself\u001b[39m,\n\u001b[32m 93\u001b[39m endpoint_name: \u001b[38;5;28mstr\u001b[39m,\n\u001b[32m (...)\u001b[39m\u001b[32m 96\u001b[39m **kwargs,\n\u001b[32m 97\u001b[39m ):\n\u001b[32m 98\u001b[39m operateur = \u001b[38;5;28mself\u001b[39m.path(endpoint_name).endpoint.assert_exists().actions[action]\n\u001b[32m---> \u001b[39m\u001b[32m99\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mRequest\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43moperateur\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[43m=\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\u001b[43m.\u001b[49m\u001b[43mhandle\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
+ "\u001b[36mFile \u001b[39m\u001b[32m~\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\web\\api.py:322\u001b[39m, in \u001b[36mRequest.handle\u001b[39m\u001b[34m(self)\u001b[39m\n\u001b[32m 321\u001b[39m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34mhandle\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[32m--> \u001b[39m\u001b[32m322\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mhandle_response\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mget_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n",
+ "\u001b[36mFile \u001b[39m\u001b[32m~\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\web\\api.py:355\u001b[39m, in \u001b[36mRequest.handle_response\u001b[39m\u001b[34m(self, response)\u001b[39m\n\u001b[32m 353\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[32m 354\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[32m--> \u001b[39m\u001b[32m355\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mraise_from_response\u001b[49m\u001b[43m(\u001b[49m\u001b[43mresponse\u001b[49m\u001b[43m)\u001b[49m\n",
+ "\u001b[36mFile \u001b[39m\u001b[32m~\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\web\\api.py:366\u001b[39m, in \u001b[36mRequest.raise_from_response\u001b[39m\u001b[34m(self, response)\u001b[39m\n\u001b[32m 364\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m json.decoder.JSONDecodeError:\n\u001b[32m 365\u001b[39m message = response.text\n\u001b[32m--> \u001b[39m\u001b[32m366\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m requests.HTTPError(response.status_code, \u001b[38;5;28mself\u001b[39m.url, message, response=response)\n",
+ "\u001b[31mHTTPError\u001b[39m: [Errno 500] http://127.0.0.1:80/sessions?date_range=%5B%272025-11-01%27%2C+%272025-11-02%27%5D&subject=ea04: '[\"“[\\'2025-11-01\\'” value has an invalid date format. It must be in YYYY-MM-DD format.\"]'"
+ ]
+ }
+ ],
+ "source": [
+ "session = connector.search(date_range = [\"2025-11-01\",\"2025-11-02\"], subject = \"ea04\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "dfc5ba2c",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "sessions = connector.search(subject = \"ea03\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "ac9ad7ba",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from alyx_connector.files.registration.rules_config import Config\n",
+ "config = Config()\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "id": "dc91895f",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "id 95fd1f97-d636-4425-9d3a-1fb359161d96\n",
+ "subject ea04\n",
+ "users [eachirou]\n",
+ "location None\n",
+ "procedures [Two photon Imaging]\n",
+ "lab HaissLab\n",
+ "projects [MotorSense]\n",
+ "type None\n",
+ "task_protocol \n",
+ "number 1\n",
+ "start_time 2024-04-03T17:25:00+02:00\n",
+ "end_time 2024-04-03T18:06:00+02:00\n",
+ "narrative stims :\\r\\n- C2 : right\\r\\n- nothing : left\\r\\...\n",
+ "parent_session None\n",
+ "n_correct_trials None\n",
+ "n_trials None\n",
+ "url http://127.0.0.1/sessions/95fd1f97-d636-4425-9...\n",
+ "extended_qc None\n",
+ "qc NOT_SET\n",
+ "wateradmin_session_related []\n",
+ "data_dataset_session_related []\n",
+ "auto_datetime 2024-04-03T19:41:41.429420+02:00\n",
+ "alias ea04/2024-04-03/001\n",
+ "u_alias ea04_2024-04-03_001\n",
+ "path //157.99.138.167/cajal_data2/ONE/MotorSense/ea...\n",
+ "json {'whisker_stims': {'Stimulus right': {'0': 'No...\n",
+ "probe_insertion []\n",
+ "notes []\n",
+ "default_data_repository_path //157.99.138.167/cajal_data2/ONE/MotorSense\n",
+ "default_data_repository_name Cajal2MotorSense\n",
+ "default_data_repository_pk 70a43e0f-09b3-4c0f-996c-12edbdaff06d\n",
+ "rel_path ea04/2024-04-03/001\n",
+ "admin_url /admin/actions/session/95fd1f97-d636-4425-9d3a...\n",
+ "Name: 29, dtype: object"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "session = sessions.iloc[-1]\n",
+ "session"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "id": "75f29292",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "file_records = config.evaluate_session(session)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "id": "989fefee",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <div class=\"table-container\">\n",
+ " <table>\n",
+ " <thead>\n",
+ " <th class=\"title\" colspan=\"10\">File :</th>\n",
+ " </thead>\n",
+ " <thead class=\"head\">\n",
+ " <tr>\n",
+ " <th>root</th>\n",
+ " <th>subject</th>\n",
+ " <th>date</th>\n",
+ " <th>number</th>\n",
+ " <th>collection</th>\n",
+ " <th>revision</th>\n",
+ " <th>object</th>\n",
+ " <th>attribute</th>\n",
+ " <th>extra</th>\n",
+ " <th>extension</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense</td>\n",
+ " <td>ea04</td>\n",
+ " <td>2024-04-03</td>\n",
+ " <td>001</td>\n",
+ " <td>behaviour_imaging\\whiskers</td>\n",
+ " <td></td>\n",
+ " <td>0</td>\n",
+ " <td></td>\n",
+ " <td></td>\n",
+ " <td>tdms</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ " </table>\n",
+ " </div>\n",
+ " <style>\n",
+ " .table-container{\n",
+ " border: 1px solid rgb(173, 173, 173);\n",
+ " border-radius: 5px;\n",
+ " overflow: hidden;\n",
+ " display: inline-block;\n",
+ " }\n",
+ " .title{\n",
+ " text-align: left;\n",
+ " white-space: pre;\n",
+ " font-weight: bolder;\n",
+ " }\n",
+ " table {\n",
+ " font-family: consolas;\n",
+ " border-collapse: collapse;\n",
+ " }\n",
+ " th, td {\n",
+ " border: 1px solid rgb(160 160 160);\n",
+ " }\n",
+ " thead:first-of-type th {\n",
+ " border-top: none;\n",
+ " }\n",
+ " td {\n",
+ " border-bottom: 0px;\n",
+ " }\n",
+ " th:first-of-type, td:first-of-type {\n",
+ " border-left: none;\n",
+ " }\n",
+ " td:last-of-type, th:last-of-type {\n",
+ " border-right: none;\n",
+ " }\n",
+ " thead > tr > th:hover, tbody > tr > td:hover{\n",
+ " background-color: rgba(111, 110, 160, 0.267);\n",
+ " }\n",
+ " </style>\n",
+ " "
+ ],
+ "text/plain": [
+ "<alyx_connector.files.parsing.files.File at 0x1f07d7a8da0>"
+ ]
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "from alyx_connector.files.parsing import File\n",
+ "File(r\"\\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea04\\2024-04-03\\001\\behaviour_imaging\\whiskers\\0.tdms\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "id": "5d2b5087",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "file_records.records[0].destination_file[\"attribute\"] = \"fesse\""
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "id": "24488d2f",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "file_records.records[0].destination_file._attribute = \"fesse\""
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "id": "bfc3e9d4",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <div class=\"table-container\">\n",
+ " <table>\n",
+ " <thead>\n",
+ " <th class=\"title\" colspan=\"10\">File :</th>\n",
+ " </thead>\n",
+ " <thead class=\"head\">\n",
+ " <tr>\n",
+ " <th>root</th>\n",
+ " <th>subject</th>\n",
+ " <th>date</th>\n",
+ " <th>number</th>\n",
+ " <th>collection</th>\n",
+ " <th>revision</th>\n",
+ " <th>object</th>\n",
+ " <th>attribute</th>\n",
+ " <th>extra</th>\n",
+ " <th>extension</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense</td>\n",
+ " <td>ea04</td>\n",
+ " <td>2024-04-03</td>\n",
+ " <td>001</td>\n",
+ " <td>behaviour_imaging\\whiskers</td>\n",
+ " <td></td>\n",
+ " <td>behaviour</td>\n",
+ " <td>fesse</td>\n",
+ " <td>whiskers.00000</td>\n",
+ " <td>tdms</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ " </table>\n",
+ " </div>\n",
+ " <style>\n",
+ " .table-container{\n",
+ " border: 1px solid rgb(173, 173, 173);\n",
+ " border-radius: 5px;\n",
+ " overflow: hidden;\n",
+ " display: inline-block;\n",
+ " }\n",
+ " .title{\n",
+ " text-align: left;\n",
+ " white-space: pre;\n",
+ " font-weight: bolder;\n",
+ " }\n",
+ " table {\n",
+ " font-family: consolas;\n",
+ " border-collapse: collapse;\n",
+ " }\n",
+ " th, td {\n",
+ " border: 1px solid rgb(160 160 160);\n",
+ " }\n",
+ " thead:first-of-type th {\n",
+ " border-top: none;\n",
+ " }\n",
+ " td {\n",
+ " border-bottom: 0px;\n",
+ " }\n",
+ " th:first-of-type, td:first-of-type {\n",
+ " border-left: none;\n",
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+ "3 [match -> rename, rename_successfull -> include] \n",
+ "4 [match -> rename, rename_successfull -> include] \n",
+ ".. ... \n",
+ "617 [match -> rename, rename_successfull -> include] \n",
+ "618 [] \n",
+ "619 [] \n",
+ "620 [] \n",
+ "621 [] \n",
+ "\n",
+ " _source_file \\\n",
+ "0 <alyx_connector.files.parsing.files.File objec... \n",
+ "1 <alyx_connector.files.parsing.files.File objec... \n",
+ "2 <alyx_connector.files.parsing.files.File objec... \n",
+ "3 <alyx_connector.files.parsing.files.File objec... \n",
+ "4 <alyx_connector.files.parsing.files.File objec... \n",
+ ".. ... \n",
+ "617 <alyx_connector.files.parsing.files.File objec... \n",
+ "618 <alyx_connector.files.parsing.files.File objec... \n",
+ "619 <alyx_connector.files.parsing.files.File objec... \n",
+ "620 <alyx_connector.files.parsing.files.File objec... \n",
+ "621 <alyx_connector.files.parsing.files.File objec... \n",
+ "\n",
+ " _destination_file \\\n",
+ "0 <alyx_connector.files.parsing.files.File objec... \n",
+ "1 <alyx_connector.files.parsing.files.File objec... \n",
+ "2 <alyx_connector.files.parsing.files.File objec... \n",
+ "3 <alyx_connector.files.parsing.files.File objec... \n",
+ "4 <alyx_connector.files.parsing.files.File objec... \n",
+ ".. ... \n",
+ "617 <alyx_connector.files.parsing.files.File objec... \n",
+ "618 <alyx_connector.files.parsing.files.File objec... \n",
+ "619 <alyx_connector.files.parsing.files.File objec... \n",
+ "620 <alyx_connector.files.parsing.files.File objec... \n",
+ "621 <alyx_connector.files.parsing.files.File objec... \n",
+ "\n",
+ " _final_path \\\n",
+ "0 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "1 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "2 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "3 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "4 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ ".. ... \n",
+ "617 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "618 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "619 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "620 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "621 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "\n",
+ " _final_pathstring \\\n",
+ "0 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "1 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "2 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "3 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "4 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ ".. ... \n",
+ "617 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "618 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "619 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "620 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "621 \\\\157.99.138.167\\cajal_data2\\ONE\\MotorSense\\ea... \n",
+ "\n",
+ " info \n",
+ "0 Will be renamed and included \n",
+ "1 Will be renamed and included \n",
+ "2 Will be renamed and included \n",
+ "3 Will be renamed and included \n",
+ "4 Will be renamed and included \n",
+ ".. ... \n",
+ "617 Will be renamed and included \n",
+ "618 Will be excluded without change dataset_type ... \n",
+ "619 Will be excluded without change dataset_type ... \n",
+ "620 Will be excluded without change dataset_type ... \n",
+ "621 Will be excluded without change dataset_type ... \n",
+ "\n",
+ "[622 rows x 17 columns]"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "df = file_records.to_dataframe()\n",
+ "# df[df[\"abort\"]==False]\n",
+ "df"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "297f4c80",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.microsoft.datawrangler.viewer.v0+json": {
+ "columns": [
+ {
+ "name": "index",
+ "rawType": "int64",
+ "type": "integer"
+ },
+ {
+ "name": "source_path",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "match",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "matching_rules",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "used_rule",
+ "rawType": "object",
+ "type": "string"
+ },
+ {
+ "name": "valid_alf",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "path_conflicts",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "dataset_type_exists",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "rename",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "delete",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "include",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "abort",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "_source_file",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "_destination_file",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "_final_path",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "_final_pathstring",
+ "rawType": "object",
+ "type": "string"
+ },
+ {
+ "name": "info",
+ "rawType": "object",
+ "type": "string"
+ }
+ ],
+ "conversionMethod": "pd.DataFrame",
+ "ref": "8149566a-d231-4833-aebf-edda2720691a",
+ "rows": [
+ [
+ "1002",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.001.txt",
+ "True",
+ "['include_test_data_rule']",
+ "include_test_data_rule ",
+ "True",
+ "False",
+ "True",
+ "False",
+ "False",
+ "True",
+ "[]",
+ "<alyx_connector.files.parsing.File object at 0x000001B396879610>",
+ "<alyx_connector.files.parsing.File object at 0x000001B396879670>",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.001.txt",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.001.txt",
+ "Will be included without change"
+ ],
+ [
+ "1003",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.002.txt",
+ "True",
+ "['include_test_data_rule']",
+ "include_test_data_rule ",
+ "True",
+ "False",
+ "True",
+ "False",
+ "False",
+ "True",
+ "[]",
+ "<alyx_connector.files.parsing.File object at 0x000001B39681BB30>",
+ "<alyx_connector.files.parsing.File object at 0x000001B396879970>",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.002.txt",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.002.txt",
+ "Will be included without change"
+ ],
+ [
+ "1004",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.003.txt",
+ "True",
+ "['include_test_data_rule']",
+ "include_test_data_rule ",
+ "True",
+ "False",
+ "True",
+ "False",
+ "False",
+ "True",
+ "[]",
+ "<alyx_connector.files.parsing.File object at 0x000001B39681B950>",
+ "<alyx_connector.files.parsing.File object at 0x000001B3968798B0>",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.003.txt",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.003.txt",
+ "Will be included without change"
+ ]
+ ],
+ "shape": {
+ "columns": 16,
+ "rows": 3
+ }
+ },
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>source_path</th>\n",
+ " <th>match</th>\n",
+ " <th>matching_rules</th>\n",
+ " <th>used_rule</th>\n",
+ " <th>valid_alf</th>\n",
+ " <th>path_conflicts</th>\n",
+ " <th>dataset_type_exists</th>\n",
+ " <th>rename</th>\n",
+ " <th>delete</th>\n",
+ " <th>include</th>\n",
+ " <th>abort</th>\n",
+ " <th>_source_file</th>\n",
+ " <th>_destination_file</th>\n",
+ " <th>_final_path</th>\n",
+ " <th>_final_pathstring</th>\n",
+ " <th>info</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>1002</th>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem...</td>\n",
+ " <td>True</td>\n",
+ " <td>[include_test_data_rule]</td>\n",
+ " <td>include_test_data_rule</td>\n",
+ " <td>True</td>\n",
+ " <td>False</td>\n",
+ " <td>True</td>\n",
+ " <td>False</td>\n",
+ " <td>False</td>\n",
+ " <td>True</td>\n",
+ " <td>[]</td>\n",
+ " <td><alyx_connector.files.parsing.File object at 0...</td>\n",
+ " <td><alyx_connector.files.parsing.File object at 0...</td>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem...</td>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem...</td>\n",
+ " <td>Will be included without change</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1003</th>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem...</td>\n",
+ " <td>True</td>\n",
+ " <td>[include_test_data_rule]</td>\n",
+ " <td>include_test_data_rule</td>\n",
+ " <td>True</td>\n",
+ " <td>False</td>\n",
+ " <td>True</td>\n",
+ " <td>False</td>\n",
+ " <td>False</td>\n",
+ " <td>True</td>\n",
+ " <td>[]</td>\n",
+ " <td><alyx_connector.files.parsing.File object at 0...</td>\n",
+ " <td><alyx_connector.files.parsing.File object at 0...</td>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem...</td>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem...</td>\n",
+ " <td>Will be included without change</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1004</th>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem...</td>\n",
+ " <td>True</td>\n",
+ " <td>[include_test_data_rule]</td>\n",
+ " <td>include_test_data_rule</td>\n",
+ " <td>True</td>\n",
+ " <td>False</td>\n",
+ " <td>True</td>\n",
+ " <td>False</td>\n",
+ " <td>False</td>\n",
+ " <td>True</td>\n",
+ " <td>[]</td>\n",
+ " <td><alyx_connector.files.parsing.File object at 0...</td>\n",
+ " <td><alyx_connector.files.parsing.File object at 0...</td>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem...</td>\n",
+ " <td>\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem...</td>\n",
+ " <td>Will be included without change</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " source_path match \\\n",
+ "1002 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... True \n",
+ "1003 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... True \n",
+ "1004 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... True \n",
+ "\n",
+ " matching_rules used_rule valid_alf \\\n",
+ "1002 [include_test_data_rule] include_test_data_rule True \n",
+ "1003 [include_test_data_rule] include_test_data_rule True \n",
+ "1004 [include_test_data_rule] include_test_data_rule True \n",
+ "\n",
+ " path_conflicts dataset_type_exists rename delete include abort \\\n",
+ "1002 False True False False True [] \n",
+ "1003 False True False False True [] \n",
+ "1004 False True False False True [] \n",
+ "\n",
+ " _source_file \\\n",
+ "1002 <alyx_connector.files.parsing.File object at 0... \n",
+ "1003 <alyx_connector.files.parsing.File object at 0... \n",
+ "1004 <alyx_connector.files.parsing.File object at 0... \n",
+ "\n",
+ " _destination_file \\\n",
+ "1002 <alyx_connector.files.parsing.File object at 0... \n",
+ "1003 <alyx_connector.files.parsing.File object at 0... \n",
+ "1004 <alyx_connector.files.parsing.File object at 0... \n",
+ "\n",
+ " _final_path \\\n",
+ "1002 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1003 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1004 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "\n",
+ " _final_pathstring \\\n",
+ "1002 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1003 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1004 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "\n",
+ " info \n",
+ "1002 Will be included without change \n",
+ "1003 Will be included without change \n",
+ "1004 Will be included without change "
+ ]
+ },
+ "execution_count": 13,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "f = file_records.to_dataframe()\n",
+ "f[f[\"used_rule\"] == \"include_test_data_rule \"]\n",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\DELETE_LATER_JUST_A_TEST\\trials.choice.001.txt"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "id": "b5e368d0",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'ihem05_2024-11-06_002'"
+ ]
+ },
+ "execution_count": 18,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "session.u_alias"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "id": "c788c08b",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{'id': '0dfed412-9b32-470f-a9d0-177b4f9f207c',\n",
+ " 'url': 'http://127.0.0.1/datasets/0dfed412-9b32-470f-a9d0-177b4f9f207c',\n",
+ " 'admin_url': '/admin/data/dataset/0dfed412-9b32-470f-a9d0-177b4f9f207c/change/',\n",
+ " 'name': 'trials.choice.txt',\n",
+ " 'created_by': 'tjostmou',\n",
+ " 'created_datetime': '2025-04-11T14:10:04.503148+02:00',\n",
+ " 'data_repository': 'Cajal2Interhem',\n",
+ " 'file_size': None,\n",
+ " 'version': None,\n",
+ " 'auto_datetime': '2025-04-11T14:10:04.504138+02:00',\n",
+ " 'dataset_type': 'trials.choice',\n",
+ " 'default_dataset': True,\n",
+ " 'tags': [],\n",
+ " 'session': 'ihem05_2024-11-06_002',\n",
+ " 'data_format': '.txt',\n",
+ " 'data_repository_pk': 'ea2cd868-ea54-4f59-a3b3-640130c44891',\n",
+ " 'data_format_pk': 'dd3f05b1-6104-4da7-be68-ffaad1b97651',\n",
+ " 'revision_pk': None,\n",
+ " 'dataset_type_pk': '378aa050-4924-4a9b-9fe7-b7cf86dff93f',\n",
+ " 'session_pk': 'dc5a61db-cbb6-48dc-bcb9-310211c8512c',\n",
+ " 'remote_root': '//157.99.138.167/cajal_data2/ONE/Interhem',\n",
+ " 'subject': 'ihem05',\n",
+ " 'date': '2024-11-06',\n",
+ " 'number': 2,\n",
+ " 'collection': 'DELETE_LATER_JUST_A_TEST',\n",
+ " 'revision': '',\n",
+ " 'object': 'trials',\n",
+ " 'attribute': 'choice',\n",
+ " 'extension': '.txt',\n",
+ " 'file_records': [{'id': 'cef2bd58-10bd-4098-a460-bc4e064817ad',\n",
+ " 'relative_path': 'ihem05/2024-11-06/002/DELETE_LATER_JUST_A_TEST/trials.choice.001.txt',\n",
+ " 'extra': '001',\n",
+ " 'exists': True,\n",
+ " 'file_name': 'trials.choice.001.txt',\n",
+ " 'hash': None},\n",
+ " {'id': '8888aece-4580-4535-90bb-a7fb85820f92',\n",
+ " 'relative_path': 'ihem05/2024-11-06/002/DELETE_LATER_JUST_A_TEST/trials.choice.002.txt',\n",
+ " 'extra': '002',\n",
+ " 'exists': True,\n",
+ " 'file_name': 'trials.choice.002.txt',\n",
+ " 'hash': None},\n",
+ " {'id': 'f4295ab5-bb26-4cec-a636-e606f62d4ecd',\n",
+ " 'relative_path': 'ihem05/2024-11-06/002/DELETE_LATER_JUST_A_TEST/trials.choice.003.txt',\n",
+ " 'extra': '003',\n",
+ " 'exists': True,\n",
+ " 'file_name': 'trials.choice.003.txt',\n",
+ " 'hash': None}]}"
+ ]
+ },
+ "execution_count": 24,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "connector.web_client.create(endpoint=\"datasets\", \n",
+ " data={\n",
+ " \"session_pk\":\"dc5a61db-cbb6-48dc-bcb9-310211c8512c\",\n",
+ " \"dataset_type\":\"trials.choice\",\n",
+ " \"collection\":\"DELETE_LATER_JUST_A_TEST\",\n",
+ " \"data_format\":\".txt\",\"set_file_records\":[{\"extra\":\"001\",\"exists\":True},\n",
+ " {\"extra\":\"002\",\"exists\":True},\n",
+ " {\"extra\":\"003\",\"exists\":True}\n",
+ " ]\n",
+ " }\n",
+ " )"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "id": "d76f2877",
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "NameError",
+ "evalue": "name 'session' is not defined",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+ "\u001b[31mNameError\u001b[39m Traceback (most recent call last)",
+ "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[1]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m \u001b[43msession\u001b[49m\n",
+ "\u001b[31mNameError\u001b[39m: name 'session' is not defined"
+ ]
+ }
+ ],
+ "source": [
+ "session"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "5ebc614f",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "used_rule info \n",
+ " Will be excluded without change 1\n",
+ " Will be excluded without change dataset_type doesn't follow alyx format dataset_type:F not existing 1\n",
+ " Will be excluded without change dataset_type doesn't follow alyx format dataset_type:F_chan2 not existing 1\n",
+ " Will be excluded without change dataset_type doesn't follow alyx format dataset_type:F_corrected not existing 1\n",
+ " Will be excluded without change dataset_type doesn't follow alyx format dataset_type:F_corrected_chan2 not existing 1\n",
+ " ... \n",
+ " Will be excluded without change dataset_type:treat2p.version not existing 1\n",
+ "behavior_cam_sessings_include_rule Will be included without change 1\n",
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+ "1 <alyx_connector.files.parsing.File object at 0... \n",
+ "2 <alyx_connector.files.parsing.File object at 0... \n",
+ "3 <alyx_connector.files.parsing.File object at 0... \n",
+ "4 <alyx_connector.files.parsing.File object at 0... \n",
+ "... ... \n",
+ "997 <alyx_connector.files.parsing.File object at 0... \n",
+ "998 <alyx_connector.files.parsing.File object at 0... \n",
+ "999 <alyx_connector.files.parsing.File object at 0... \n",
+ "1000 <alyx_connector.files.parsing.File object at 0... \n",
+ "1001 <alyx_connector.files.parsing.File object at 0... \n",
+ "\n",
+ " _final_path \\\n",
+ "0 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "2 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "3 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "4 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "... ... \n",
+ "997 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "998 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "999 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1000 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1001 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "\n",
+ " _final_pathstring \\\n",
+ "0 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "2 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "3 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "4 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "... ... \n",
+ "997 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "998 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "999 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1000 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "1001 \\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem... \n",
+ "\n",
+ " info \n",
+ "0 Will be included without change \n",
+ "1 Will be included without change \n",
+ "2 Will be included without change \n",
+ "3 Will be included without change \n",
+ "4 Will be included without change \n",
+ "... ... \n",
+ "997 Will be excluded without change dataset_type n... \n",
+ "998 Will be excluded without change dataset_type n... \n",
+ "999 Will be excluded without change dataset_type n... \n",
+ "1000 Will be excluded without change dataset_type n... \n",
+ "1001 Will be excluded without change dataset_type d... \n",
+ "\n",
+ "[1002 rows x 16 columns]"
+ ]
+ },
+ "execution_count": 5,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "file_records_to_df(file_records, details = True)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "0b42a8be",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "sessions = connector.search(subject=\"wm32\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "9fcc38e7",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from alyx_connector.files.transfers.transfers import FileTransferManager"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "id": "1dd01e13",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from alyx_connector.files.parsing import File, Matcher\n",
+ "from alyx_connector.files.expressions import Expressions\n",
+ "\n",
+ "from alyx_registrator import Config, file_records_to_df\n",
+ "config = Config()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "id": "5713ac7c",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " Ordered by: internal time\n",
+ " List reduced from 219 to 1 due to restriction <'{built-in method builtins.isinstance}'>\n",
+ "\n",
+ "Function was called by...\n",
+ " ncalls tottime cumtime\n",
+ "{built-in method builtins.isinstance} <- 3 0.000 0.000 <frozen importlib._bootstrap>:1384(_handle_fromlist)\n",
+ " 1013 0.000 0.000 <frozen ntpath>:107(join)\n",
+ " 54242 0.008 0.008 <frozen ntpath>:179(splitroot)\n",
+ " 1002 0.000 0.000 <frozen ntpath>:564(normpath)\n",
+ " 2003 0.000 0.000 C:\\Python312\\Lib\\copy.py:61(copy)\n",
+ " 2003 0.000 0.000 C:\\Python312\\Lib\\copy.py:247(_reconstruct)\n",
+ " 16 0.000 0.000 C:\\Python312\\Lib\\enum.py:1528(__or__)\n",
+ " 10 0.000 0.000 C:\\Python312\\Lib\\enum.py:1538(__and__)\n",
+ " 194820 0.031 0.031 C:\\Python312\\Lib\\pathlib.py:358(__init__)\n",
+ " 4 0.000 0.000 C:\\Python312\\Lib\\typing.py:1439(__subclasscheck__)\n",
+ " 11457 0.003 0.003 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\ONE-registrator\\alyx_registrator\\registration.py:381(evaluate)\n",
+ " 128612 0.019 0.019 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\expressions.py:228(search)\n",
+ " 32153 0.005 0.005 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:146(date)\n",
+ " 32153 0.007 0.007 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:228(extra)\n",
+ " 1 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\IPython\\core\\interactiveshell.py:3513(run_code)\n",
+ " 64 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\ipykernel\\ipkernel.py:775(_clean_thread_parent_frames)\n",
+ " 1 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\pandas\\core\\dtypes\\common.py:1040(needs_i8_conversion)\n",
+ " 1 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\pandas\\core\\dtypes\\common.py:1434(_is_dtype_type)\n",
+ " 2 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:842(_engine)\n",
+ " 3 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:5170(_get_engine_target)\n",
+ " 4 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\pandas\\core\\indexing.py:2765(check_dict_or_set_indexers)\n",
+ " 1 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\pandas\\core\\series.py:1095(__getitem__)\n",
+ " 1 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\traitlets\\traitlets.py:1527(_notify_observers)\n",
+ " 2 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\traitlets\\traitlets.py:2304(validate)\n",
+ " 2 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\traitlets\\traitlets.py:3474(validate)\n",
+ " 2 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\traitlets\\traitlets.py:3631(set)\n",
+ " 1 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\zmq\\eventloop\\zmqstream.py:546(_run_callback)\n",
+ " 7 0.000 0.000 c:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\.venv\\Lib\\site-packages\\zmq\\sugar\\socket.py:712(send_multipart)\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "<pstats.Stats at 0x17bdfe13b60>"
+ ]
+ },
+ "execution_count": 6,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "stats.print_callers('{built-in method builtins.isinstance}')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "562c659a",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " 4955759 function calls (4925591 primitive calls) in 3.411 seconds\n",
+ "\n",
+ " Ordered by: internal time\n",
+ " List reduced from 219 to 50 due to restriction <50>\n",
+ "\n",
+ " ncalls tottime percall cumtime percall filename:lineno(function)\n",
+ " 1014 0.404 0.000 0.404 0.000 {built-in method nt._path_isfile}\n",
+ " 352385 0.298 0.000 0.298 0.000 {method 'search' of 're.Pattern' objects}\n",
+ " 32153 0.186 0.000 2.097 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:77(from_parts)\n",
+ " 321530 0.176 0.000 0.279 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:60(_check_unallowed_chars)\n",
+ " 321530 0.154 0.000 1.800 0.000 {built-in method builtins.setattr}\n",
+ " 97410 0.154 0.000 0.223 0.000 C:\\Python312\\Lib\\pathlib.py:358(__init__)\n",
+ " 64306 0.145 0.000 0.601 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\expressions.py:228(search)\n",
+ " 32153 0.111 0.000 0.953 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:108(root)\n",
+ " 54242 0.103 0.000 0.161 0.000 <frozen ntpath>:179(splitroot)\n",
+ " 43186 0.102 0.000 0.291 0.000 C:\\Python312\\Lib\\pathlib.py:387(_parse_path)\n",
+ " 105489 0.086 0.000 0.242 0.000 C:\\Python312\\Lib\\pathlib.py:437(__str__)\n",
+ " 351680 0.081 0.000 0.081 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:100(_raise_if_not_partname)\n",
+ "459583/459579 0.073 0.000 0.073 0.000 {built-in method builtins.isinstance}\n",
+ " 32153 0.070 0.000 0.099 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:179(revision)\n",
+ " 97410 0.065 0.000 0.288 0.000 C:\\Python312\\Lib\\pathlib.py:1158(__init__)\n",
+ " 12 0.062 0.005 0.062 0.005 {built-in method nt.listdir}\n",
+ " 75339 0.059 0.000 0.410 0.000 C:\\Python312\\Lib\\pathlib.py:551(drive)\n",
+ " 32153 0.059 0.000 0.203 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:166(collection)\n",
+ " 32153 0.057 0.000 2.507 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:87(from_path)\n",
+ " 128612 0.049 0.000 0.067 0.000 C:\\Python312\\Lib\\enum.py:197(__get__)\n",
+ " 64306 0.048 0.000 0.048 0.000 {method 'groupdict' of 're.Match' objects}\n",
+ " 43186 0.046 0.000 0.350 0.000 C:\\Python312\\Lib\\pathlib.py:407(_load_parts)\n",
+ " 97410 0.043 0.000 0.063 0.000 C:\\Python312\\Lib\\pathlib.py:1165(__new__)\n",
+ " 32153 0.042 0.000 2.554 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\ONE-registrator\\alyx_registrator\\registration.py:87(source_file)\n",
+ " 30150 0.039 0.000 2.597 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\ONE-registrator\\alyx_registrator\\registration.py:308(evaluate)\n",
+ "164780/134629 0.036 0.000 0.046 0.000 {built-in method builtins.getattr}\n",
+ " 32153 0.036 0.000 0.072 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:157(number)\n",
+ " 11457 0.032 0.000 2.640 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\ONE-registrator\\alyx_registrator\\registration.py:381(evaluate)\n",
+ " 32153 0.031 0.000 0.066 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:248(extension)\n",
+ " 131566 0.030 0.000 0.030 0.000 {built-in method __new__ of type object at 0x00007FFDAF9F13D0}\n",
+ " 106490 0.028 0.000 0.028 0.000 {method 'startswith' of 'str' objects}\n",
+ " 129463 0.027 0.000 0.027 0.000 {method 'append' of 'list' objects}\n",
+ " 153667 0.025 0.000 0.025 0.000 {built-in method nt.fspath}\n",
+ " 32153 0.025 0.000 0.344 0.000 C:\\Python312\\Lib\\pathlib.py:749(is_absolute)\n",
+ " 42185 0.025 0.000 0.057 0.000 C:\\Python312\\Lib\\pathlib.py:429(_format_parsed_parts)\n",
+ " 68336 0.023 0.000 0.023 0.000 {method 'find' of 'str' objects}\n",
+ " 97428 0.022 0.000 0.022 0.000 {method 'replace' of 'str' objects}\n",
+ " 34156 0.022 0.000 0.031 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:69(__new__)\n",
+ " 32153 0.021 0.000 0.057 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:228(extra)\n",
+ " 87638 0.021 0.000 0.021 0.000 {built-in method sys.intern}\n",
+ " 32153 0.020 0.000 0.055 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:146(date)\n",
+ " 32153 0.018 0.000 0.050 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:194(object)\n",
+ " 32153 0.017 0.000 0.045 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:205(attribute)\n",
+ " 64306 0.016 0.000 0.016 0.000 {method 'endswith' of 'str' objects}\n",
+ " 30150 0.016 0.000 0.051 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:96(__getitem__)\n",
+ " 43186 0.015 0.000 0.015 0.000 {method 'split' of 'str' objects}\n",
+ " 86380 0.013 0.000 0.013 0.000 {built-in method builtins.len}\n",
+ " 32153 0.013 0.000 0.044 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:137(subject)\n",
+ " 42185 0.011 0.000 0.011 0.000 {method 'join' of 'str' objects}\n",
+ " 75339 0.011 0.000 0.011 0.000 C:\\Python312\\Lib\\pathlib.py:560(root)\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "<pstats.Stats at 0x17bdfe13b60>"
+ ]
+ },
+ "execution_count": 4,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "import cProfile\n",
+ "import pstats\n",
+ "\n",
+ "profiler = cProfile.Profile()\n",
+ "profiler.enable()\n",
+ "\n",
+ "file_records = config.evaluate_session(session)\n",
+ "\n",
+ "profiler.disable()\n",
+ "stats = pstats.Stats(profiler).sort_stats('tottime')\n",
+ "stats.print_stats(50) # print top 10 functions by cumulative time"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "id": "27308329",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "application/vnd.microsoft.datawrangler.viewer.v0+json": {
+ "columns": [
+ {
+ "name": "index",
+ "rawType": "int64",
+ "type": "integer"
+ },
+ {
+ "name": "source_path",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "match",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "matching_rules",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "used_rule",
+ "rawType": "object",
+ "type": "string"
+ },
+ {
+ "name": "valid_alf",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "path_conflicts",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "dataset_type_exists",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "rename",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "delete",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "include",
+ "rawType": "bool",
+ "type": "boolean"
+ },
+ {
+ "name": "abort",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "_source_file",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "_destination_file",
+ "rawType": "object",
+ "type": "unknown"
+ },
+ {
+ "name": "info",
+ "rawType": "object",
+ "type": "string"
+ }
+ ],
+ "conversionMethod": "pd.DataFrame",
+ "ref": "be605038-92d9-43b1-b299-0a6afce0e54b",
+ "rows": [
+ [
+ "0",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\behaviour_imaging\\whiskers\\behaviour.camera_settings.whiskers.txt",
+ "True",
+ "['behavior_cam_sessings_include_rule']",
+ "",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "[]",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594F800>",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594F7D0>",
+ "Will be excluded without change dataset_type doesn't follow alyx format dataset_type not existing "
+ ],
+ [
+ "1",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\behaviour_imaging\\whiskers\\behaviour.video.whiskers.00000.tdms",
+ "True",
+ "['behavior_whiskers_rule1']",
+ "",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "[]",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594F950>",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594F9B0>",
+ "Will be excluded without change dataset_type doesn't follow alyx format dataset_type not existing "
+ ],
+ [
+ "2",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\behaviour_imaging\\whiskers\\behaviour.video.whiskers.00001.tdms",
+ "True",
+ "['behavior_whiskers_rule1']",
+ "",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "[]",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594FC20>",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594FB90>",
+ "Will be excluded without change dataset_type doesn't follow alyx format dataset_type not existing "
+ ],
+ [
+ "3",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\behaviour_imaging\\whiskers\\behaviour.video.whiskers.00002.tdms",
+ "True",
+ "['behavior_whiskers_rule1']",
+ "",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "[]",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594FE00>",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594FD70>",
+ "Will be excluded without change dataset_type doesn't follow alyx format dataset_type not existing "
+ ],
+ [
+ "4",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\behaviour_imaging\\whiskers\\behaviour.video.whiskers.00003.tdms",
+ "True",
+ "['behavior_whiskers_rule1']",
+ "",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "[]",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594F7A0>",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE594FF50>",
+ "Will be excluded without change dataset_type doesn't follow alyx format dataset_type not existing "
+ ],
+ [
+ "5",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\behaviour_imaging\\whiskers\\behaviour.video.whiskers.00004.tdms",
+ "True",
+ "['behavior_whiskers_rule1']",
+ "",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "False",
+ "[]",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE598C200>",
+ "<alyx_connector.files.parsing.File object at 0x000001EEE598C170>",
+ "Will be excluded without change dataset_type doesn't follow alyx format dataset_type not existing "
+ ],
+ [
+ "6",
+ "\\\\157.99.138.167\\cajal_data2\\ONE\\Interhem\\ihem05\\2024-11-06\\002\\behaviour_imaging\\whiskers\\behaviour.video.whiskers.00005.tdms",
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+ " 26343 0.006 0.000 0.006 0.000 {built-in method __new__ of type object at 0x00007FFDAF9F13D0}\n",
+ " 4809 0.006 0.000 0.401 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\ONE-registrator\\alyx_registrator\\registration.py:87(source_file)\n",
+ " 4809 0.006 0.000 0.011 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:143(number)\n",
+ " 3807 0.006 0.000 0.015 0.000 C:\\Python312\\Lib\\copy.py:247(_reconstruct)\n",
+ " 8616 0.006 0.000 0.008 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:55(__new__)\n",
+ "33678/33670 0.005 0.000 0.005 0.000 {built-in method builtins.len}\n",
+ " 4809 0.005 0.000 0.010 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:231(extension)\n",
+ " 25233 0.004 0.000 0.004 0.000 {built-in method nt.fspath}\n",
+ " 20838 0.004 0.000 0.004 0.000 {method 'get' of 'dict' objects}\n",
+ " 17425 0.004 0.000 0.004 0.000 {method 'append' of 'list' objects}\n",
+ " 15027 0.004 0.000 0.004 0.000 {method 'startswith' of 'str' objects}\n",
+ " 4809 0.004 0.000 0.056 0.000 C:\\Python312\\Lib\\pathlib.py:749(is_absolute)\n",
+ " 10818 0.004 0.000 0.004 0.000 {method 'find' of 'str' objects}\n",
+ " 3807 0.004 0.000 0.004 0.000 {method '__reduce_ex__' of 'object' objects}\n",
+ " 5409 0.003 0.000 0.006 0.000 C:\\Python312\\Lib\\pathlib.py:429(_format_parsed_parts)\n",
+ " 12918 0.003 0.000 0.003 0.000 {built-in method sys.intern}\n",
+ " 4809 0.003 0.000 0.009 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:132(date)\n",
+ " 13518 0.003 0.000 0.003 0.000 {method 'replace' of 'str' objects}\n",
+ " 5109 0.003 0.000 0.008 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:180(object)\n",
+ " 5109 0.003 0.000 0.007 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:191(attribute)\n",
+ " 300 0.003 0.000 0.205 0.001 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\ONE-registrator\\alyx_registrator\\registration.py:592(rename)\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "<pstats.Stats at 0x19eb2a892b0>"
+ ]
+ },
+ "execution_count": 6,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "import cProfile\n",
+ "import pstats\n",
+ "\n",
+ "profiler = cProfile.Profile()\n",
+ "profiler.enable()\n",
+ "\n",
+ "file_records = config.actions_cascade(file_records)\n",
+ "\n",
+ "profiler.disable()\n",
+ "stats = pstats.Stats(profiler).sort_stats('tottime')\n",
+ "stats.print_stats(50) # print top 10 functions by cumulative time"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "f4d50053",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "FileTransferManager(sessions).push_request(policies={\"destination_older\":\"ignore\"}).transfer()"
+ ]
+ },
{
"cell_type": "code",
"execution_count": 15,
@@ -112,12 +11387,12 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "id": "d21b3e1e",
+ "execution_count": 4,
+ "id": "780cf946",
"metadata": {},
"outputs": [],
"source": [
- "connector."
+ "existing_dst = connector.search(\"dataset-types\", details = False)"
]
},
{
@@ -450,60 +11725,6 @@
"sessions"
]
},
- {
- "cell_type": "code",
- "execution_count": 18,
- "id": "0ce5699f",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "subject wm32\n",
- "users []\n",
- "location None\n",
- "procedures []\n",
- "lab HaissLab\n",
- "projects []\n",
- "type None\n",
- "task_protocol \n",
- "number 1\n",
- "start_time 2025-04-09T20:36:41.648138+02:00\n",
- "end_time None\n",
- "narrative \n",
- "parent_session None\n",
- "n_correct_trials None\n",
- "n_trials None\n",
- "url http://127.0.0.1/sessions/a977f70d-38f7-4da8-a...\n",
- "extended_qc None\n",
- "qc NOT_SET\n",
- "wateradmin_session_related []\n",
- "data_dataset_session_related []\n",
- "auto_datetime 2025-04-09T20:36:41.656298+02:00\n",
- "alias wm32/2025-04-09/001\n",
- "u_alias wm32_2025-04-09_001\n",
- "path //157.99.138.167/cajal_data2/ONE/Adaptation/wm...\n",
- "json None\n",
- "probe_insertion []\n",
- "notes []\n",
- "default_data_repository_path //157.99.138.167/cajal_data2/ONE/Adaptation\n",
- "default_data_repository_name Cajal2Adaptation\n",
- "default_data_repository_pk 05baa8e4-5eb5-4214-a008-c9e5331004b0\n",
- "rel_path wm32/2025-04-09/001\n",
- "admin_url /admin/actions/session/a977f70d-38f7-4da8-adfd...\n",
- "Name: a977f70d-38f7-4da8-adfd-8884dd42b5b3, dtype: object"
- ]
- },
- "execution_count": 18,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "sessions = connector.search(id = \"a977f70d-38f7-4da8-adfd-8884dd42b5b3\")\n",
- "sessions"
- ]
- },
{
"cell_type": "code",
"execution_count": 19,
@@ -559,23 +11780,262 @@
},
{
"cell_type": "code",
- "execution_count": 2,
- "id": "2a732e40",
+ "execution_count": 9,
+ "id": "c1d6ee83",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'//157.99.138.167/cajal_data2/ONE/Interhem/ihem05/2024-11-06/002'"
+ ]
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
- "from alyx_connector.files.parsing import File, Matcher\n",
- "from alyx_connector.files.expressions import Expressions\n"
+ "session.path"
]
},
{
"cell_type": "code",
- "execution_count": 7,
- "id": "1dd01e13",
+ "execution_count": 17,
+ "id": "f1638466",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "79.7198255"
+ ]
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "sum([v[2] for k,v in stats.stats.items()])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "id": "ac88c9fd",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Set: 2.646561099914834\n",
+ "Regexp: 0.3690903000533581\n"
+ ]
+ }
+ ],
+ "source": [
+ "import re\n",
+ "import timeit\n",
+ "\n",
+ "_unallowed_chars_set = {\"?\", \"*\", \":\", '\"', \"<\", \">\"}\n",
+ "_unallowed_chars_re = re.compile(r'[?*:\"><]')\n",
+ "\n",
+ "def check_set(variable):\n",
+ " return any(char in _unallowed_chars_set for char in variable)\n",
+ "\n",
+ "def check_re(variable):\n",
+ " return bool(_unallowed_chars_re.search(variable))\n",
+ "\n",
+ "test_str = \"this_is_a_test_string_with_no_unallowed_chars\"\n",
+ "\n",
+ "print(\"Set:\", timeit.timeit(lambda: check_set(test_str), number=1000000))\n",
+ "print(\"Regexp:\", timeit.timeit(lambda: check_re(test_str), number=1000000))\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "id": "a19154bc",
"metadata": {},
"outputs": [],
"source": [
- "from alyx_registrator import Config"
+ "profiler.dump_stats(\"profile_results.prof\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "id": "ac400b74",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " 145726694 function calls (144967324 primitive calls) in 79.720 seconds\n",
+ "\n",
+ " Ordered by: internal time\n",
+ " List reduced from 228 to 50 due to restriction <50>\n",
+ "\n",
+ " ncalls tottime percall cumtime percall filename:lineno(function)\n",
+ " 4744322 5.847 0.000 9.579 0.000 C:\\Python312\\Lib\\pathlib.py:358(__init__)\n",
+ " 4373811 5.533 0.000 8.682 0.000 <frozen ntpath>:179(splitroot)\n",
+ " 1095930 3.514 0.000 8.529 0.000 C:\\Python312\\Lib\\pathlib.py:387(_parse_path)\n",
+ " 4744322 3.376 0.000 12.955 0.000 C:\\Python312\\Lib\\pathlib.py:1158(__init__)\n",
+ " 3676320 2.972 0.000 3.680 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:45(_check_unallowed_chars)\n",
+ "17528008/17528004 2.672 0.000 2.672 0.000 {built-in method builtins.isinstance}\n",
+ " 735324 2.518 0.000 2.518 0.000 {method 'search' of 're.Pattern' objects}\n",
+ " 728418 2.467 0.000 7.767 0.000 <frozen ntpath>:107(join)\n",
+ " 367512 2.310 0.000 25.677 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:63(from_parts)\n",
+ " 1463442 2.199 0.000 20.365 0.000 C:\\Python312\\Lib\\pathlib.py:437(__str__)\n",
+ " 2185254 1.973 0.000 9.861 0.000 C:\\Python312\\Lib\\pathlib.py:380(with_segments)\n",
+ " 3676320 1.883 0.000 21.958 0.000 {built-in method builtins.setattr}\n",
+ " 4744322 1.878 0.000 2.874 0.000 C:\\Python312\\Lib\\pathlib.py:1165(__new__)\n",
+ " 735024 1.691 0.000 7.130 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\expressions.py:228(search)\n",
+ " 1095930 1.557 0.000 18.186 0.000 C:\\Python312\\Lib\\pathlib.py:407(_load_parts)\n",
+ " 10218550 1.472 0.000 1.472 0.000 {built-in method builtins.getattr}\n",
+ " 1463442 1.409 0.000 19.595 0.000 C:\\Python312\\Lib\\pathlib.py:551(drive)\n",
+ " 367512 1.379 0.000 11.507 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:94(root)\n",
+ " 2185254 1.342 0.000 11.202 0.000 C:\\Python312\\Lib\\pathlib.py:712(joinpath)\n",
+ " 8390318 1.305 0.000 1.305 0.000 {built-in method nt.fspath}\n",
+ " 364209 1.300 0.000 15.796 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:244(session_name)\n",
+ " 364209 1.259 0.000 4.625 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:274(filename)\n",
+ " 5469741 1.221 0.000 1.221 0.000 {method 'replace' of 'str' objects}\n",
+ " 4559217 1.146 0.000 1.146 0.000 {built-in method sys.intern}\n",
+ " 5114834 1.099 0.000 1.099 0.000 {built-in method __new__ of type object at 0x00007FFDAF9F13D0}\n",
+ " 3676320 0.951 0.000 0.951 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:86(_raise_if_not_partname)\n",
+ " 1092627 0.932 0.000 2.061 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:219(extras)\n",
+ " 367512 0.866 0.000 1.203 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:165(revision)\n",
+ "367511/70 0.865 0.000 0.011 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\ONE-registrator\\alyx_registrator\\registration.py:85(source_file)\n",
+ " 2185254 0.829 0.000 12.031 0.000 C:\\Python312\\Lib\\pathlib.py:720(__truediv__)\n",
+ " 726612 0.821 0.000 11.932 0.000 C:\\Python312\\Lib\\pathlib.py:484(_str_normcase)\n",
+ " 3675112 0.802 0.000 0.802 0.000 {built-in method builtins.any}\n",
+ " 3641489 0.787 0.000 0.787 0.000 {method 'extend' of 'list' objects}\n",
+ " 3289592 0.786 0.000 0.786 0.000 {method 'append' of 'list' objects}\n",
+ " 2186748 0.758 0.000 0.758 0.000 {method 'split' of 'str' objects}\n",
+ "367511/70 0.734 0.000 0.011 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:73(from_path)\n",
+ " 1095930 0.728 0.000 1.898 0.000 C:\\Python312\\Lib\\pathlib.py:429(_format_parsed_parts)\n",
+ " 364209 0.724 0.000 21.270 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:315(session_path)\n",
+ " 367812 0.722 0.000 2.583 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:152(collection)\n",
+ " 2191860 0.713 0.000 0.713 0.000 {method 'find' of 'str' objects}\n",
+ " 364209 0.708 0.000 4.167 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:297(collection_subpath)\n",
+ " 735024 0.610 0.000 0.610 0.000 {method 'groupdict' of 're.Match' objects}\n",
+ " 1470048 0.600 0.000 0.823 0.000 C:\\Python312\\Lib\\enum.py:197(__get__)\n",
+ " 2183445 0.570 0.000 0.856 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:210(extra)\n",
+ " 603 0.549 0.001 79.129 0.131 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\ONE-registrator\\alyx_registrator\\registration.py:134(check_path_conflicts)\n",
+ " 1460139 0.513 0.000 0.513 0.000 {method 'join' of 'str' objects}\n",
+ " 367512 0.465 0.000 0.948 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:143(number)\n",
+ " 1467045 0.409 0.000 0.409 0.000 {method 'startswith' of 'str' objects}\n",
+ " 364209 0.406 0.000 17.381 0.000 C:\\Users\\tjostmou\\Documents\\Python\\__packages__\\alyx-connector\\src\\alyx_connector\\files\\parsing.py:240(session_name_as_path)\n",
+ " 363609 0.405 0.000 0.405 0.000 <string>:2(__eq__)\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "<pstats.Stats at 0x13b62e3e0c0>"
+ ]
+ },
+ "execution_count": 8,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "stats = pstats.Stats(profiler).sort_stats('tottime')\n",
+ "stats.print_stats(50) # print top 10 functions by cumulative time"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 22,
+ "id": "82ac9520",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "['behaviour.camera_settings',\n",
+ " 'behaviour.video',\n",
+ " 'behaviour.video_compressed',\n",
+ " 'behaviour.video_compressed_meta']"
+ ]
+ },
+ "execution_count": 22,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "[name for name in config.dataset_types if \"behaviour\" in name]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 25,
+ "id": "d7f4ab2a",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "True"
+ ]
+ },
+ "execution_count": 25,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "file_records[0].destination_file.dataset_type in config.dataset_types"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "id": "7d20d10b",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "True"
+ ]
+ },
+ "execution_count": 26,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "file_records[0].destination_file.is_dataset_type_valid"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "id": "4bf7852a",
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "NameError",
+ "evalue": "name 'file_records' is not defined",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+ "\u001b[31mNameError\u001b[39m Traceback (most recent call last)",
+ "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[4]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m file_records_to_df(\u001b[43mfile_records\u001b[49m, details = \u001b[38;5;28;01mTrue\u001b[39;00m)\n",
+ "\u001b[31mNameError\u001b[39m: name 'file_records' is not defined"
+ ]
+ }
+ ],
+ "source": [
+ "file_records_to_df(file_records, details = True)"
]
},
{
diff --git a/src/alyx_connector/__init__.py b/src/alyx_connector/__init__.py
index d779abe4871623ba0c2296b27a03028790e964ba..b50460a23500b536163b92af22a5d79d57156ad4 100644
--- a/src/alyx_connector/__init__.py
+++ b/src/alyx_connector/__init__.py
@@ -1,3 +1,3 @@
-__version__ = "2.1.30"
+__version__ = "2.1.31"
from .connector.core import Connector
diff --git a/src/alyx_connector/connector/core.py b/src/alyx_connector/connector/core.py
index f6ae37ead99e4bf5589d682965c883c7b4b89359..ec25aeebe58e397e3237600334da6e2ddef47e46 100644
--- a/src/alyx_connector/connector/core.py
+++ b/src/alyx_connector/connector/core.py
@@ -5,6 +5,7 @@ from tqdm import tqdm
from ..utils import Singleton
from ..web.clients import WebClient
+from ..files.registration.rules_config import Config
from typing import overload, Optional, NoReturn
@@ -12,6 +13,36 @@ logger = getLogger(__name__)
class Connector(metaclass=Singleton):
+ """Connector class for managing a singleton web client connection.
+
+ This class provides methods to interact with a web client, including searching for sessions, registering sessions,
+ and converting results to pandas DataFrames or Series. It ensures that only one instance
+ of the Connector exists at any time.
+
+ Attributes:
+ username (str): The username associated with the web client.
+ url (str): The URL of the web client.
+
+ Methods:
+ setup(*args, **kwargs):
+ Sets up the web client and returns a Connector instance.
+
+ search(endpoint="sessions", details=True, raises=True, **kwargs):
+ Searches for sessions or other resources at the specified endpoint.
+
+ register(session_or_sessions):
+ Registers a session or multiple sessions with the connector.
+
+ raise_if_search_empty(search_result):
+ Raises a ValueError if the search result is empty.
+
+ results_to_pandas(request_result):
+ Converts the results from a request into a pandas DataFrame or Series.
+
+ details_aggregation(search_result, endpoint):
+ Aggregates detailed results from a list of search results by retrieving additional
+ information from a specified endpoint.
+ """
_singleton_no_argument_only = True
@@ -41,6 +72,12 @@ class Connector(metaclass=Singleton):
search_result = self.raise_if_search_empty(search_result)
return self.results_to_pandas(search_result)
+ def register(self, session_or_sessions=DataFrame | Series):
+ if isinstance(session_or_sessions, Series):
+ return Config(connector=self, session=session_or_sessions)
+ for _, session in session_or_sessions.iterrows():
+ return Config(connector=self, session=session).registration_pipeline(session)
+
# @overload
# def search(self, endpoint=..., id: str = ..., **kwargs) -> Series: ...
@@ -158,1498 +195,1497 @@ class Connector(metaclass=Singleton):
return detailed_results
-if __name__ == "__main__":
-
- class WebConnector(metaclass=Singleton):
- """An API for searching and loading data through the Alyx database"""
-
- def __init__(
- self,
- username=None,
- password=None,
- base_url=None,
- cache_dir=None,
- mode="auto",
- data_access_mode="local",
- wildcards=True,
- **kwargs,
- ):
- """An API for searching and loading data through the Alyx database
-
- Parameters
- ----------
- mode : str
- Query mode, options include 'auto', 'local' (offline) and 'remote' (online only). Most
- methods have a `query_type` parameter that can override the class mode.
- wildcards : bool
- If true, methods allow unix shell style pattern matching, otherwise regular
- expressions are supported
- cache_dir : str, Path
- Path to the data files. If Alyx parameters have been set up for this location,
- an OneAlyx instance is returned. If data_dir and base_url are None, the default
- location is used.
- base_url : str
- An Alyx database URL. The URL must start with 'http'.
- username : str
- An Alyx database login username.
- password : str
- An Alyx database password.
- cache_rest : str
- If not in 'local' mode, this determines which http request types to cache. Default is
- 'GET'. Use None to deactivate cache (not recommended).
- """
-
- # Load Alyx Web client
- self.web_client = AlyxClient(
- username=username,
- password=password,
- base_url=base_url,
- cache_dir=cache_dir,
- **kwargs,
- )
-
- self._registration_client = RegistrationClient(self)
-
- self.data_access_mode = data_access_mode
-
- self._search_endpoint = "sessions"
-
- # get parameters override if inputs provided
- super().__init__(mode=mode, wildcards=wildcards, cache_dir=cache_dir)
-
- def set_data_access_mode(self, mode):
- available_modes = [
- "local",
- "remote",
- ] # TODO : add ability to go auto mode later. (if possible, still have to think about it)
- if mode in available_modes:
- self.data_access_mode = mode
- self.alyx.delete_cache() # delete rest cache in case there is local / remote path stored inside
- else:
- raise ValueError(f"data_access_mode must be one of : {available_modes}")
-
- def __repr__(self):
- return f'One ({"off" if self.offline else "on"}line, {self.alyx.base_url})'
-
- def load_cache(self, cache_dir=None, clobber=False, tag=None):
- """
- Load parquet cache files. If the local cache is sufficiently old, this method will query
- the database for the location and creation date of the remote cache. If newer, it will be
- download and loaded.
-
- Note: Unlike refresh_cache, this will always reload the local files at least once.
-
- Parameters
- ----------
- cache_dir : str, pathlib.Path
- An optional directory location of the parquet files, defaults to One.cache_dir.
- clobber : bool
- If True, query Alyx for a newer cache even if current (local) cache is recent.
- tag : str
- An optional Alyx dataset tag for loading cache tables containing a subset of datasets.
- """
- _logger = logging.getLogger("load_cache")
- cache_meta = self._cache.get("_meta", {})
- cache_dir = cache_dir or self.cache_dir
- # If user provides tag that doesn't match current cache's tag, always download.
- # NB: In the future 'database_tags' may become a list.
- current_tags = [x.get("database_tags") for x in cache_meta.get("raw", {}).values() or [{}]]
- tag = tag or current_tags[0] # For refreshes take the current tag as default
- different_tag = any(x != tag for x in current_tags)
- if not clobber or different_tag:
- super().load_cache(cache_dir) # Load any present cache
- cache_meta = self._cache.get("_meta", {}) # TODO Make walrus when we drop 3.7 support
- expired = self._cache and cache_meta["expired"]
- if not expired or self.mode in ("local", "remote"):
- return
-
- # Warn user if expired
- if cache_meta["expired"] and cache_meta.get("created_time", False) and not self.alyx.silent:
- age = datetime.now() - cache_meta["created_time"]
- t_str = f"{age.days} day(s)" if age.days >= 1 else f"{np.floor(age.seconds / (60 * 2))} hour(s)"
- _logger.info(f"cache over {t_str} old")
-
- try:
- # Determine whether a newer cache is available
- cache_info = self.alyx.get(f'cache/info/{tag or ""}'.strip("/"), expires=True)
- assert tag == cache_info.get("database_tags")
-
- # Check version compatibility
- min_version = packaging.version.parse(cache_info.get("min_api_version", "0.0.0"))
- if packaging.version.parse(alyx_connector.__version__) < min_version:
- warnings.warn(f"Newer cache tables require ONE version {min_version} or greater")
- return
-
- # Check whether remote cache more recent
- remote_created = datetime.fromisoformat(cache_info["date_created"])
- local_created = cache_meta.get("created_time", None)
- if local_created and (remote_created - local_created) < timedelta(minutes=1):
- _logger.info("No newer cache available")
- return
-
- # Download the remote cache files
- _logger.info("Downloading remote caches...")
- files = self.alyx.download_cache_tables(cache_info.get("location"), cache_dir)
- assert any(files)
- super().load_cache(cache_dir) # Reload cache after download
- except (requests.exceptions.HTTPError, HTTPError) as ex:
- _logger.debug(ex)
- ## REMOVED THIS WARNING FOR NOW AS I CAN'T FIND IF IT IS ACTUALLY USEFULL TO HAVE A REMOTE CACHE WHEN
- # SETUPING A LOCAL USE OF ALYX LIKE WE DO
- # _logger.error('Failed to load the remote cache file')
- self.mode = "remote"
- except (ConnectionError, requests.exceptions.ConnectionError) as ex:
- _logger.debug(ex)
- _logger.error("Failed to connect to Alyx")
- self.mode = "local"
-
- @property
- def alyx(self):
- """one.webclient.AlyxClient: The Alyx Web client"""
- return self.web_client
-
- @property
- def register(self):
- return self._registration_client
-
- @property
- def cache_dir(self):
- """pathlib.Path: The location of the downloaded file cache"""
- return self.web_client.cache_dir
-
- @util.refresh
- def search_terms(self, query_type=None):
- """
- Returns a list of search terms to be passed as kwargs to the search method
-
- Parameters
- ----------
- query_type : str
- If 'remote', the search terms are largely determined by the REST endpoint used
-
- Returns
- -------
- tuple
- Tuple of search strings
- """
- if (query_type or self.mode) != "remote":
- # Return search terms from REST schema
- return self._search_terms
- fields = self.alyx.rest_schemes[self._search_endpoint]["list"]["fields"]
- # 'laboratory' already in search terms
- excl = ("lab",)
- return tuple({*self._search_terms, *(x["name"] for x in fields if x["name"] not in excl)})
-
- def describe_dataset(self, dataset_type=None):
- """Print a dataset type description.
-
- NB: This requires an Alyx database connection.
-
- Parameters
- ----------
- dataset_type : str
- A dataset type or dataset name
-
- Returns
- -------
- dict
- The Alyx dataset type record
- """
- _logger = logging.getLogger("describe_dataset")
- assert self.mode != "local" and not self.offline, "Unable to connect to Alyx in local mode"
- if not dataset_type:
- return self.alyx.rest("dataset-types", "list")
- try:
- assert isinstance(dataset_type, str) and not is_uuid_string(dataset_type)
- _logger.disabled = True
- out = self.alyx.rest("dataset-types", "read", dataset_type)
- except (AssertionError, requests.exceptions.HTTPError):
- # Try to get dataset type from dataset name
- out = self.alyx.rest("dataset-types", "read", self.dataset2type(dataset_type))
- finally:
- _logger.disabled = False
- print(out["description"])
- return out
-
- def change_session_data_mode(self, session_details, mode):
- session_details["full_path"] = session_details[mode + "_full_path"]
- return session_details
-
- #### LIST DATASETS
- @util.refresh
- def list_datasets(
- self,
- eid=None,
- details=False,
- query_type=None,
- as_mode=None,
- no_cache=False,
- **filters,
- ) -> np.ndarray | pd.DataFrame | List[str]:
- """_summary_
-
- Args:
- eid (str, optional): Session id (alias or pk). Does not need to be supplied only if
- using session_details. Defaults to None.
- details (bool, optional): If False, will only return a list of absolute file paths
- (obtained from the column full_path of the dataset dataframe).
- Otherwise will return a full dataframe of all datasets found for this session
- Defaults to False.
- query_type (str or None, optional): Wether to perform the metadata fetch
- (only if using eid) from local cache or on alyx. If None, uses the current mode of
- the connector instance. Defaults to None.
- as_mode (str or None, optional): Wether to perform the full_path construction using
- default current (None), 'local' or 'remote' mode. Defaults to None.
- session_details (pd.Series, optional): The pandas series containing
- data_dataset_session_related information.
- If not supplied, the function must be supplied a session id (eid, first argument)
- to get this session_details variable internally. Defaults to None.
-
- Other filtering keys are accepted :
- (the value on wich you search must match perfectly. Key must also match any of the
- below. key and values are case sensitive)
- - extra
- - object
- - attribute
- - subject
- - date
- - number
- - revision
- - collection
- - extension
-
- - dataset_type
- - name (from dataset, ex trials.eventTimelines)
- - file_name
-
- - relative_path
- - exists
- - created_by
- - created_datetime
- - data_repository
- - hash
- - file_size
- - tags
-
- Raises:
- NotImplementedError: For now, using mode (metadata) local will not work as the cache system to retrive data
- has not been tested for.
-
- Returns:
- Union[list, pd.DataFrame]: A list of matching files full_paths (if details = False) or a dataframe of all
- matching file records components and metadata.
- """
-
- import natsort
-
- _logger = logging.getLogger("list_datasets")
-
- def flatten_pathlist(x):
- if isinstance(x, (list, tuple)):
- return natsort.natsorted([a for i in x for a in flatten(i)])
- else:
- return natsort.natsorted([x])
-
- # OBTAINING A SESSION_DETAILS (IN WHICH RESIDES FILES INFO)
-
- data_access_mode = as_mode or self.data_access_mode
- if hasattr(eid, "keys") and "data_dataset_session_related" in eid.keys():
- session_details = (
- eid.copy()
- ) # either a pd.series of dict, copy and key getters/setters works both cases
- try:
- eid = session_details["id"]
- except KeyError:
- eid = session_details.name
- session_details["id"] = eid
- else:
- _eid = eid
- # Ensure we have a UUID str
- eid = self.to_eid(eid)
- if eid is None:
- raise ValueError(
- f"The session id {_eid} supplied seem to not be existing. Check that you are in 'remote' mode "
- "(not data_access_mode) and check that the session exists on a webpage."
- )
- if (query_type or self.mode) != "remote":
- raise NotImplementedError
- ## TODO : GET BACK THE DATA FROM THE CACHE AFTER CHANGE IN DATA MANAGEMENT METHODOLOGY
- # return super().list_datasets(eid, details=details, query_type=query_type, **filters)
-
- session_details = self.to_session_details(
- self.alyx.rest("sessions", "read", id=eid, query_type=query_type, no_cache=no_cache)
- )
- # session, datasets = util.ses2records(self.alyx.rest('sessions', 'read', id=eid))
- # self._update_cache_from_records(sessions=session, datasets=datasets.copy()
- # if datasets is not None else datasets)
- # Add to cache tables # TODO : DO ADD THAT FUNCTIONNALITY AGAIN
-
- datasets = copy.deepcopy(session_details["data_dataset_session_related"])
- # copy to not change the session_details in case they are suplied by user as input
-
- file_records = []
- for dataset in datasets:
- files = dataset.pop("file_records")
- dataset["session#"] = dataset.pop("session")
- dataset["dataset#"] = dataset.pop("id")
- dataset["dataset_url"] = dataset.pop("url")
- dataset["dataset_admin_url"] = dataset.pop("admin_url")
- dataset["local_root"] = alyx_connector.params.get().LOCAL_ROOT
- for file in files:
- # file["file_url"] = file.pop("url")
- # file["file_admin_url"] = file.pop("admin_url")
- file["file#"] = file.pop("id")
- file.update(
- {
- "remote_full_path": os.path.normpath(
- os.path.join(dataset["remote_root"], file["relative_path"])
- ),
- "local_full_path": os.path.normpath(
- os.path.join(dataset["local_root"], file["relative_path"])
- ),
- }
- )
- # remote or local depending on current mode
- file["full_path"] = file[data_access_mode + "_full_path"]
- file.update(dataset)
- file_records.append(file)
-
- dataframe = pd.DataFrame(file_records)
- if dataframe.empty:
- _logger.warning(
- "No dataset found for this session. Are you sure you ran the file registration routine ?"
- )
- return dataframe if details else []
-
- dataframe.set_index(["session#", "dataset#", "file#"])
-
- # FILTERING THE ROWS BASED ON USER INPUT
- # query_string = ' & '.join([f'{k} == {repr(v)}' for k, v in filters.items()])
- if filters:
- if "filename" in filters.keys():
- # allowing filename for retrocompatibility
- filters["file_name"] = filters.pop("filename")
- queries = []
- for key, value in filters.items():
- # if the columns correspunding to filter is object or string, we try to match using wildcard type
- # syntax as input
- # to do that we convert * wildcards to .* in regex and add a ^ and $ at start and end of pattern
- # to force a complete string length match.
-
- if dataframe[key].dtype is npdtype("O") or dataframe[key].dtype is npdtype(str):
- queries.append(f"{key}.str.match('^' + {repr(value).replace('*', '.*')} + '$') ") #
- # if the columns is not a sting, we match it directly.
- else:
- queries.append(f"{key} == {value}")
-
- # example of a query string : query_string = "exists == True & subject.str.match('wm.*$')"
- query_string = " & ".join(queries)
-
- try:
- dataframe = dataframe.query(query_string, engine="python")
- except (KeyError, pd.errors.UndefinedVariableError) as e:
- raise KeyError(f"Cannot use the key {str(e)} to filter for datasets")
-
- return dataframe if details else list(dataframe["full_path"])
-
- @util.refresh
- def pid2eid(self, pid: str, query_type=None) -> Tuple[str, str]:
- """
- Given an Alyx probe UUID string, returns the session id string and the probe label
- (i.e. the ALF collection).
-
- NB: Requires a connection to the Alyx database.
-
- Parameters
- ----------
- pid : str, uuid.UUID
- A probe UUID
- query_type : str
- Query mode - options include 'remote', and 'refresh'
-
- Returns
- -------
- str
- Experiment ID (eid)
- str
- Probe label
- """
- query_type = query_type or self.mode
- if query_type != "remote":
- self.refresh_cache(query_type)
- if query_type == "local" and "insertions" not in self._cache.keys():
- raise NotImplementedError("Converting probe IDs required remote connection")
- rec = self.alyx.rest("insertions", "read", id=str(pid))
- return rec["session"], rec["name"]
-
- #### SEARCH
- def search(
- self,
- id=None,
- *,
- details=False,
- query_type=None,
- as_mode=None,
- no_cache=False,
- **kwargs,
- ):
- """
- Searches sessions matching the given criteria and returns a list of matching eids
-
- For a list of search terms, use the method
-
- one.search_terms(query_type='remote')
-
- For all of the search parameters, a single value or list may be provided. For dataset,
- the sessions returned will contain all listed datasets. For the other parameters,
- the session must contain at least one of the entries. NB: Wildcards are not permitted,
- however if wildcards property is False, regular expressions may be used for all but
- number and date_range.
-
- Parameters
- ----------
- dataset : str, list
- List of dataset names. Returns sessions containing all these datasets.
- A dataset matches if it contains the search string e.g. 'wheel.position' matches
- '_ibl_wheel.position.npy'
- date_range : str, list, datetime.datetime, datetime.date, pandas.timestamp
- A single date to search or a list of 2 dates that define the range (inclusive). To
- define only the upper or lower date bound, set the other element to None.
- lab : str, list
- A str or list of lab names, returns sessions from any of these labs
- number : str, int
- Number of session to be returned, i.e. number in sequence for a given date
- subject : str, list
- A list of subject nicknames, returns sessions for any of these subjects
- task_protocol : str, list
- The task protocol name (can be partial, i.e. any task protocol containing that str
- will be found)
- project(s) : str, list
- The project name (can be partial, i.e. any task protocol containing that str
- will be found)
- performance_lte / performance_gte : float
- Search only for sessions whose performance is less equal or greater equal than a
- pre-defined threshold as a percentage (0-100)
- users : str, list
- A list of users
- location : str, list
- A str or list of lab location (as per Alyx definition) name
- Note: this corresponds to the specific rig, not the lab geographical location per se
- json : dict
- example :
- ```python
- json = {
- "whisker_stims": {
- "amplitudes": {
- "abstract__contains": ['10-0','10-10','10_90-0']
- }
- }
- }
- ```
- allowed filter looups are listed here :
- https://docs.djangoproject.com/en/5.0/ref/models/querysets/#field-lookups
-
-
- dataset_types : str, list
- One or more of dataset_types
- details : bool
- If true also returns a dict of dataset details
- query_type : str, None
- Query cache ('local') or Alyx database ('remote')
- limit : int
- The number of results to fetch in one go (if pagination enabled on server)
-
-
-
-
- Returns
- -------
- list
- List of eids
- (list of dicts)
- If details is True, also returns a list of dictionaries, each entry corresponding to a
- matching session
- """
- _logger = logging.getLogger("search")
- query_type = query_type or self.mode # we set query_type = self.mode if query_type is None
- if query_type != "remote":
- return super().search(details=details, query_type=query_type, **kwargs)
-
- # loop over input arguments and build the url
- search_terms = self.search_terms(query_type=query_type)
- params = {} # {"django": kwargs.pop("django", "")}
-
- if isinstance(id, (list, tuple)):
- sessions = []
- for i in id:
- sessions.append(
- self.search(
- id=i, details=details, as_mode=as_mode, no_cache=no_cache, query_type=query_type, **kwargs
- )
- )
- return pd.DataFrame(sessions)
-
- if id is not None:
- params["id"] = self.to_eid(id)
- if params["id"] is None: # this means the id we supplied is not a valid eid
- raise ValueError(f"{id} is not a valid identifier, could not convert it to session uuid.")
- _logger.debug(f"kwargs : {kwargs}")
- for key, value in sorted(kwargs.items()):
- field = util.autocomplete(key, search_terms) # Validate and get full name
- _logger.debug(f"field : {field}")
- # check that the input matches one of the defined filters
- if field == "date_range":
- params[field] = [x.date().isoformat() for x in util.validate_date_range(value)]
- elif field == "laboratory":
- params["lab"] = value
- else:
- params[field] = value
- _logger.debug(f"params : {params}")
- # Make GET request
- ses = self.alyx.rest(
- self._search_endpoint,
- "list",
- no_cache=no_cache,
- query_type=query_type,
- **params,
- )
- if len(ses) > 1:
- _logger.info(f"Found {len(ses)} sessions.")
-
- if not details:
- return [item["id"] for item in ses]
- # list(util.LazyId(ses))
-
- sess_df = []
- for session_short_info in tqdm(ses, total=len(ses), delay=2, desc="Loading session details", file=stdout):
- session_detailed_info = self.alyx.rest(
- "sessions",
- "read",
- id=session_short_info["id"],
- no_cache=no_cache,
- query_type=query_type,
- )
- formated_session = self.to_session_details(session_detailed_info, as_mode=as_mode)
- sess_df.append(formated_session)
-
- try:
- sess_df = pd.DataFrame(sess_df)
- sess_df.index = sess_df.index.set_names("id")
- sess_df["start_datetime"] = pd.to_datetime(sess_df["start_datetime"], utc=True)
- except (ValueError, KeyError):
- warnings.warn("search result contained no entry")
- pass # could not create a dataframe form session details. Returning dict instead
- if id is not None:
- return sess_df.iloc[0]
- return sess_df
-
- def to_session_details(self, session_dict, as_mode=None):
- data_access_mode = (
- as_mode or self.data_access_mode
- ) # we set data_access_mode = self.data_access_mode if as_mode is None
-
- session_dict["date"] = str(datetime.fromisoformat(session_dict["start_time"]).date())
- session_dict["extended_qc"] = session_dict["extended_qc"] if session_dict["extended_qc"] is not None else {}
- session_dict["local_path"] = os.path.normpath(
- os.path.join(alyx_connector.params.get().LOCAL_ROOT, session_dict["rel_path"])
- )
- session_dict["remote_path"] = os.path.normpath(
- session_dict["path"]
- ) # path is the remote path initially (out from the database)
- # we set path depending on the data_access_mode
- session_dict["path"] = session_dict[data_access_mode + "_path"]
- session_dict["rel_path"] = Path(session_dict["rel_path"])
-
- session_dict["start_datetime"] = datetime.strptime(session_dict["start_time"], "%Y-%m-%dT%H:%M:%S%z")
-
- id = session_dict.pop("id")
-
- session_details = pd.Series(session_dict, name=id)
- return session_details
-
- def _download_datasets(self, dsets, **kwargs) -> List[Path]:
- """
- Download a single or multitude of datasets if stored on AWS, otherwise calls
- OneAlyx._download_dataset.
-
- NB: This will not skip files that are already present. Use check_filesystem instead.
-
- Parameters
- ----------
- dset : dict, str, pd.Series
- A single or multitude of dataset dictionaries
-
- Returns
- -------
- pathlib.Path
- A local file path or list of paths
- """
- # If all datasets exist on AWS, download from there.
- _logger = logging.getLogger("_download_datasets")
- try:
- if "exists_aws" in dsets and np.all(np.equal(dsets["exists_aws"].values, True)):
- _logger.info("Downloading from AWS")
- return self._download_aws(map(lambda x: x[1], dsets.iterrows()), **kwargs)
- except Exception as ex:
- _logger.debug(ex)
- return self._download_dataset(dsets, **kwargs)
-
- def _dset2url(self, dset, update_cache=True):
- """
- Converts a dataset into a remote HTTP server URL. The dataset may be one or more of the
- following: a dict from returned by the sessions endpoint or dataset endpoint, a record
- from the datasets cache table, or a file path. Unlike record2url, this method can convert
- dicts and paths to URLs.
-
- Parameters
- ----------
- dset : dict, str, pd.Series, pd.DataFrame, list
- A single or multitude of dataset dictionary from an Alyx REST query OR URL string
- update_cache : bool
- If True (default) and the dataset is from Alyx and cannot be converted to a URL,
- 'exists' will be set to False in the corresponding entry in the cache table.
-
- Returns
- -------
- str
- The remote URL of the dataset
- """
- _logger = logging.getLogger("_dset2url")
- did = None
- if isinstance(dset, str) and dset.startswith("http"):
- url = dset
- elif isinstance(dset, (str, Path)):
- url = self.path2url(dset)
- if not url:
- _logger.warning(f"Dataset {dset} not found in cache")
- return
- elif isinstance(dset, (list, tuple)):
- dset2url = partial(self._dset2url, update_cache=update_cache)
- return list(flatten(map(dset2url, dset)))
- else:
- # check if dset is dataframe, iterate over rows
- if hasattr(dset, "iterrows"):
- dset2url = partial(self._dset2url, update_cache=update_cache)
- url = list(map(lambda x: dset2url(x[1]), dset.iterrows()))
- elif "data_url" in dset: # data_dataset_session_related dict
- url = dset["data_url"]
- did = dset["id"]
- elif "file_records" not in dset: # Convert dataset Series to alyx dataset dict
- url = self.record2url(dset) # NB: URL will always be returned but may not exist
- is_int = all(isinstance(x, (int, np.int64)) for x in util.ensure_list(dset.name))
- did = np.array(dset.name)[-2:] if is_int else util.ensure_list(dset.name)[-1]
- else: # from datasets endpoint
- repo = getattr(getattr(self.web_client, "_par", None), "HTTP_DATA_SERVER", None)
- url = next(
- (
- fr["data_url"]
- for fr in dset["file_records"]
- if fr["data_url"] and fr["exists"] and fr["data_url"].startswith(repo or fr["data_url"])
- ),
- None,
- )
- did = dset["url"][-36:]
-
- # Update cache if url not found
- if did is not None and not url and update_cache:
- _logger.debug("Updating cache")
- if isinstance(did, str) and self._index_type("datasets") is int:
- (did,) = parquet.str2np(did).tolist()
- elif self._index_type("datasets") is str and not isinstance(did, str):
- did = parquet.np2str(did)
- # NB: This will be considerably easier when IndexSlice supports Ellipsis
- idx = [slice(None)] * int(self._cache["datasets"].index.nlevels / 2)
- self._cache["datasets"].loc[(*idx, *util.ensure_list(did)), "exists"] = False
- self._cache["_meta"]["modified_time"] = datetime.now()
-
- return url
-
- def _download_dataset(self, dset, cache_dir=None, update_cache=True, **kwargs) -> List[Path | None]:
- """
- Download a single or multitude of dataset from an Alyx REST dictionary.
-
- NB: This will not skip files that are already present. Use check_filesystem instead.
-
- Parameters
- ----------
- dset : dict, str, pd.Series, pd.DataFrame, list
- A single or multitude of dataset dictionary from an Alyx REST query OR URL string
- cache_dir : str, pathlib.Path
- The root directory to save the data to (default taken from ONE parameters)
- update_cache : bool
- If true, the cache is updated when filesystem discrepancies are encountered
-
- Returns
- -------
- pathlib.Path, list
- A local file path or list of paths
- """
- cache_dir = cache_dir or self.cache_dir
- url = self._dset2url(dset, update_cache=update_cache)
- if not url:
- return
- if isinstance(url, str):
- target_dir = str(Path(cache_dir, get_alf_path(url)).parent)
- return self._download_file(url, target_dir, **kwargs)
- # must be list of URLs
- valid_urls = list(filter(None, url))
- if not valid_urls:
- return [None] * len(url)
- target_dir = [str(Path(cache_dir, get_alf_path(x)).parent) for x in valid_urls]
- files = self._download_file(valid_urls, target_dir, **kwargs)
- # Return list of file paths or None if we failed to extract URL from dataset
- return [None if not x else files.pop(0) for x in url]
-
- def _tag_mismatched_file_record(self, url):
- fr = self.alyx.rest(
- "files",
- "list",
- django=f'dataset,{Path(url).name.split(".")[-2]},data_repository__globus_is_personal,False',
- no_cache=True,
- )
- if len(fr) > 0:
- json_field = fr[0]["json"]
- if json_field is None:
- json_field = {"mismatch_hash": True}
- else:
- json_field.update({"mismatch_hash": True})
- try:
- self.alyx.rest(
- "files",
- "partial_update",
- id=fr[0]["url"][-36:],
- data={"json": json_field},
- )
- except requests.exceptions.HTTPError as ex:
- warnings.warn(
- f"Failed to tag remote file record mismatch: {ex}\nPlease contact the database administrator."
- )
-
- def _download_file(self, url, target_dir, keep_uuid=False, file_size=None, hash=None) -> Path | List[Path]:
- """
- Downloads a single file or multitude of files from an HTTP webserver.
- The webserver in question is set by the AlyxClient object.
-
- Parameters
- ----------
- url : str, list
- An absolute or relative URL for a remote dataset
- target_dir : str, list
- Absolute path of directory to download file to (including alf path)
- keep_uuid : bool
- If true, the UUID is not removed from the file name (default is False)
- file_size : int, list
- The expected file size or list of file sizes to compare with downloaded file
- hash : str, list
- The expected file hash or list of file hashes to compare with downloaded file
-
- Returns
- -------
- pathlib.Path
- The file path of the downloaded file or files.
-
- Example
- -------
- >>> file_path = OneAlyx._download_file(
- ... 'https://example.com/data.file.npy', '/home/Downloads/subj/1900-01-01/001/alf')
- """
- assert not self.offline
- # Ensure all target directories exist
- [Path(x).mkdir(parents=True, exist_ok=True) for x in set(util.ensure_list(target_dir))]
-
- # download file(s) from url(s), returns file path(s) with UUID
- local_path, md5 = self.alyx.download_file(url, target_dir=target_dir, return_md5=True)
-
- # check if url, hash, and file_size are lists
- if isinstance(url, (tuple, list)):
- assert (file_size is None) or len(file_size) == len(url)
- assert (hash is None) or len(hash) == len(url)
- for args in zip(*map(util.ensure_list, (file_size, md5, hash, local_path, url))):
- self._check_hash_and_file_size_mismatch(*args)
-
- # check if we are keeping the uuid on the list of file names
- if keep_uuid:
- return local_path
-
- # remove uuids from list of file names
- if isinstance(local_path, (list, tuple)):
- return [alfio.remove_uuid_file(x) for x in local_path]
- else:
- return alfio.remove_uuid_file(local_path)
-
- def _check_hash_and_file_size_mismatch(self, file_size, hash, expected_hash, local_path, url):
- """
- Check to ensure the hash and file size of a downloaded file matches what is on disk
-
- Parameters
- ----------
- file_size : int
- The expected file size to compare with downloaded file
- hash : str
- The expected file hash to compare with downloaded file
- local_path: str
- The path of the downloaded file
- url : str
- An absolute or relative URL for a remote dataset
- """
- _logger = logging.getLogger("_check_hash_and_file_size_mismatch")
- # verify hash size
- hash = hash or hashfile.md5(local_path)
- hash_mismatch = hash and hash != expected_hash
- # verify file size
- file_size_mismatch = file_size and Path(local_path).stat().st_size != file_size
- # check if there is a mismatch in hash or file_size
- if hash_mismatch or file_size_mismatch:
- # post download, if there is a mismatch between Alyx and the newly downloaded file size
- # or hash, flag the offending file record in Alyx for database for maintenance
- hash_mismatch = expected_hash and expected_hash != hash
- file_size_mismatch = file_size and Path(local_path).stat().st_size != file_size
- if hash_mismatch or file_size_mismatch:
- url = url or self.path2url(local_path)
- _logger.debug(f"Tagging mismatch for {url}")
- # tag the mismatched file records
- self._tag_mismatched_file_record(url)
-
- @staticmethod
- def setup(base_url=None, **kwargs):
- """
- Set up OneAlyx for a given database
-
- Parameters
- ----------
- base_url : str
- An Alyx database URL. If None, the current default database is used.
- **kwargs
- Optional arguments to pass to one.params.setup.
-
- Returns
- -------
- OneAlyx
- An instance of OneAlyx for the newly set up database URL
- """
- base_url = base_url or alyx_connector.params.get_default_client()
- cache_map = alyx_connector.params.setup(client=base_url, **kwargs)
- return OneAlyx(base_url=base_url or alyx_connector.params.get(cache_map.DEFAULT).ALYX_URL)
-
- @util.refresh
- @util.parse_id
- def eid2path(self, eid, query_type=None) -> util.Listable(Path):
- """
- From an experiment ID gets the local session path
-
- Parameters
- ----------
- eid : str, UUID, pathlib.Path, dict, list
- Experiment session identifier; may be a UUID, URL, experiment reference string
- details dict or Path.
- query_type : str
- If set to 'remote', will force database connection
-
- Returns
- -------
- pathlib.Path, list
- A session path or list of session paths
- """
-
- # first try avoid hitting the database
- mode = query_type or self.mode
- if mode != "remote":
- cache_path = super().eid2path(eid)
- if cache_path or mode == "local":
- return cache_path
-
- # If eid is a list recurse through it and return a list
- if isinstance(eid, list):
- unwrapped = unwrap(self.path2eid)
- return [unwrapped(self, e, query_type="remote") for e in eid]
-
- # if it wasn't successful, query Alyx
- ses = self.alyx.rest("sessions", "list", django=f"pk,{eid}")
-
- if len(ses) == 0:
- return None
-
- data_repository = ses[0]["default_data_repository"]
- if data_repository is None:
- data_repository = ""
-
- return os.path.join(
- data_repository,
- ses[0]["subject"],
- ses[0]["start_time"][:10],
- str(ses[0]["number"]).zfill(3),
- )
-
- @util.refresh
- def path2eid(self, path_obj: Union[str, Path], query_type=None) -> util.Listable(Path):
- import re
-
- """
- From a local path, gets the experiment ID
-
- Parameters
- ----------
- path_obj : str, pathlib.Path, list
- Local path or list of local paths
- query_type : str
- If set to 'remote', will force database connection
-
- Returns
- -------
- str, list
- An eid or list of eids
- """
- # If path_obj is a list recurse through it and return a list
- if isinstance(path_obj, list):
- path_obj = [Path(x) for x in path_obj]
- eid_list = []
- unwrapped = unwrap(self.path2eid)
- for p in path_obj:
- eid_list.append(unwrapped(self, p))
- return eid_list
- # else ensure the path ends with mouse,date, number
- try:
- path_obj = re.findall(r"(\w+(?:\\|\/)\d{4}-\d{2}-\d{2}(?:\\|\/)\d+)", path_obj)[0]
- except IndexError: # could not match anything
- pass
-
- path_obj = Path(path_obj)
-
- # try the cached info to possibly avoid hitting database
- mode = query_type or self.mode
- if mode != "remote":
- cache_eid = super().path2eid(path_obj)
- if cache_eid or mode == "local":
- return cache_eid
-
- session_path = get_session_path(path_obj)
- # if path does not have a date and a number return None
- if session_path is None:
- return None
-
- # if not search for subj, date, number XXX: hits the DB
- search = unwrap(self.search)
- uuid = search(
- subject=session_path.parts[-3],
- date_range=session_path.parts[-2],
- number=session_path.parts[-1],
- query_type="remote",
- )
-
- # Return the uuid if any
- return uuid[0] if uuid else None
-
- @util.refresh
- def path2url(self, filepath, query_type=None) -> str:
- """
- Given a local file path, returns the URL of the remote file.
-
- Parameters
- ----------
- filepath : str, pathlib.Path
- A local file path
- query_type : str
- If set to 'remote', will force database connection
-
- Returns
- -------
- str
- A URL string
- """
- query_type = query_type or self.mode
- if query_type != "remote":
- return super().path2url(filepath)
- eid = self.path2eid(filepath)
- try:
- (dataset,) = self.alyx.rest("datasets", "list", session=eid, name=Path(filepath).name)
- return next(r["data_url"] for r in dataset["file_records"] if r["data_url"] and r["exists"])
- except (ValueError, StopIteration):
- raise alferr.ALFObjectNotFound(f"File record for {filepath} not found on Alyx")
-
- @util.parse_id
- def type2datasets(self, eid, dataset_type, details=False):
- """
- Get list of datasets belonging to a given dataset type for a given session
-
- Parameters
- ----------
- eid : str, UUID, pathlib.Path, dict
- Experiment session identifier; may be a UUID, URL, experiment reference string
- details dict or Path.
- dataset_type : str, list
- An Alyx dataset type, e.g. camera.times or a list of dtypes
- details : bool
- If True, a datasets DataFrame is returned
-
- Returns
- -------
- np.ndarray, dict
- A numpy array of data, or DataFrame if details is true
- """
- assert self.mode != "local" and not self.offline, "Unable to connect to Alyx in local mode"
- if isinstance(dataset_type, str):
- restriction = f"session__id,{eid},dataset_type__name,{dataset_type}"
- elif isinstance(dataset_type, collections.abc.Sequence):
- restriction = f"session__id,{eid},dataset_type__name__in,{dataset_type}"
- else:
- raise TypeError("dataset_type must be a str or str list")
- datasets = util.datasets2records(self.alyx.rest("datasets", "list", django=restriction))
- return datasets if details else datasets["rel_path"].sort_values().values
-
- def dataset2type(self, dset) -> str:
- """Return dataset type from dataset.
-
- NB: Requires an Alyx database connection
-
- Parameters
- ----------
- dset : str, np.ndarray, tuple
- A dataset name, dataset uuid or dataset integer id
-
- Returns
- -------
- str
- The dataset type
- """
- assert self.mode != "local" and not self.offline, "Unable to connect to Alyx in local mode"
- # Ensure dset is a str uuid
- if isinstance(dset, str) and not is_uuid_string(dset):
- dset = self._dataset_name2id(dset)
- if isinstance(dset, np.ndarray):
- dset = parquet.np2str(dset)[0]
- if isinstance(dset, tuple) and all(isinstance(x, int) for x in dset):
- dset = parquet.np2str(np.array(dset))
- if not is_uuid_string(dset):
- raise ValueError("Unrecognized name or UUID")
- return self.alyx.rest("datasets", "read", id=dset)["dataset_type"]
-
- def describe_revision(self, revision, full=False):
- """Print description of a revision
-
- Parameters
- ----------
- revision : str
- The name of the revision (without '#')
- full : bool
- If true, returns the matching record
-
- Returns
- -------
- None, dict
- None if full is false or no record found, otherwise returns record as dict
- """
- assert self.mode != "local" and not self.offline, "Unable to connect to Alyx in local mode"
- try:
- rec = self.alyx.rest("revisions", "read", id=revision)
- print(rec["description"])
- if full:
- return rec
- except requests.exceptions.HTTPError as ex:
- if ex.response.status_code != 404:
- raise ex
- print(f'revision "{revision}" not found')
-
- def _dataset_name2id(self, dset_name, eid=None):
- # TODO finish function
- datasets = self.list_datasets(eid) if eid else self._cache["datasets"]
- # Get ID of fist matching dset
- for idx, rel_path in datasets["rel_path"].items():
- if rel_path.endswith(dset_name):
- return idx[-1] # (eid, did)
- raise ValueError(f"Dataset {dset_name} not found in cache")
-
- @util.refresh
- @util.parse_id
- def get_details(self, eid: str, full: bool = False, query_type=None):
- """Return session details for a given session
-
- Parameters
- ----------
- eid : str, UUID, pathlib.Path, dict, list
- Experiment session identifier; may be a UUID, URL, experiment reference string
- details dict or Path.
- full : bool
- If True, returns a DataFrame of session and dataset info
- query_type : {'local', 'refresh', 'auto', 'remote'}
- The query mode - if 'local' the details are taken from the cache tables; if 'remote'
- the details are returned from the sessions REST endpoint; if 'auto' uses whichever
- mode ONE is in; if 'refresh' reloads the cache before querying.
-
- Returns
- -------
- pd.Series, pd.DataFrame, dict
- in local mode - a session record or full DataFrame with dataset information if full is
- True; in remote mode - a full or partial session dict
-
- Raises
- ------
- ValueError
- Invalid experiment ID (failed to parse into eid string)
- requests.exceptions.HTTPError
- [Errno 404] Remote session not found on Alyx
- """
- if (query_type or self.mode) == "local":
- return super().get_details(eid, full=full)
- # If eid is a list of eIDs recurse through list and return the results
- if isinstance(eid, list):
- details_list = []
- for p in eid:
- details_list.append(self.get_details(p, full=full))
- return details_list
- # load all details
- dets = self.alyx.rest("sessions", "read", eid)
- if full:
- return dets
- # If it's not full return the normal output like from a one.search
- det_fields = [
- "subject",
- "start_time",
- "number",
- "lab",
- "projects",
- "url",
- "task_protocol",
- "local_path",
- ]
- out = {k: v for k, v in dets.items() if k in det_fields}
- out["projects"] = ",".join(out["projects"])
- out.update(
- {
- "local_path": self.eid2path(eid),
- "date": datetime.fromisoformat(out["start_time"]).date(),
- }
- )
- return out
-
- ### METHODS ADDED BY TIMOTHE TO EXTEND THE USE OF THE API
-
- def get_data_repository_path(self, repository_name):
- repo_data = self.alyx.rest("data-repository", "read", repository_name)
- repo_path = r"\\" + os.path.join(repo_data["hostname"], repo_data["globus_path"].lstrip("/"))
- return os.path.normpath(repo_path)
-
- def read_sql(self, query):
- raise NotImplementedError
-
- def create_session(self, data_dict):
- import re
-
- data_dict = data_dict.copy()
- data_dict["number"] = str(int(data_dict["number"])) # remove leading zeros if any
- try: # a session have been found with same 3 parameters, don't allow to process to registering.
- _searched_session = self.search(
- subject=data_dict["subject"],
- number=data_dict["number"],
- date_range=data_dict["start_time"][:10],
- users=data_dict["users"],
- details=True,
- )
- url = re.sub(r"\/sessions", r"/actions/session", _searched_session["url"].item())
- raise ValueError(
- f"This session path is already registered ! See here : {url}\n You probably need to change the number "
- "of the session for this animald/date combo"
- )
- except KeyError: # no session have benn found, all is well, can proceed
- pass
-
- self.alyx.rest("sessions", "create", data=data_dict)
-
- def default_session_data(self):
- return {"lab": "HaissLab", "task_protocol": ""}
-
- @staticmethod
- def explorer(path):
- import subprocess
-
- path = os.path.normpath(path)
- if not os.path.exists(path):
- raise IOError(f"Path {path} does not exist")
- if os.path.isfile(path):
- path = os.path.dirname(path)
-
- pre_cmd = f"explorer.exe {path}"
- subprocess.call(pre_cmd)
- return
- # this part is to open in atab instead of window. Buggy for now.
- if path[:2] == r"\\":
- pre_cmd = f"pushd {path}; "
- # path = os.path.join(*[item for item in selected_folder.split(os.sep) if item != ''][1:])
- # #this removes the first object of the path
- else:
- pre_cmd = 'cd "{pateh}; "'
- subprocess.call(pre_cmd + r"start .")
- # subprocess.Popen(r'explorer '+f'{os.path.dirname(path)},select,{os.path.basename(path)}')
-
- def collection_path(self, eid, collections):
- return os.path.join(self.current_remote_repository_path, self.eid2path(eid), collections)
-
- def set_current_remote_repository(self, repo_name):
- self.current_remote_repository_path = self.get_data_repository_path(repo_name)
-
- def get_parts_from_path(self, input_path):
- import re
-
- subject, date, number = re.findall(r"(\w+)(?:\\|\/)(\d{4}-\d{2}-\d{2})(?:\\|\/)(\d+)", input_path)[0]
- return {"subject": subject, "date": date, "number": number}
-
- def get_json_params(self, eid):
- return self.alyx.rest("sessions", "read", eid)["json"]
-
- def get_extended_qc(self, eid):
- return self.alyx.rest("sessions", "read", eid)["extended_qc"]
-
- def display_session_info(self, session_details):
- from IPython.display import Markdown, display
-
- session_data_link = f"[Data pathes](file:{os.path.normpath(session_details.path)}) pointing in {self.data_access_mode} mode."
- metadatas_link = f"[Metadatas]({session_details.url}) obtained in {self.mode} mode."
- uuid = f"(uuid is '{session_details.name}')"
- display(Markdown(f"Session {session_details.rel_path}. {session_data_link} {metadatas_link} {uuid}"))
-
- @wraps(MultiSessionPlaceholder)
- def multisession(*args, **kwargs):
- return MultiSessionPlaceholder(*args, **kwargs)
-
- def update_session_info(self, session_details, json={}, extended_qc={}, **kwargs):
- _logger = logging.getLogger("update_session_info")
-
- data = {}
- if len(json):
- base_json = session_details.json
- if base_json is None:
- base_json = {}
- base_json.update(json)
- data["json"] = base_json
-
- if len(extended_qc):
- base_ext_qc = session_details.extended_qc
- if base_ext_qc is None:
- base_ext_qc = {}
- base_ext_qc.update(extended_qc)
- data["extended_qc"] = base_ext_qc
-
- data.update(kwargs)
-
- _logger.info(f"Updating session {session_details.rel_path}")
- ans = input(f"Data OK ? (OK or Cancel) : {data}")
- if ans != "OK":
- _logger.info("Aborting")
- return
- _logger.info("Applying changes")
- self.alyx.rest("sessions", "partial_update", id=session_details.name, data=data)
- self.alyx.delete_cache()
-
- def push_files(self, file_list, *, session_details, relative=False, overwrite_policy="raise"):
- """
- The function push_processed_files copies a list of files to a remote session directory,
- and handles various overwrite policies.
-
- Args:
-
- - file_list (list of str): a list of local file paths to be copied to the remote session directory.
- - session_details (SessionDetails): an object containing the session details.
- - relative: If the string representing the path of the files are absolute or relative from
- INSIDE the session folder (ex : 'D:\\LOCAL_DATA\\wm25\\2022-08-05\\001\\a_folder\\test.file'
- is an absolute path and 'a_folder\test.file' is a relative path)
- - overwrite_policy (str, optional): the overwrite policy. Possibilities are:
- - "raise" (raise an exception if a file with the same name already exists in the remote directory),
- - "skip" (skip copying the file if a file with the same name already exists in the remote directory),
- - "overwrite" (overwrite the file with the same name in the remote directory),
- - "most_recent" (copy the file only if it is more recent than the file
- with the same name in the remote directory),
- - "erase" (erase the existing file in the remote directory if a file with the same name already exists,
- then copy a new one in place.) Prefer choosing overwrite in most situations).
-
- Default is "raise".
-
- Returns:
-
- a dictionary with two keys:
- - "copied" : a list of file paths that have been copied to the remote session directory.
- - "ignored" : a list of file paths that could not be copied (either because they were not found or
- because they were excluded by the overwrite policy).
- """
-
- import shutil
-
- def get_relative_path(absolute_path, common_root_path):
- """Compare an input path and a path with a common root with the input path, and returns only the part of
- the input path that is not shared with the _common_root_path.
-
- Args:
- input_path (TYPE): DESCRIPTION.
- common_root_base (TYPE): DESCRIPTION.
-
- Returns:
- TYPE: DESCRIPTION.
-
- """
- absolute_path = os.path.normpath(absolute_path)
- common_root_path = os.path.normpath(common_root_path)
-
- commonprefix = os.path.commonprefix([common_root_path, absolute_path])
- if commonprefix == "":
- raise IOError(f"These two pathes have no common root path : {absolute_path} and {common_root_path}")
- return os.path.relpath(absolute_path, start=commonprefix)
-
- overwrite_policies = ["raise", "skip", "erase", "most_recent", "overwrite"]
- if overwrite_policy not in overwrite_policies:
- raise NotImplementedError(
- f"Value {overwrite_policy} for overwrite_policy is not supported. "
- f"Possibilities are : {overwrite_policies}"
- )
-
- session_local_root = session_details["local_path"]
- session_remote_root = session_details["remote_path"]
-
- if not isinstance(file_list, (list, tuple, np.ndarray)):
- file_list = [file_list]
-
- if relative:
- file_list = [os.path.join(session_local_root, session_details.rel_path, file) for file in file_list]
-
- source_files = [] # file paths that have been copied
- # files paths of the copies of the one in the list above (ordered similarly)
- dest_files = []
-
- overwrite_raise_list = (
- []
- ) # stores files that already exist in remote folder in case we have 'raise' overwrite_policy, to print to user
- file_not_found_warning = []
-
- # MAKE THE LIST OF FILES THAT WILL BE COPIED
- for local_path in file_list:
- if not os.path.isfile(local_path):
- file_not_found_warning.append(local_path)
- continue
-
- try:
- relative_path = get_relative_path(local_path, session_local_root)
- except IOError:
- file_not_found_warning.append(local_path)
- continue
-
- remote_path = os.path.join(session_remote_root, relative_path)
-
- if os.path.isfile(remote_path):
- if overwrite_policy == "raise":
- overwrite_raise_list.append(local_path)
- elif overwrite_policy == "skip":
- logging.getLogger().info(f"Skipping file {remote_path}")
- continue
- elif overwrite_policy == "erase":
- os.remove(remote_path)
- elif overwrite_policy == "most_recent":
- if (
- os.stat(remote_path).st_mtime > os.stat(local_path).st_mtime
- ): # remote_path is more recent (higher time value)
- continue
- elif overwrite_policy == "overwrite":
- pass
- # else if overwrite, we just do nothing and files will be overwritten during shutil.copy operation
-
- source_files.append(local_path)
- dest_files.append(remote_path)
-
- if len(file_not_found_warning):
- logging.getLogger().warning(
- "These files were not found or are not inside the session local folder, "
- f"and therefore cannot be copied :\nFiles:\n{file_not_found_warning}"
- )
-
- if len(overwrite_raise_list):
- raise IOError(
- f"The files listed below already exist in the destination : {session_remote_root}\n"
- "No file have been copied to avoid mistakes. "
- "You can check the content of the destination folder manually, "
- "or change the 'overwrite_policy' argument of this function (beware of data losses !).\n"
- f"Files :\n {overwrite_raise_list}"
- )
-
- # APPLY THE COPY
- for local_path, remote_path in zip(source_files, dest_files):
- container_dir = os.path.dirname(remote_path)
- # make destination dir if it doesn't exist already
- os.makedirs(container_dir, exist_ok=True)
- shutil.copy(local_path, remote_path)
-
- return {
- "copied": source_files,
- "ignored": list(set(file_list).difference(set(source_files))),
- }
-
- def copy_files(self, source_file_list, source_root, destination_root, overwrite_policy="raise"):
- def get_relative_path(absolute_path, common_root_path):
- """
- Compare an input path and a path with a common root with the input path, and returns only the part of the
- input path that is not shared with the _common_root_path.
-
- Args:
- input_path (TYPE): DESCRIPTION.
- common_root_base (TYPE): DESCRIPTION.
-
- Returns:
- TYPE: DESCRIPTION.
-
- """
- absolute_path = os.path.normpath(absolute_path)
- common_root_path = os.path.normpath(common_root_path)
-
- commonprefix = os.path.commonprefix([common_root_path, absolute_path])
- if commonprefix == "":
- raise IOError(f"These two pathes have no common root path : {absolute_path} and {common_root_path}")
- return os.path.relpath(absolute_path, start=commonprefix)
-
- # Check if the overwrite_policy is supported
- overwrite_policies = ["raise", "skip", "erase", "most_recent", "overwrite"]
- if overwrite_policy not in overwrite_policies:
- raise ValueError(
- f"Unsupported value for overwrite_policy: {overwrite_policy}. Possibilities are: {overwrite_policies}"
- )
-
- # Iterate through the list of source files and copy them to the destination
- copied_files = []
- ignored_files = []
-
- for source_file_path in source_file_list:
- # Get the relative path of the source file with respect to the source root
- relative_path = get_relative_path(source_file_path, source_root)
-
- # Create the destination path by joining the destination root and the relative path
- destination_path = os.path.join(destination_root, relative_path)
-
- # Check if the file exists at the source location and is a file
- if not os.path.isfile(source_file_path):
- ignored_files.append(source_file_path)
- continue
-
- # Check if the file exists at the destination location and apply the overwrite policy accordingly
- if os.path.isfile(destination_path):
- if overwrite_policy == "raise":
- raise ValueError(f"File already exists at the destination: {destination_path}")
- elif overwrite_policy == "skip":
- ignored_files.append(source_file_path)
- continue
- elif overwrite_policy == "erase":
- os.remove(destination_path)
- elif overwrite_policy == "most_recent":
- if os.stat(destination_path).st_mtime > os.stat(source_file_path).st_mtime:
- ignored_files.append(source_file_path)
- continue
- elif overwrite_policy == "overwrite":
- pass
-
- # Create the directory structure at the destination if it does not exist already
- os.makedirs(os.path.dirname(destination_path), exist_ok=True)
-
- # Copy the file from source to destination
- shutil.copy(source_file_path, destination_path)
-
- # Append the copied file to the list of copied files
- copied_files.append(source_file_path)
-
- # Return a dictionary with the list of copied and ignored files
- return {"copied": copied_files, "ignored": ignored_files}
-
- def pull_files(self, file_list, *, session_details, relative=False, overwrite_policy="raise"):
- pass
+# if __name__ == "__main__":
+
+# class WebConnector(metaclass=Singleton):
+# """An API for searching and loading data through the Alyx database"""
+
+# def __init__(
+# self,
+# username=None,
+# password=None,
+# base_url=None,
+# cache_dir=None,
+# mode="auto",
+# data_access_mode="local",
+# wildcards=True,
+# **kwargs,
+# ):
+# """An API for searching and loading data through the Alyx database
+
+# Parameters
+# ----------
+# mode : str
+# Query mode, options include 'auto', 'local' (offline) and 'remote' (online only). Most
+# methods have a `query_type` parameter that can override the class mode.
+# wildcards : bool
+# If true, methods allow unix shell style pattern matching, otherwise regular
+# expressions are supported
+# cache_dir : str, Path
+# Path to the data files. If Alyx parameters have been set up for this location,
+# an OneAlyx instance is returned. If data_dir and base_url are None, the default
+# location is used.
+# base_url : str
+# An Alyx database URL. The URL must start with 'http'.
+# username : str
+# An Alyx database login username.
+# password : str
+# An Alyx database password.
+# cache_rest : str
+# If not in 'local' mode, this determines which http request types to cache. Default is
+# 'GET'. Use None to deactivate cache (not recommended).
+# """
+
+# # Load Alyx Web client
+# self.web_client = AlyxClient(
+# username=username,
+# password=password,
+# base_url=base_url,
+# cache_dir=cache_dir,
+# **kwargs,
+# )
+
+# self._registration_client = RegistrationClient(self)
+
+# self.data_access_mode = data_access_mode
+
+# self._search_endpoint = "sessions"
+
+# # get parameters override if inputs provided
+# super().__init__(mode=mode, wildcards=wildcards, cache_dir=cache_dir)
+
+# def set_data_access_mode(self, mode):
+# available_modes = [
+# "local",
+# "remote",
+# ] # TODO : add ability to go auto mode later. (if possible, still have to think about it)
+# if mode in available_modes:
+# self.data_access_mode = mode
+# self.alyx.delete_cache() # delete rest cache in case there is local / remote path stored inside
+# else:
+# raise ValueError(f"data_access_mode must be one of : {available_modes}")
+
+# def __repr__(self):
+# return f'One ({"off" if self.offline else "on"}line, {self.alyx.base_url})'
+
+# def load_cache(self, cache_dir=None, clobber=False, tag=None):
+# """
+# Load parquet cache files. If the local cache is sufficiently old, this method will query
+# the database for the location and creation date of the remote cache. If newer, it will be
+# download and loaded.
+
+# Note: Unlike refresh_cache, this will always reload the local files at least once.
+
+# Parameters
+# ----------
+# cache_dir : str, pathlib.Path
+# An optional directory location of the parquet files, defaults to One.cache_dir.
+# clobber : bool
+# If True, query Alyx for a newer cache even if current (local) cache is recent.
+# tag : str
+# An optional Alyx dataset tag for loading cache tables containing a subset of datasets.
+# """
+# _logger = logging.getLogger("load_cache")
+# cache_meta = self._cache.get("_meta", {})
+# cache_dir = cache_dir or self.cache_dir
+# # If user provides tag that doesn't match current cache's tag, always download.
+# # NB: In the future 'database_tags' may become a list.
+# current_tags = [x.get("database_tags") for x in cache_meta.get("raw", {}).values() or [{}]]
+# tag = tag or current_tags[0] # For refreshes take the current tag as default
+# different_tag = any(x != tag for x in current_tags)
+# if not clobber or different_tag:
+# super().load_cache(cache_dir) # Load any present cache
+# cache_meta = self._cache.get("_meta", {}) # TODO Make walrus when we drop 3.7 support
+# expired = self._cache and cache_meta["expired"]
+# if not expired or self.mode in ("local", "remote"):
+# return
+
+# # Warn user if expired
+# if cache_meta["expired"] and cache_meta.get("created_time", False) and not self.alyx.silent:
+# age = datetime.now() - cache_meta["created_time"]
+# t_str = f"{age.days} day(s)" if age.days >= 1 else f"{np.floor(age.seconds / (60 * 2))} hour(s)"
+# _logger.info(f"cache over {t_str} old")
+
+# try:
+# # Determine whether a newer cache is available
+# cache_info = self.alyx.get(f'cache/info/{tag or ""}'.strip("/"), expires=True)
+# assert tag == cache_info.get("database_tags")
+
+# # Check version compatibility
+# min_version = packaging.version.parse(cache_info.get("min_api_version", "0.0.0"))
+# if packaging.version.parse(alyx_connector.__version__) < min_version:
+# warnings.warn(f"Newer cache tables require ONE version {min_version} or greater")
+# return
+
+# # Check whether remote cache more recent
+# remote_created = datetime.fromisoformat(cache_info["date_created"])
+# local_created = cache_meta.get("created_time", None)
+# if local_created and (remote_created - local_created) < timedelta(minutes=1):
+# _logger.info("No newer cache available")
+# return
+
+# # Download the remote cache files
+# _logger.info("Downloading remote caches...")
+# files = self.alyx.download_cache_tables(cache_info.get("location"), cache_dir)
+# assert any(files)
+# super().load_cache(cache_dir) # Reload cache after download
+# except (requests.exceptions.HTTPError, HTTPError) as ex:
+# _logger.debug(ex)
+# ## REMOVED THIS WARNING FOR NOW AS I CAN'T FIND IF IT IS ACTUALLY USEFULL TO HAVE A REMOTE CACHE WHEN
+# # SETUPING A LOCAL USE OF ALYX LIKE WE DO
+# # _logger.error('Failed to load the remote cache file')
+# self.mode = "remote"
+# except (ConnectionError, requests.exceptions.ConnectionError) as ex:
+# _logger.debug(ex)
+# _logger.error("Failed to connect to Alyx")
+# self.mode = "local"
+
+# @property
+# def alyx(self):
+# """one.webclient.AlyxClient: The Alyx Web client"""
+# return self.web_client
+
+# @property
+# def register(self):
+# return self._registration_client
+
+# @property
+# def cache_dir(self):
+# """pathlib.Path: The location of the downloaded file cache"""
+# return self.web_client.cache_dir
+
+# @util.refresh
+# def search_terms(self, query_type=None):
+# """
+# Returns a list of search terms to be passed as kwargs to the search method
+
+# Parameters
+# ----------
+# query_type : str
+# If 'remote', the search terms are largely determined by the REST endpoint used
+
+# Returns
+# -------
+# tuple
+# Tuple of search strings
+# """
+# if (query_type or self.mode) != "remote":
+# # Return search terms from REST schema
+# return self._search_terms
+# fields = self.alyx.rest_schemes[self._search_endpoint]["list"]["fields"]
+# # 'laboratory' already in search terms
+# excl = ("lab",)
+# return tuple({*self._search_terms, *(x["name"] for x in fields if x["name"] not in excl)})
+
+# def describe_dataset(self, dataset_type=None):
+# """Print a dataset type description.
+
+# NB: This requires an Alyx database connection.
+
+# Parameters
+# ----------
+# dataset_type : str
+# A dataset type or dataset name
+
+# Returns
+# -------
+# dict
+# The Alyx dataset type record
+# """
+# _logger = logging.getLogger("describe_dataset")
+# assert self.mode != "local" and not self.offline, "Unable to connect to Alyx in local mode"
+# if not dataset_type:
+# return self.alyx.rest("dataset-types", "list")
+# try:
+# assert isinstance(dataset_type, str) and not is_uuid_string(dataset_type)
+# _logger.disabled = True
+# out = self.alyx.rest("dataset-types", "read", dataset_type)
+# except (AssertionError, requests.exceptions.HTTPError):
+# # Try to get dataset type from dataset name
+# out = self.alyx.rest("dataset-types", "read", self.dataset2type(dataset_type))
+# finally:
+# _logger.disabled = False
+# print(out["description"])
+# return out
+
+# def change_session_data_mode(self, session_details, mode):
+# session_details["full_path"] = session_details[mode + "_full_path"]
+# return session_details
+
+# #### LIST DATASETS
+# @util.refresh
+# def list_datasets(
+# self,
+# eid=None,
+# details=False,
+# query_type=None,
+# as_mode=None,
+# no_cache=False,
+# **filters,
+# ) -> np.ndarray | pd.DataFrame | List[str]:
+# """_summary_
+
+# Args:
+# eid (str, optional): Session id (alias or pk). Does not need to be supplied only if
+# using session_details. Defaults to None.
+# details (bool, optional): If False, will only return a list of absolute file paths
+# (obtained from the column full_path of the dataset dataframe).
+# Otherwise will return a full dataframe of all datasets found for this session
+# Defaults to False.
+# query_type (str or None, optional): Wether to perform the metadata fetch
+# (only if using eid) from local cache or on alyx. If None, uses the current mode of
+# the connector instance. Defaults to None.
+# as_mode (str or None, optional): Wether to perform the full_path construction using
+# default current (None), 'local' or 'remote' mode. Defaults to None.
+# session_details (pd.Series, optional): The pandas series containing
+# data_dataset_session_related information.
+# If not supplied, the function must be supplied a session id (eid, first argument)
+# to get this session_details variable internally. Defaults to None.
+
+# Other filtering keys are accepted :
+# (the value on wich you search must match perfectly. Key must also match any of the
+# below. key and values are case sensitive)
+# - extra
+# - object
+# - attribute
+# - subject
+# - date
+# - number
+# - revision
+# - collection
+# - extension
+
+# - dataset_type
+# - name (from dataset, ex trials.eventTimelines)
+# - file_name
+
+# - relative_path
+# - exists
+# - created_by
+# - created_datetime
+# - data_repository
+# - hash
+# - file_size
+# - tags
+
+# Raises:
+# NotImplementedError: For now, using mode (metadata) local will not work as the cache system to retrive data
+# has not been tested for.
+
+# Returns:
+# Union[list, pd.DataFrame]: A list of matching files full_paths (if details = False) or a dataframe of all
+# matching file records components and metadata.
+# """
+
+# import natsort
+
+# _logger = logging.getLogger("list_datasets")
+
+# def flatten_pathlist(x):
+# if isinstance(x, (list, tuple)):
+# return natsort.natsorted([a for i in x for a in flatten(i)])
+# else:
+# return natsort.natsorted([x])
+
+# # OBTAINING A SESSION_DETAILS (IN WHICH RESIDES FILES INFO)
+
+# data_access_mode = as_mode or self.data_access_mode
+# if hasattr(eid, "keys") and "data_dataset_session_related" in eid.keys():
+# session_details = (
+# eid.copy()
+# ) # either a pd.series of dict, copy and key getters/setters works both cases
+# try:
+# eid = session_details["id"]
+# except KeyError:
+# eid = session_details.name
+# session_details["id"] = eid
+# else:
+# _eid = eid
+# # Ensure we have a UUID str
+# eid = self.to_eid(eid)
+# if eid is None:
+# raise ValueError(
+# f"The session id {_eid} supplied seem to not be existing. Check that you are in 'remote' mode "
+# "(not data_access_mode) and check that the session exists on a webpage."
+# )
+# if (query_type or self.mode) != "remote":
+# raise NotImplementedError
+# ## TODO : GET BACK THE DATA FROM THE CACHE AFTER CHANGE IN DATA MANAGEMENT METHODOLOGY
+# # return super().list_datasets(eid, details=details, query_type=query_type, **filters)
+
+# session_details = self.to_session_details(
+# self.alyx.rest("sessions", "read", id=eid, query_type=query_type, no_cache=no_cache)
+# )
+# # session, datasets = util.ses2records(self.alyx.rest('sessions', 'read', id=eid))
+# # self._update_cache_from_records(sessions=session, datasets=datasets.copy()
+# # if datasets is not None else datasets)
+# # Add to cache tables # TODO : DO ADD THAT FUNCTIONNALITY AGAIN
+
+# datasets = copy.deepcopy(session_details["data_dataset_session_related"])
+# # copy to not change the session_details in case they are suplied by user as input
+
+# file_records = []
+# for dataset in datasets:
+# files = dataset.pop("file_records")
+# dataset["session#"] = dataset.pop("session")
+# dataset["dataset#"] = dataset.pop("id")
+# dataset["dataset_url"] = dataset.pop("url")
+# dataset["dataset_admin_url"] = dataset.pop("admin_url")
+# dataset["local_root"] = alyx_connector.params.get().LOCAL_ROOT
+# for file in files:
+# # file["file_url"] = file.pop("url")
+# # file["file_admin_url"] = file.pop("admin_url")
+# file["file#"] = file.pop("id")
+# file.update(
+# {
+# "remote_full_path": os.path.normpath(
+# os.path.join(dataset["remote_root"], file["relative_path"])
+# ),
+# "local_full_path": os.path.normpath(
+# os.path.join(dataset["local_root"], file["relative_path"])
+# ),
+# }
+# )
+# # remote or local depending on current mode
+# file["full_path"] = file[data_access_mode + "_full_path"]
+# file.update(dataset)
+# file_records.append(file)
+
+# dataframe = pd.DataFrame(file_records)
+# if dataframe.empty:
+# _logger.warning(
+# "No dataset found for this session. Are you sure you ran the file registration routine ?"
+# )
+# return dataframe if details else []
+
+# dataframe.set_index(["session#", "dataset#", "file#"])
+
+# # FILTERING THE ROWS BASED ON USER INPUT
+# # query_string = ' & '.join([f'{k} == {repr(v)}' for k, v in filters.items()])
+# if filters:
+# if "filename" in filters.keys():
+# # allowing filename for retrocompatibility
+# filters["file_name"] = filters.pop("filename")
+# queries = []
+# for key, value in filters.items():
+# # if the columns correspunding to filter is object or string, we try to match using wildcard type
+# # syntax as input
+# # to do that we convert * wildcards to .* in regex and add a ^ and $ at start and end of pattern
+# # to force a complete string length match.
+
+# if dataframe[key].dtype is npdtype("O") or dataframe[key].dtype is npdtype(str):
+# queries.append(f"{key}.str.match('^' + {repr(value).replace('*', '.*')} + '$') ") #
+# # if the columns is not a sting, we match it directly.
+# else:
+# queries.append(f"{key} == {value}")
+
+# # example of a query string : query_string = "exists == True & subject.str.match('wm.*$')"
+# query_string = " & ".join(queries)
+
+# try:
+# dataframe = dataframe.query(query_string, engine="python")
+# except (KeyError, pd.errors.UndefinedVariableError) as e:
+# raise KeyError(f"Cannot use the key {str(e)} to filter for datasets")
+
+# return dataframe if details else list(dataframe["full_path"])
+
+# @util.refresh
+# def pid2eid(self, pid: str, query_type=None) -> Tuple[str, str]:
+# """
+# Given an Alyx probe UUID string, returns the session id string and the probe label
+# (i.e. the ALF collection).
+
+# NB: Requires a connection to the Alyx database.
+
+# Parameters
+# ----------
+# pid : str, uuid.UUID
+# A probe UUID
+# query_type : str
+# Query mode - options include 'remote', and 'refresh'
+
+# Returns
+# -------
+# str
+# Experiment ID (eid)
+# str
+# Probe label
+# """
+# query_type = query_type or self.mode
+# if query_type != "remote":
+# self.refresh_cache(query_type)
+# if query_type == "local" and "insertions" not in self._cache.keys():
+# raise NotImplementedError("Converting probe IDs required remote connection")
+# rec = self.alyx.rest("insertions", "read", id=str(pid))
+# return rec["session"], rec["name"]
+
+# #### SEARCH
+# def search(
+# self,
+# id=None,
+# *,
+# details=False,
+# query_type=None,
+# as_mode=None,
+# no_cache=False,
+# **kwargs,
+# ):
+# """
+# Searches sessions matching the given criteria and returns a list of matching eids
+
+# For a list of search terms, use the method
+
+# one.search_terms(query_type='remote')
+
+# For all of the search parameters, a single value or list may be provided. For dataset,
+# the sessions returned will contain all listed datasets. For the other parameters,
+# the session must contain at least one of the entries. NB: Wildcards are not permitted,
+# however if wildcards property is False, regular expressions may be used for all but
+# number and date_range.
+
+# Parameters
+# ----------
+# dataset : str, list
+# List of dataset names. Returns sessions containing all these datasets.
+# A dataset matches if it contains the search string e.g. 'wheel.position' matches
+# '_ibl_wheel.position.npy'
+# date_range : str, list, datetime.datetime, datetime.date, pandas.timestamp
+# A single date to search or a list of 2 dates that define the range (inclusive). To
+# define only the upper or lower date bound, set the other element to None.
+# lab : str, list
+# A str or list of lab names, returns sessions from any of these labs
+# number : str, int
+# Number of session to be returned, i.e. number in sequence for a given date
+# subject : str, list
+# A list of subject nicknames, returns sessions for any of these subjects
+# task_protocol : str, list
+# The task protocol name (can be partial, i.e. any task protocol containing that str
+# will be found)
+# project(s) : str, list
+# The project name (can be partial, i.e. any task protocol containing that str
+# will be found)
+# performance_lte / performance_gte : float
+# Search only for sessions whose performance is less equal or greater equal than a
+# pre-defined threshold as a percentage (0-100)
+# users : str, list
+# A list of users
+# location : str, list
+# A str or list of lab location (as per Alyx definition) name
+# Note: this corresponds to the specific rig, not the lab geographical location per se
+# json : dict
+# example :
+# ```python
+# json = {
+# "whisker_stims": {
+# "amplitudes": {
+# "abstract__contains": ['10-0','10-10','10_90-0']
+# }
+# }
+# }
+# ```
+# allowed filter looups are listed here :
+# https://docs.djangoproject.com/en/5.0/ref/models/querysets/#field-lookups
+
+
+# dataset_types : str, list
+# One or more of dataset_types
+# details : bool
+# If true also returns a dict of dataset details
+# query_type : str, None
+# Query cache ('local') or Alyx database ('remote')
+# limit : int
+# The number of results to fetch in one go (if pagination enabled on server)
+
+
+# Returns
+# -------
+# list
+# List of eids
+# (list of dicts)
+# If details is True, also returns a list of dictionaries, each entry corresponding to a
+# matching session
+# """
+# _logger = logging.getLogger("search")
+# query_type = query_type or self.mode # we set query_type = self.mode if query_type is None
+# if query_type != "remote":
+# return super().search(details=details, query_type=query_type, **kwargs)
+
+# # loop over input arguments and build the url
+# search_terms = self.search_terms(query_type=query_type)
+# params = {} # {"django": kwargs.pop("django", "")}
+
+# if isinstance(id, (list, tuple)):
+# sessions = []
+# for i in id:
+# sessions.append(
+# self.search(
+# id=i, details=details, as_mode=as_mode, no_cache=no_cache, query_type=query_type, **kwargs
+# )
+# )
+# return pd.DataFrame(sessions)
+
+# if id is not None:
+# params["id"] = self.to_eid(id)
+# if params["id"] is None: # this means the id we supplied is not a valid eid
+# raise ValueError(f"{id} is not a valid identifier, could not convert it to session uuid.")
+# _logger.debug(f"kwargs : {kwargs}")
+# for key, value in sorted(kwargs.items()):
+# field = util.autocomplete(key, search_terms) # Validate and get full name
+# _logger.debug(f"field : {field}")
+# # check that the input matches one of the defined filters
+# if field == "date_range":
+# params[field] = [x.date().isoformat() for x in util.validate_date_range(value)]
+# elif field == "laboratory":
+# params["lab"] = value
+# else:
+# params[field] = value
+# _logger.debug(f"params : {params}")
+# # Make GET request
+# ses = self.alyx.rest(
+# self._search_endpoint,
+# "list",
+# no_cache=no_cache,
+# query_type=query_type,
+# **params,
+# )
+# if len(ses) > 1:
+# _logger.info(f"Found {len(ses)} sessions.")
+
+# if not details:
+# return [item["id"] for item in ses]
+# # list(util.LazyId(ses))
+
+# sess_df = []
+# for session_short_info in tqdm(ses, total=len(ses), delay=2, desc="Loading session details", file=stdout):
+# session_detailed_info = self.alyx.rest(
+# "sessions",
+# "read",
+# id=session_short_info["id"],
+# no_cache=no_cache,
+# query_type=query_type,
+# )
+# formated_session = self.to_session_details(session_detailed_info, as_mode=as_mode)
+# sess_df.append(formated_session)
+
+# try:
+# sess_df = pd.DataFrame(sess_df)
+# sess_df.index = sess_df.index.set_names("id")
+# sess_df["start_datetime"] = pd.to_datetime(sess_df["start_datetime"], utc=True)
+# except (ValueError, KeyError):
+# warnings.warn("search result contained no entry")
+# pass # could not create a dataframe form session details. Returning dict instead
+# if id is not None:
+# return sess_df.iloc[0]
+# return sess_df
+
+# def to_session_details(self, session_dict, as_mode=None):
+# data_access_mode = (
+# as_mode or self.data_access_mode
+# ) # we set data_access_mode = self.data_access_mode if as_mode is None
+
+# session_dict["date"] = str(datetime.fromisoformat(session_dict["start_time"]).date())
+# session_dict["extended_qc"] = session_dict["extended_qc"] if session_dict["extended_qc"] is not None else {}
+# session_dict["local_path"] = os.path.normpath(
+# os.path.join(alyx_connector.params.get().LOCAL_ROOT, session_dict["rel_path"])
+# )
+# session_dict["remote_path"] = os.path.normpath(
+# session_dict["path"]
+# ) # path is the remote path initially (out from the database)
+# # we set path depending on the data_access_mode
+# session_dict["path"] = session_dict[data_access_mode + "_path"]
+# session_dict["rel_path"] = Path(session_dict["rel_path"])
+
+# session_dict["start_datetime"] = datetime.strptime(session_dict["start_time"], "%Y-%m-%dT%H:%M:%S%z")
+
+# id = session_dict.pop("id")
+
+# session_details = pd.Series(session_dict, name=id)
+# return session_details
+
+# def _download_datasets(self, dsets, **kwargs) -> List[Path]:
+# """
+# Download a single or multitude of datasets if stored on AWS, otherwise calls
+# OneAlyx._download_dataset.
+
+# NB: This will not skip files that are already present. Use check_filesystem instead.
+
+# Parameters
+# ----------
+# dset : dict, str, pd.Series
+# A single or multitude of dataset dictionaries
+
+# Returns
+# -------
+# pathlib.Path
+# A local file path or list of paths
+# """
+# # If all datasets exist on AWS, download from there.
+# _logger = logging.getLogger("_download_datasets")
+# try:
+# if "exists_aws" in dsets and np.all(np.equal(dsets["exists_aws"].values, True)):
+# _logger.info("Downloading from AWS")
+# return self._download_aws(map(lambda x: x[1], dsets.iterrows()), **kwargs)
+# except Exception as ex:
+# _logger.debug(ex)
+# return self._download_dataset(dsets, **kwargs)
+
+# def _dset2url(self, dset, update_cache=True):
+# """
+# Converts a dataset into a remote HTTP server URL. The dataset may be one or more of the
+# following: a dict from returned by the sessions endpoint or dataset endpoint, a record
+# from the datasets cache table, or a file path. Unlike record2url, this method can convert
+# dicts and paths to URLs.
+
+# Parameters
+# ----------
+# dset : dict, str, pd.Series, pd.DataFrame, list
+# A single or multitude of dataset dictionary from an Alyx REST query OR URL string
+# update_cache : bool
+# If True (default) and the dataset is from Alyx and cannot be converted to a URL,
+# 'exists' will be set to False in the corresponding entry in the cache table.
+
+# Returns
+# -------
+# str
+# The remote URL of the dataset
+# """
+# _logger = logging.getLogger("_dset2url")
+# did = None
+# if isinstance(dset, str) and dset.startswith("http"):
+# url = dset
+# elif isinstance(dset, (str, Path)):
+# url = self.path2url(dset)
+# if not url:
+# _logger.warning(f"Dataset {dset} not found in cache")
+# return
+# elif isinstance(dset, (list, tuple)):
+# dset2url = partial(self._dset2url, update_cache=update_cache)
+# return list(flatten(map(dset2url, dset)))
+# else:
+# # check if dset is dataframe, iterate over rows
+# if hasattr(dset, "iterrows"):
+# dset2url = partial(self._dset2url, update_cache=update_cache)
+# url = list(map(lambda x: dset2url(x[1]), dset.iterrows()))
+# elif "data_url" in dset: # data_dataset_session_related dict
+# url = dset["data_url"]
+# did = dset["id"]
+# elif "file_records" not in dset: # Convert dataset Series to alyx dataset dict
+# url = self.record2url(dset) # NB: URL will always be returned but may not exist
+# is_int = all(isinstance(x, (int, np.int64)) for x in util.ensure_list(dset.name))
+# did = np.array(dset.name)[-2:] if is_int else util.ensure_list(dset.name)[-1]
+# else: # from datasets endpoint
+# repo = getattr(getattr(self.web_client, "_par", None), "HTTP_DATA_SERVER", None)
+# url = next(
+# (
+# fr["data_url"]
+# for fr in dset["file_records"]
+# if fr["data_url"] and fr["exists"] and fr["data_url"].startswith(repo or fr["data_url"])
+# ),
+# None,
+# )
+# did = dset["url"][-36:]
+
+# # Update cache if url not found
+# if did is not None and not url and update_cache:
+# _logger.debug("Updating cache")
+# if isinstance(did, str) and self._index_type("datasets") is int:
+# (did,) = parquet.str2np(did).tolist()
+# elif self._index_type("datasets") is str and not isinstance(did, str):
+# did = parquet.np2str(did)
+# # NB: This will be considerably easier when IndexSlice supports Ellipsis
+# idx = [slice(None)] * int(self._cache["datasets"].index.nlevels / 2)
+# self._cache["datasets"].loc[(*idx, *util.ensure_list(did)), "exists"] = False
+# self._cache["_meta"]["modified_time"] = datetime.now()
+
+# return url
+
+# def _download_dataset(self, dset, cache_dir=None, update_cache=True, **kwargs) -> List[Path | None]:
+# """
+# Download a single or multitude of dataset from an Alyx REST dictionary.
+
+# NB: This will not skip files that are already present. Use check_filesystem instead.
+
+# Parameters
+# ----------
+# dset : dict, str, pd.Series, pd.DataFrame, list
+# A single or multitude of dataset dictionary from an Alyx REST query OR URL string
+# cache_dir : str, pathlib.Path
+# The root directory to save the data to (default taken from ONE parameters)
+# update_cache : bool
+# If true, the cache is updated when filesystem discrepancies are encountered
+
+# Returns
+# -------
+# pathlib.Path, list
+# A local file path or list of paths
+# """
+# cache_dir = cache_dir or self.cache_dir
+# url = self._dset2url(dset, update_cache=update_cache)
+# if not url:
+# return
+# if isinstance(url, str):
+# target_dir = str(Path(cache_dir, get_alf_path(url)).parent)
+# return self._download_file(url, target_dir, **kwargs)
+# # must be list of URLs
+# valid_urls = list(filter(None, url))
+# if not valid_urls:
+# return [None] * len(url)
+# target_dir = [str(Path(cache_dir, get_alf_path(x)).parent) for x in valid_urls]
+# files = self._download_file(valid_urls, target_dir, **kwargs)
+# # Return list of file paths or None if we failed to extract URL from dataset
+# return [None if not x else files.pop(0) for x in url]
+
+# def _tag_mismatched_file_record(self, url):
+# fr = self.alyx.rest(
+# "files",
+# "list",
+# django=f'dataset,{Path(url).name.split(".")[-2]},data_repository__globus_is_personal,False',
+# no_cache=True,
+# )
+# if len(fr) > 0:
+# json_field = fr[0]["json"]
+# if json_field is None:
+# json_field = {"mismatch_hash": True}
+# else:
+# json_field.update({"mismatch_hash": True})
+# try:
+# self.alyx.rest(
+# "files",
+# "partial_update",
+# id=fr[0]["url"][-36:],
+# data={"json": json_field},
+# )
+# except requests.exceptions.HTTPError as ex:
+# warnings.warn(
+# f"Failed to tag remote file record mismatch: {ex}\nPlease contact the database administrator."
+# )
+
+# def _download_file(self, url, target_dir, keep_uuid=False, file_size=None, hash=None) -> Path | List[Path]:
+# """
+# Downloads a single file or multitude of files from an HTTP webserver.
+# The webserver in question is set by the AlyxClient object.
+
+# Parameters
+# ----------
+# url : str, list
+# An absolute or relative URL for a remote dataset
+# target_dir : str, list
+# Absolute path of directory to download file to (including alf path)
+# keep_uuid : bool
+# If true, the UUID is not removed from the file name (default is False)
+# file_size : int, list
+# The expected file size or list of file sizes to compare with downloaded file
+# hash : str, list
+# The expected file hash or list of file hashes to compare with downloaded file
+
+# Returns
+# -------
+# pathlib.Path
+# The file path of the downloaded file or files.
+
+# Example
+# -------
+# >>> file_path = OneAlyx._download_file(
+# ... 'https://example.com/data.file.npy', '/home/Downloads/subj/1900-01-01/001/alf')
+# """
+# assert not self.offline
+# # Ensure all target directories exist
+# [Path(x).mkdir(parents=True, exist_ok=True) for x in set(util.ensure_list(target_dir))]
+
+# # download file(s) from url(s), returns file path(s) with UUID
+# local_path, md5 = self.alyx.download_file(url, target_dir=target_dir, return_md5=True)
+
+# # check if url, hash, and file_size are lists
+# if isinstance(url, (tuple, list)):
+# assert (file_size is None) or len(file_size) == len(url)
+# assert (hash is None) or len(hash) == len(url)
+# for args in zip(*map(util.ensure_list, (file_size, md5, hash, local_path, url))):
+# self._check_hash_and_file_size_mismatch(*args)
+
+# # check if we are keeping the uuid on the list of file names
+# if keep_uuid:
+# return local_path
+
+# # remove uuids from list of file names
+# if isinstance(local_path, (list, tuple)):
+# return [alfio.remove_uuid_file(x) for x in local_path]
+# else:
+# return alfio.remove_uuid_file(local_path)
+
+# def _check_hash_and_file_size_mismatch(self, file_size, hash, expected_hash, local_path, url):
+# """
+# Check to ensure the hash and file size of a downloaded file matches what is on disk
+
+# Parameters
+# ----------
+# file_size : int
+# The expected file size to compare with downloaded file
+# hash : str
+# The expected file hash to compare with downloaded file
+# local_path: str
+# The path of the downloaded file
+# url : str
+# An absolute or relative URL for a remote dataset
+# """
+# _logger = logging.getLogger("_check_hash_and_file_size_mismatch")
+# # verify hash size
+# hash = hash or hashfile.md5(local_path)
+# hash_mismatch = hash and hash != expected_hash
+# # verify file size
+# file_size_mismatch = file_size and Path(local_path).stat().st_size != file_size
+# # check if there is a mismatch in hash or file_size
+# if hash_mismatch or file_size_mismatch:
+# # post download, if there is a mismatch between Alyx and the newly downloaded file size
+# # or hash, flag the offending file record in Alyx for database for maintenance
+# hash_mismatch = expected_hash and expected_hash != hash
+# file_size_mismatch = file_size and Path(local_path).stat().st_size != file_size
+# if hash_mismatch or file_size_mismatch:
+# url = url or self.path2url(local_path)
+# _logger.debug(f"Tagging mismatch for {url}")
+# # tag the mismatched file records
+# self._tag_mismatched_file_record(url)
+
+# @staticmethod
+# def setup(base_url=None, **kwargs):
+# """
+# Set up OneAlyx for a given database
+
+# Parameters
+# ----------
+# base_url : str
+# An Alyx database URL. If None, the current default database is used.
+# **kwargs
+# Optional arguments to pass to one.params.setup.
+
+# Returns
+# -------
+# OneAlyx
+# An instance of OneAlyx for the newly set up database URL
+# """
+# base_url = base_url or alyx_connector.params.get_default_client()
+# cache_map = alyx_connector.params.setup(client=base_url, **kwargs)
+# return OneAlyx(base_url=base_url or alyx_connector.params.get(cache_map.DEFAULT).ALYX_URL)
+
+# @util.refresh
+# @util.parse_id
+# def eid2path(self, eid, query_type=None) -> util.Listable(Path):
+# """
+# From an experiment ID gets the local session path
+
+# Parameters
+# ----------
+# eid : str, UUID, pathlib.Path, dict, list
+# Experiment session identifier; may be a UUID, URL, experiment reference string
+# details dict or Path.
+# query_type : str
+# If set to 'remote', will force database connection
+
+# Returns
+# -------
+# pathlib.Path, list
+# A session path or list of session paths
+# """
+
+# # first try avoid hitting the database
+# mode = query_type or self.mode
+# if mode != "remote":
+# cache_path = super().eid2path(eid)
+# if cache_path or mode == "local":
+# return cache_path
+
+# # If eid is a list recurse through it and return a list
+# if isinstance(eid, list):
+# unwrapped = unwrap(self.path2eid)
+# return [unwrapped(self, e, query_type="remote") for e in eid]
+
+# # if it wasn't successful, query Alyx
+# ses = self.alyx.rest("sessions", "list", django=f"pk,{eid}")
+
+# if len(ses) == 0:
+# return None
+
+# data_repository = ses[0]["default_data_repository"]
+# if data_repository is None:
+# data_repository = ""
+
+# return os.path.join(
+# data_repository,
+# ses[0]["subject"],
+# ses[0]["start_time"][:10],
+# str(ses[0]["number"]).zfill(3),
+# )
+
+# @util.refresh
+# def path2eid(self, path_obj: Union[str, Path], query_type=None) -> util.Listable(Path):
+# import re
+
+# """
+# From a local path, gets the experiment ID
+
+# Parameters
+# ----------
+# path_obj : str, pathlib.Path, list
+# Local path or list of local paths
+# query_type : str
+# If set to 'remote', will force database connection
+
+# Returns
+# -------
+# str, list
+# An eid or list of eids
+# """
+# # If path_obj is a list recurse through it and return a list
+# if isinstance(path_obj, list):
+# path_obj = [Path(x) for x in path_obj]
+# eid_list = []
+# unwrapped = unwrap(self.path2eid)
+# for p in path_obj:
+# eid_list.append(unwrapped(self, p))
+# return eid_list
+# # else ensure the path ends with mouse,date, number
+# try:
+# path_obj = re.findall(r"(\w+(?:\\|\/)\d{4}-\d{2}-\d{2}(?:\\|\/)\d+)", path_obj)[0]
+# except IndexError: # could not match anything
+# pass
+
+# path_obj = Path(path_obj)
+
+# # try the cached info to possibly avoid hitting database
+# mode = query_type or self.mode
+# if mode != "remote":
+# cache_eid = super().path2eid(path_obj)
+# if cache_eid or mode == "local":
+# return cache_eid
+
+# session_path = get_session_path(path_obj)
+# # if path does not have a date and a number return None
+# if session_path is None:
+# return None
+
+# # if not search for subj, date, number XXX: hits the DB
+# search = unwrap(self.search)
+# uuid = search(
+# subject=session_path.parts[-3],
+# date_range=session_path.parts[-2],
+# number=session_path.parts[-1],
+# query_type="remote",
+# )
+
+# # Return the uuid if any
+# return uuid[0] if uuid else None
+
+# @util.refresh
+# def path2url(self, filepath, query_type=None) -> str:
+# """
+# Given a local file path, returns the URL of the remote file.
+
+# Parameters
+# ----------
+# filepath : str, pathlib.Path
+# A local file path
+# query_type : str
+# If set to 'remote', will force database connection
+
+# Returns
+# -------
+# str
+# A URL string
+# """
+# query_type = query_type or self.mode
+# if query_type != "remote":
+# return super().path2url(filepath)
+# eid = self.path2eid(filepath)
+# try:
+# (dataset,) = self.alyx.rest("datasets", "list", session=eid, name=Path(filepath).name)
+# return next(r["data_url"] for r in dataset["file_records"] if r["data_url"] and r["exists"])
+# except (ValueError, StopIteration):
+# raise alferr.ALFObjectNotFound(f"File record for {filepath} not found on Alyx")
+
+# @util.parse_id
+# def type2datasets(self, eid, dataset_type, details=False):
+# """
+# Get list of datasets belonging to a given dataset type for a given session
+
+# Parameters
+# ----------
+# eid : str, UUID, pathlib.Path, dict
+# Experiment session identifier; may be a UUID, URL, experiment reference string
+# details dict or Path.
+# dataset_type : str, list
+# An Alyx dataset type, e.g. camera.times or a list of dtypes
+# details : bool
+# If True, a datasets DataFrame is returned
+
+# Returns
+# -------
+# np.ndarray, dict
+# A numpy array of data, or DataFrame if details is true
+# """
+# assert self.mode != "local" and not self.offline, "Unable to connect to Alyx in local mode"
+# if isinstance(dataset_type, str):
+# restriction = f"session__id,{eid},dataset_type__name,{dataset_type}"
+# elif isinstance(dataset_type, collections.abc.Sequence):
+# restriction = f"session__id,{eid},dataset_type__name__in,{dataset_type}"
+# else:
+# raise TypeError("dataset_type must be a str or str list")
+# datasets = util.datasets2records(self.alyx.rest("datasets", "list", django=restriction))
+# return datasets if details else datasets["rel_path"].sort_values().values
+
+# def dataset2type(self, dset) -> str:
+# """Return dataset type from dataset.
+
+# NB: Requires an Alyx database connection
+
+# Parameters
+# ----------
+# dset : str, np.ndarray, tuple
+# A dataset name, dataset uuid or dataset integer id
+
+# Returns
+# -------
+# str
+# The dataset type
+# """
+# assert self.mode != "local" and not self.offline, "Unable to connect to Alyx in local mode"
+# # Ensure dset is a str uuid
+# if isinstance(dset, str) and not is_uuid_string(dset):
+# dset = self._dataset_name2id(dset)
+# if isinstance(dset, np.ndarray):
+# dset = parquet.np2str(dset)[0]
+# if isinstance(dset, tuple) and all(isinstance(x, int) for x in dset):
+# dset = parquet.np2str(np.array(dset))
+# if not is_uuid_string(dset):
+# raise ValueError("Unrecognized name or UUID")
+# return self.alyx.rest("datasets", "read", id=dset)["dataset_type"]
+
+# def describe_revision(self, revision, full=False):
+# """Print description of a revision
+
+# Parameters
+# ----------
+# revision : str
+# The name of the revision (without '#')
+# full : bool
+# If true, returns the matching record
+
+# Returns
+# -------
+# None, dict
+# None if full is false or no record found, otherwise returns record as dict
+# """
+# assert self.mode != "local" and not self.offline, "Unable to connect to Alyx in local mode"
+# try:
+# rec = self.alyx.rest("revisions", "read", id=revision)
+# print(rec["description"])
+# if full:
+# return rec
+# except requests.exceptions.HTTPError as ex:
+# if ex.response.status_code != 404:
+# raise ex
+# print(f'revision "{revision}" not found')
+
+# def _dataset_name2id(self, dset_name, eid=None):
+# # TODO finish function
+# datasets = self.list_datasets(eid) if eid else self._cache["datasets"]
+# # Get ID of fist matching dset
+# for idx, rel_path in datasets["rel_path"].items():
+# if rel_path.endswith(dset_name):
+# return idx[-1] # (eid, did)
+# raise ValueError(f"Dataset {dset_name} not found in cache")
+
+# @util.refresh
+# @util.parse_id
+# def get_details(self, eid: str, full: bool = False, query_type=None):
+# """Return session details for a given session
+
+# Parameters
+# ----------
+# eid : str, UUID, pathlib.Path, dict, list
+# Experiment session identifier; may be a UUID, URL, experiment reference string
+# details dict or Path.
+# full : bool
+# If True, returns a DataFrame of session and dataset info
+# query_type : {'local', 'refresh', 'auto', 'remote'}
+# The query mode - if 'local' the details are taken from the cache tables; if 'remote'
+# the details are returned from the sessions REST endpoint; if 'auto' uses whichever
+# mode ONE is in; if 'refresh' reloads the cache before querying.
+
+# Returns
+# -------
+# pd.Series, pd.DataFrame, dict
+# in local mode - a session record or full DataFrame with dataset information if full is
+# True; in remote mode - a full or partial session dict
+
+# Raises
+# ------
+# ValueError
+# Invalid experiment ID (failed to parse into eid string)
+# requests.exceptions.HTTPError
+# [Errno 404] Remote session not found on Alyx
+# """
+# if (query_type or self.mode) == "local":
+# return super().get_details(eid, full=full)
+# # If eid is a list of eIDs recurse through list and return the results
+# if isinstance(eid, list):
+# details_list = []
+# for p in eid:
+# details_list.append(self.get_details(p, full=full))
+# return details_list
+# # load all details
+# dets = self.alyx.rest("sessions", "read", eid)
+# if full:
+# return dets
+# # If it's not full return the normal output like from a one.search
+# det_fields = [
+# "subject",
+# "start_time",
+# "number",
+# "lab",
+# "projects",
+# "url",
+# "task_protocol",
+# "local_path",
+# ]
+# out = {k: v for k, v in dets.items() if k in det_fields}
+# out["projects"] = ",".join(out["projects"])
+# out.update(
+# {
+# "local_path": self.eid2path(eid),
+# "date": datetime.fromisoformat(out["start_time"]).date(),
+# }
+# )
+# return out
+
+# ### METHODS ADDED BY TIMOTHE TO EXTEND THE USE OF THE API
+
+# def get_data_repository_path(self, repository_name):
+# repo_data = self.alyx.rest("data-repository", "read", repository_name)
+# repo_path = r"\\" + os.path.join(repo_data["hostname"], repo_data["globus_path"].lstrip("/"))
+# return os.path.normpath(repo_path)
+
+# def read_sql(self, query):
+# raise NotImplementedError
+
+# def create_session(self, data_dict):
+# import re
+
+# data_dict = data_dict.copy()
+# data_dict["number"] = str(int(data_dict["number"])) # remove leading zeros if any
+# try: # a session have been found with same 3 parameters, don't allow to process to registering.
+# _searched_session = self.search(
+# subject=data_dict["subject"],
+# number=data_dict["number"],
+# date_range=data_dict["start_time"][:10],
+# users=data_dict["users"],
+# details=True,
+# )
+# url = re.sub(r"\/sessions", r"/actions/session", _searched_session["url"].item())
+# raise ValueError(
+# f"This session path is already registered ! See here : {url}\n You probably need to change the number "
+# "of the session for this animald/date combo"
+# )
+# except KeyError: # no session have benn found, all is well, can proceed
+# pass
+
+# self.alyx.rest("sessions", "create", data=data_dict)
+
+# def default_session_data(self):
+# return {"lab": "HaissLab", "task_protocol": ""}
+
+# @staticmethod
+# def explorer(path):
+# import subprocess
+
+# path = os.path.normpath(path)
+# if not os.path.exists(path):
+# raise IOError(f"Path {path} does not exist")
+# if os.path.isfile(path):
+# path = os.path.dirname(path)
+
+# pre_cmd = f"explorer.exe {path}"
+# subprocess.call(pre_cmd)
+# return
+# # this part is to open in atab instead of window. Buggy for now.
+# if path[:2] == r"\\":
+# pre_cmd = f"pushd {path}; "
+# # path = os.path.join(*[item for item in selected_folder.split(os.sep) if item != ''][1:])
+# # #this removes the first object of the path
+# else:
+# pre_cmd = 'cd "{pateh}; "'
+# subprocess.call(pre_cmd + r"start .")
+# # subprocess.Popen(r'explorer '+f'{os.path.dirname(path)},select,{os.path.basename(path)}')
+
+# def collection_path(self, eid, collections):
+# return os.path.join(self.current_remote_repository_path, self.eid2path(eid), collections)
+
+# def set_current_remote_repository(self, repo_name):
+# self.current_remote_repository_path = self.get_data_repository_path(repo_name)
+
+# def get_parts_from_path(self, input_path):
+# import re
+
+# subject, date, number = re.findall(r"(\w+)(?:\\|\/)(\d{4}-\d{2}-\d{2})(?:\\|\/)(\d+)", input_path)[0]
+# return {"subject": subject, "date": date, "number": number}
+
+# def get_json_params(self, eid):
+# return self.alyx.rest("sessions", "read", eid)["json"]
+
+# def get_extended_qc(self, eid):
+# return self.alyx.rest("sessions", "read", eid)["extended_qc"]
+
+# def display_session_info(self, session_details):
+# from IPython.display import Markdown, display
+
+# session_data_link = f"[Data pathes](file:{os.path.normpath(session_details.path)}) pointing in {self.data_access_mode} mode."
+# metadatas_link = f"[Metadatas]({session_details.url}) obtained in {self.mode} mode."
+# uuid = f"(uuid is '{session_details.name}')"
+# display(Markdown(f"Session {session_details.rel_path}. {session_data_link} {metadatas_link} {uuid}"))
+
+# @wraps(MultiSessionPlaceholder)
+# def multisession(*args, **kwargs):
+# return MultiSessionPlaceholder(*args, **kwargs)
+
+# def update_session_info(self, session_details, json={}, extended_qc={}, **kwargs):
+# _logger = logging.getLogger("update_session_info")
+
+# data = {}
+# if len(json):
+# base_json = session_details.json
+# if base_json is None:
+# base_json = {}
+# base_json.update(json)
+# data["json"] = base_json
+
+# if len(extended_qc):
+# base_ext_qc = session_details.extended_qc
+# if base_ext_qc is None:
+# base_ext_qc = {}
+# base_ext_qc.update(extended_qc)
+# data["extended_qc"] = base_ext_qc
+
+# data.update(kwargs)
+
+# _logger.info(f"Updating session {session_details.rel_path}")
+# ans = input(f"Data OK ? (OK or Cancel) : {data}")
+# if ans != "OK":
+# _logger.info("Aborting")
+# return
+# _logger.info("Applying changes")
+# self.alyx.rest("sessions", "partial_update", id=session_details.name, data=data)
+# self.alyx.delete_cache()
+
+# def push_files(self, file_list, *, session_details, relative=False, overwrite_policy="raise"):
+# """
+# The function push_processed_files copies a list of files to a remote session directory,
+# and handles various overwrite policies.
+
+# Args:
+
+# - file_list (list of str): a list of local file paths to be copied to the remote session directory.
+# - session_details (SessionDetails): an object containing the session details.
+# - relative: If the string representing the path of the files are absolute or relative from
+# INSIDE the session folder (ex : 'D:\\LOCAL_DATA\\wm25\\2022-08-05\\001\\a_folder\\test.file'
+# is an absolute path and 'a_folder\test.file' is a relative path)
+# - overwrite_policy (str, optional): the overwrite policy. Possibilities are:
+# - "raise" (raise an exception if a file with the same name already exists in the remote directory),
+# - "skip" (skip copying the file if a file with the same name already exists in the remote directory),
+# - "overwrite" (overwrite the file with the same name in the remote directory),
+# - "most_recent" (copy the file only if it is more recent than the file
+# with the same name in the remote directory),
+# - "erase" (erase the existing file in the remote directory if a file with the same name already exists,
+# then copy a new one in place.) Prefer choosing overwrite in most situations).
+
+# Default is "raise".
+
+# Returns:
+
+# a dictionary with two keys:
+# - "copied" : a list of file paths that have been copied to the remote session directory.
+# - "ignored" : a list of file paths that could not be copied (either because they were not found or
+# because they were excluded by the overwrite policy).
+# """
+
+# import shutil
+
+# def get_relative_path(absolute_path, common_root_path):
+# """Compare an input path and a path with a common root with the input path, and returns only the part of
+# the input path that is not shared with the _common_root_path.
+
+# Args:
+# input_path (TYPE): DESCRIPTION.
+# common_root_base (TYPE): DESCRIPTION.
+
+# Returns:
+# TYPE: DESCRIPTION.
+
+# """
+# absolute_path = os.path.normpath(absolute_path)
+# common_root_path = os.path.normpath(common_root_path)
+
+# commonprefix = os.path.commonprefix([common_root_path, absolute_path])
+# if commonprefix == "":
+# raise IOError(f"These two pathes have no common root path : {absolute_path} and {common_root_path}")
+# return os.path.relpath(absolute_path, start=commonprefix)
+
+# overwrite_policies = ["raise", "skip", "erase", "most_recent", "overwrite"]
+# if overwrite_policy not in overwrite_policies:
+# raise NotImplementedError(
+# f"Value {overwrite_policy} for overwrite_policy is not supported. "
+# f"Possibilities are : {overwrite_policies}"
+# )
+
+# session_local_root = session_details["local_path"]
+# session_remote_root = session_details["remote_path"]
+
+# if not isinstance(file_list, (list, tuple, np.ndarray)):
+# file_list = [file_list]
+
+# if relative:
+# file_list = [os.path.join(session_local_root, session_details.rel_path, file) for file in file_list]
+
+# source_files = [] # file paths that have been copied
+# # files paths of the copies of the one in the list above (ordered similarly)
+# dest_files = []
+
+# overwrite_raise_list = (
+# []
+# ) # stores files that already exist in remote folder in case we have 'raise' overwrite_policy, to print to user
+# file_not_found_warning = []
+
+# # MAKE THE LIST OF FILES THAT WILL BE COPIED
+# for local_path in file_list:
+# if not os.path.isfile(local_path):
+# file_not_found_warning.append(local_path)
+# continue
+
+# try:
+# relative_path = get_relative_path(local_path, session_local_root)
+# except IOError:
+# file_not_found_warning.append(local_path)
+# continue
+
+# remote_path = os.path.join(session_remote_root, relative_path)
+
+# if os.path.isfile(remote_path):
+# if overwrite_policy == "raise":
+# overwrite_raise_list.append(local_path)
+# elif overwrite_policy == "skip":
+# logging.getLogger().info(f"Skipping file {remote_path}")
+# continue
+# elif overwrite_policy == "erase":
+# os.remove(remote_path)
+# elif overwrite_policy == "most_recent":
+# if (
+# os.stat(remote_path).st_mtime > os.stat(local_path).st_mtime
+# ): # remote_path is more recent (higher time value)
+# continue
+# elif overwrite_policy == "overwrite":
+# pass
+# # else if overwrite, we just do nothing and files will be overwritten during shutil.copy operation
+
+# source_files.append(local_path)
+# dest_files.append(remote_path)
+
+# if len(file_not_found_warning):
+# logging.getLogger().warning(
+# "These files were not found or are not inside the session local folder, "
+# f"and therefore cannot be copied :\nFiles:\n{file_not_found_warning}"
+# )
+
+# if len(overwrite_raise_list):
+# raise IOError(
+# f"The files listed below already exist in the destination : {session_remote_root}\n"
+# "No file have been copied to avoid mistakes. "
+# "You can check the content of the destination folder manually, "
+# "or change the 'overwrite_policy' argument of this function (beware of data losses !).\n"
+# f"Files :\n {overwrite_raise_list}"
+# )
+
+# # APPLY THE COPY
+# for local_path, remote_path in zip(source_files, dest_files):
+# container_dir = os.path.dirname(remote_path)
+# # make destination dir if it doesn't exist already
+# os.makedirs(container_dir, exist_ok=True)
+# shutil.copy(local_path, remote_path)
+
+# return {
+# "copied": source_files,
+# "ignored": list(set(file_list).difference(set(source_files))),
+# }
+
+# def copy_files(self, source_file_list, source_root, destination_root, overwrite_policy="raise"):
+# def get_relative_path(absolute_path, common_root_path):
+# """
+# Compare an input path and a path with a common root with the input path, and returns only the part of the
+# input path that is not shared with the _common_root_path.
+
+# Args:
+# input_path (TYPE): DESCRIPTION.
+# common_root_base (TYPE): DESCRIPTION.
+
+# Returns:
+# TYPE: DESCRIPTION.
+
+# """
+# absolute_path = os.path.normpath(absolute_path)
+# common_root_path = os.path.normpath(common_root_path)
+
+# commonprefix = os.path.commonprefix([common_root_path, absolute_path])
+# if commonprefix == "":
+# raise IOError(f"These two pathes have no common root path : {absolute_path} and {common_root_path}")
+# return os.path.relpath(absolute_path, start=commonprefix)
+
+# # Check if the overwrite_policy is supported
+# overwrite_policies = ["raise", "skip", "erase", "most_recent", "overwrite"]
+# if overwrite_policy not in overwrite_policies:
+# raise ValueError(
+# f"Unsupported value for overwrite_policy: {overwrite_policy}. Possibilities are: {overwrite_policies}"
+# )
+
+# # Iterate through the list of source files and copy them to the destination
+# copied_files = []
+# ignored_files = []
+
+# for source_file_path in source_file_list:
+# # Get the relative path of the source file with respect to the source root
+# relative_path = get_relative_path(source_file_path, source_root)
+
+# # Create the destination path by joining the destination root and the relative path
+# destination_path = os.path.join(destination_root, relative_path)
+
+# # Check if the file exists at the source location and is a file
+# if not os.path.isfile(source_file_path):
+# ignored_files.append(source_file_path)
+# continue
+
+# # Check if the file exists at the destination location and apply the overwrite policy accordingly
+# if os.path.isfile(destination_path):
+# if overwrite_policy == "raise":
+# raise ValueError(f"File already exists at the destination: {destination_path}")
+# elif overwrite_policy == "skip":
+# ignored_files.append(source_file_path)
+# continue
+# elif overwrite_policy == "erase":
+# os.remove(destination_path)
+# elif overwrite_policy == "most_recent":
+# if os.stat(destination_path).st_mtime > os.stat(source_file_path).st_mtime:
+# ignored_files.append(source_file_path)
+# continue
+# elif overwrite_policy == "overwrite":
+# pass
+
+# # Create the directory structure at the destination if it does not exist already
+# os.makedirs(os.path.dirname(destination_path), exist_ok=True)
+
+# # Copy the file from source to destination
+# shutil.copy(source_file_path, destination_path)
+
+# # Append the copied file to the list of copied files
+# copied_files.append(source_file_path)
+
+# # Return a dictionary with the list of copied and ignored files
+# return {"copied": copied_files, "ignored": ignored_files}
+
+# def pull_files(self, file_list, *, session_details, relative=False, overwrite_policy="raise"):
+# pass
+#
diff --git a/src/alyx_connector/files/parsing/__init__.py b/src/alyx_connector/files/parsing/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..5887dae15e259662d08bbf7ac542b372f2b46032
--- /dev/null
+++ b/src/alyx_connector/files/parsing/__init__.py
@@ -0,0 +1 @@
+from .files import File, UUID
diff --git a/src/alyx_connector/files/expressions.py b/src/alyx_connector/files/parsing/expressions.py
similarity index 100%
rename from src/alyx_connector/files/expressions.py
rename to src/alyx_connector/files/parsing/expressions.py
diff --git a/src/alyx_connector/files/parsing.py b/src/alyx_connector/files/parsing/files.py
similarity index 92%
rename from src/alyx_connector/files/parsing.py
rename to src/alyx_connector/files/parsing/files.py
index 2d0169b1580b18e70ff6f8b51a03fe80480bd4d3..e5871c93c1e4fefec0c92be1805aa0f36a94cdfc 100644
--- a/src/alyx_connector/files/parsing.py
+++ b/src/alyx_connector/files/parsing/files.py
@@ -1,5 +1,5 @@
from pathlib import Path
-from re import split
+from re import split, compile
from uuid import UUID as OriginalUUID
from datetime import datetime
from pandas import Series
@@ -7,7 +7,21 @@ from copy import copy
from .expressions import Part, Matcher
-from typing import Optional, Any
+from typing import Optional, Any, TypedDict, List, Tuple, Unpack, Union, cast
+
+
+class PartsDict(TypedDict, total=False):
+ root: Union[str, Path]
+ drive: Union[str, Path]
+ subject: str
+ date: Union[datetime, str]
+ number: Union[str, int]
+ collection: Union[str, Path]
+ revision: Union[str, Path]
+ object: str
+ attribute: str
+ extra: Union[str, List[str], Tuple[str, ...]]
+ extension: str
class UUID(OriginalUUID):
@@ -41,27 +55,27 @@ class File:
partsnames = Part._member_names_
_unallowed_chars = ["?", "*", ":", '"', "<", ">"]
+ _unallowed_chars_pattern = compile(rf'[{"".join([char for char in _unallowed_chars])}]')
def _check_unallowed_chars(self, variable: Any):
if not variable:
return
- variable = str(variable)
- if any([char in variable for char in self._unallowed_chars]):
+ if bool(self._unallowed_chars_pattern.search(str(variable))):
raise ValueError(f"A path cannot contain any of these characters {self._unallowed_chars}")
def copy(self) -> "File":
return copy(self)
- def __new__(cls, path: Optional[str | Path] = None, *args, **kwargs: Optional[str | Path]):
+ def __new__(cls, path: Optional[str | Path] = None, **kwargs: Unpack[PartsDict]):
if path is None and not kwargs:
return super().__new__(cls)
if path is not None:
obj = cls.from_path(path, pattern="fullpath")
return obj
- return cls.from_parts(*args, **kwargs)
+ return cls.from_parts(**kwargs)
@classmethod
- def from_parts(cls, **kwargs: Optional[str | Path]) -> "File":
+ def from_parts(cls, **kwargs: Unpack[PartsDict]) -> "File":
obj = cls()
for partname, partvalue in kwargs.items():
if partname == "drive":
@@ -72,7 +86,7 @@ class File:
@classmethod
def from_path(cls, fullpath: str | Path, pattern="fullpath") -> "File":
- parts = Matcher.search(pattern, fullpath)
+ parts = cast(PartsDict, Matcher.search(pattern, fullpath))
return cls.from_parts(**parts)
def __setitem__(self, partname: str, value: Path | str | int | None):
@@ -109,7 +123,7 @@ class File:
self._root = rootpath
@property
- def drive(self):
+ def drive(self) -> Optional[Path]:
return getattr(self, "_drive", None)
@drive.setter
@@ -121,7 +135,7 @@ class File:
return getattr(self, "_subject", None)
@subject.setter
- def subject(self, subject: Optional[str | Path]):
+ def subject(self, subject: Optional[str]):
self._check_unallowed_chars(subject)
self._subject = subject if subject is not None else None
@@ -212,7 +226,10 @@ class File:
return getattr(self, "_extra", None)
@extra.setter
- def extra(self, extra: Optional[str]):
+ def extra(self, extra: Optional[str | List[str] | Tuple[str, ...]]):
+ if isinstance(extra, (list, tuple)):
+ self.extras = extra
+ return
self._check_unallowed_chars(extra)
self._extra = extra if extra else None
@@ -221,7 +238,7 @@ class File:
return str(self.extra).split(".") if self.extra else []
@extras.setter
- def extras(self, extras: list[str] | tuple[str]):
+ def extras(self, extras: List[str] | Tuple[str, ...]):
self.extra = ".".join(extras)
@property
@@ -414,6 +431,7 @@ class File:
def to_dict(self) -> dict:
return dict(
root=self.root,
+ drive=self.drive,
subject=self.subject,
date=self.date,
number=self.number,
diff --git a/src/alyx_connector/files/parsing/rulesets.py b/src/alyx_connector/files/parsing/rulesets.py
new file mode 100644
index 0000000000000000000000000000000000000000..0ea604f2a109f2b096e7ae4c8efd9d3e68ea685b
--- /dev/null
+++ b/src/alyx_connector/files/parsing/rulesets.py
@@ -0,0 +1,623 @@
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Literal, List, Dict, Tuple, Optional, Union, Callable, Protocol, Iterator, cast
+
+
+class ActionFunction(Protocol):
+ def __call__(self, file_record: "FileRecord", source: str, *, message: str = "") -> "FileRecord": ...
+
+
+class OperationFunction(Protocol):
+ def __call__(
+ self,
+ value: str,
+ ) -> bool: ...
+
+
+@dataclass
+class FileRecord:
+ # source_path is the original path from disk scan. will never change
+ source_path: Path
+
+ match: bool = False
+ matching_rules: list = field(default_factory=list)
+ used_rule: str = ""
+
+ valid_alf: bool = False
+ path_conflicts: bool = False
+ dataset_type_exists: bool = False
+ rename: bool = False
+ delete: bool = False
+ include: bool = False
+ abort: list = field(default_factory=list)
+
+ frozen = False
+
+ executed_actions = []
+
+ # source file
+ @property
+ def source_file(self) -> File:
+ source_file = getattr("self", "_source_file", None)
+ if source_file is None:
+ try:
+ source_file = File.from_path(self.source_path)
+ except Exception as e:
+ raise ValueError(f"File from {self.source_path} was not parseable ! {type(e)}:{e}")
+ self._source_file = source_file
+ return source_file
+
+ # was alf_info
+ @property
+ def destination_file(self) -> File:
+ destination_file = getattr("self", "_destination_file", None)
+ if destination_file is None:
+ destination_file = self.source_file.copy()
+ self._destination_file = destination_file
+ return destination_file
+
+ @property
+ def final_path(self) -> Path:
+ if not hasattr("self", "_final_path"):
+ self._final_path = self.destination_file.fullpath if self.rename else self.source_path
+ return self._final_path
+
+ @property
+ def final_file(self) -> "File":
+ if not hasattr("self", "_final_file"):
+ self._final_file = self.destination_file if self.rename else self.source_file
+ return self._final_file
+
+ @property
+ def final_pathstring(self):
+ if not hasattr("self", "_final_pathstring"):
+ self._final_pathstring = str(self.final_path)
+ return self._final_pathstring
+
+ def actions_cascade(self, config: "Config"):
+ for rule in config.rules.values():
+ rule.actions_cascade(self)
+
+ def finish_cascade(self, config: "Config"):
+ # change the values of the filre record after all other actions have been resolved.
+ # finish actions include calculating ,
+
+ self.valid_alf = self.destination_file.is_dataset_type_valid
+
+ if self.valid_alf and self.destination_file.dataset_type in config.dataset_types:
+ self.dataset_type_exists = True
+
+ @property
+ def inclusion_accepted(self):
+ if (
+ self.include
+ and self.valid_alf
+ and self.dataset_type_exists
+ and not self.path_conflicts
+ and not self.abort
+ and not self.delete
+ ):
+ return True
+ return False
+
+ @property
+ def rename_accepted(self):
+ if self.rename and self.valid_alf and not self.path_conflicts and not self.abort and not self.delete:
+ return True
+ return False
+
+ def apply_changes(self, do_deletes=True, do_renames=True): # apply changes to file_record
+ if self.delete and self.rename:
+ raise ValueError("Cannot rename AND delete the same entry.")
+
+ if self.rename_accepted and do_renames:
+ file_directory = self.destination_file.fullpath.parent
+ file_directory.mkdir(parents=True, exist_ok=True)
+ self.source_file.fullpath.rename(self.destination_file.fullpath)
+
+ elif self.delete and do_deletes:
+ self.source_file.fullpath.unlink()
+ self.include = False
+
+ def to_user_dict(self):
+ return {
+ "source_path": self.source_path,
+ "dest_path": str(self.destination_file.fullpath) if self.rename_accepted else "",
+ "info": self.info_message,
+ }
+
+ @property
+ def info_message(
+ self,
+ ): # message to make from action booleans to help the use understand what happened
+ message = ""
+ if self.inclusion_accepted and not self.rename_accepted:
+ message = " included without change"
+
+ if self.inclusion_accepted and self.rename_accepted:
+ message = " renamed and included"
+
+ if not self.inclusion_accepted and self.rename_accepted:
+ message = " renamed and excluded"
+
+ if not self.inclusion_accepted and not self.rename_accepted:
+ message = " excluded without change"
+
+ if not self.valid_alf:
+ message = message + " dataset_type doesn't follow alyx format"
+
+ if not self.dataset_type_exists:
+ message = message + f" dataset_type:{self.destination_file.dataset_type} not existing"
+
+ if self.delete:
+ message = " auto deleted"
+
+ if self.abort:
+ message_prefix = " Aborting due to errors : "
+ abort_messages = []
+ for ab_msg in self.abort:
+ if ab_msg == " filepath_conflicts":
+ ab_msg = " File name conflicts with a current file or another file that will be renamed identically"
+ abort_messages.append(ab_msg)
+
+ message = (
+ message_prefix
+ + ", ".join(abort_messages)
+ # + " --- Without Abort, would have been "
+ # + message
+ )
+ else:
+ message = "Will be " + message
+
+ return str(message)
+
+
+class Statement:
+ allowed_operations: List[CheckOperation] = ["exact", "contain", "match"]
+ allowed_elements = [
+ "source_path",
+ "subject",
+ "date",
+ "number",
+ "root",
+ "object",
+ "attribute",
+ "extension",
+ "extra",
+ "collection",
+ "revision",
+ ]
+ conditions: List[str] | List[Pattern]
+ operation: CheckOperation
+ operation_method: OperationFunction
+
+ def __init__(
+ self, element: Element, operation_detail: str | List[str] | Dict[CheckFullOperation, str | list[str]], parent
+ ):
+ self.inverted = False
+ self.parent = parent
+
+ for el in self.allowed_elements:
+ if element == el:
+ self.tested_element = element
+ break
+ else:
+ raise ValueError(
+ f"Tested element is {self.tested_element} wich is invalid value. "
+ f"If must be one of :({''.join(self.allowed_elements)})"
+ )
+
+ if isinstance(operation_detail, dict):
+ # if the operation detail is a dict, if should contain a single key, wich is the check operation type
+ if len(operation_detail) != 1:
+ raise ValueError(
+ f"Content of tested element {self.tested_element} is a dict. "
+ "Then it must contain only one key ({''.join(self.allowed_operations)})"
+ )
+
+ operation = list(operation_detail.keys())[0]
+ conditions = operation_detail[operation]
+
+ for op in self.allowed_operations:
+ if op in operation:
+ self.inverted = True if "_not" in operation else False
+ self.operation = op
+ break
+ else:
+ raise ValueError(
+ f"Content of tested element {self.tested_element} is a dict and the key present was : {operation}. "
+ "It must contain one of : ({''.join(self.allowed_operations)}). "
+ )
+ else:
+ # If the operation detail is not a dict, then we asume that the check operation
+ # is : "exact" matching of the string or strings
+ self.operation = "exact"
+ conditions = operation_detail
+
+ if not isinstance(conditions, list):
+ conditions = [conditions]
+
+ if self.operation == "match":
+ existing_patterns = self.patterns
+ patterns = []
+ for pattern_name in conditions:
+ try:
+ patterns.append(existing_patterns[pattern_name])
+ except KeyError:
+ raise ValueError(
+ f"Pattern {pattern_name} was asked in condition statement {self.tested_element} "
+ "but was not defined in re_patterns."
+ )
+ conditions = patterns
+
+ # self.operation is a string name of a method of the class that handles boolean matchong a condition.
+ # self.operation_method is the actual bound method object that corresponds to that string
+ self.operation_method = getattr(self, self.operation)
+ self.conditions = conditions
+
+ @property
+ def patterns(self):
+ return self.parent.patterns
+
+ def evaluate(self, file_record: FileRecord):
+ if self.tested_element == "source_path":
+ value = str(file_record.source_path)
+ else:
+ value = file_record.source_file[self.tested_element]
+ if value is None:
+ return False
+ value = str(value)
+ # we invert the result of the boolean check if Statement.inverted is True, or not if not inverted
+ return self.operation_method(value) != self.inverted
+
+ def exact(self, value):
+ return value in self.conditions
+
+ def contain(self, value):
+ for item in self.conditions:
+ if item in value:
+ return True
+ return False
+
+ def match(self, value):
+ for pattern in self.conditions:
+ if pattern.search(value):
+ return True
+ return False
+
+ def __str__(self):
+ return (
+ f"{self.tested_element} {'~' if self.inverted else ''}{self.operation} -> "
+ f"{', '.join([str(value) for value in self.conditions])}"
+ )
+
+
+class RuleConditions:
+ def __init__(
+ self,
+ rule_dict: dict,
+ parent: "Rule | RuleConditions",
+ rule_name: Optional[str] = None,
+ rule_type: Literal["all", "any"] = "all",
+ inverted: bool = False,
+ ):
+ allowed_types: List[Literal["all", "any"]] = ["all", "any"]
+ rule_methods = [all, any]
+ if rule_type not in allowed_types:
+ raise ValueError(f"rule_type must be one of : {','. join(allowed_types)}")
+
+ self.parent = parent
+ self.rule_name = rule_name
+ self.rule_type = rule_type
+ self.rule_method = rule_methods[
+ allowed_types.index(self.rule_type)
+ ] # get the actual python object corresponding to the rule type
+ self.inverted = inverted
+ self.sub_rules: List[RuleConditions | Statement] = []
+
+ for key, value in rule_dict.items():
+ allowed_types = ["all", "any"]
+ for ty in allowed_types:
+ if ty in key:
+ _rule_type = ty
+ _inverted = True if "_not" in key else False
+ sub_rule = RuleConditions(value, self, rule_type=_rule_type, inverted=_inverted)
+ break
+ else:
+ sub_rule = Statement(key, value, self)
+
+ self.sub_rules.append(sub_rule)
+
+ @property
+ def patterns(self):
+ return self.parent.patterns
+
+ def evaluate(self, file_record: FileRecord | str | Path) -> FileRecord | bool:
+ if isinstance(file_record, (str, Path)):
+ file_record = FileRecord(Path(file_record))
+ evaluations = []
+ for condition in self.sub_rules:
+ boolean_return = condition.evaluate(file_record)
+ evaluations.append(boolean_return)
+ boolean_return = self.rule_method(evaluations)
+
+ boolean_return = not boolean_return if self.inverted else boolean_return
+ if self.rule_name is None:
+ return boolean_return
+
+ file_record.match |= boolean_return
+ if boolean_return:
+ file_record.matching_rules.append(self.rule_name)
+ return file_record
+
+ def __str__(self):
+ spacer = "\n - "
+ line_return = "\n"
+ sub_rules_str = spacer + spacer.join(str(value) for value in self.sub_rules)
+ type_str = self.rule_type
+ type_str += "~" if self.inverted else ""
+ return f"{' Conditions :' if self.rule_name else ' ' + type_str}{sub_rules_str}"
+
+
+class RuleActions:
+ allowed_actions = ["rename", "include", "delete", "exclude", "abort"]
+ allowed_triggers = ["match", "destination_exists", "rename_unchanged", "rename_error", "rename_successfull"]
+ triggers: Dict[Triggers, Actions]
+
+ def __init__(self, rule_dict: dict, rule_name: str, parent: "Rule"):
+ self.rule_name = rule_name
+ self.parent = parent
+ if "on" not in rule_dict.keys():
+ raise ValueError(f'The rule {rule_name} defined no "on" triggers !')
+
+ self.triggers = rule_dict["on"]
+
+ if "match" not in self.triggers.keys():
+ raise ValueError(
+ f"match action was not defined in rule {rule_name}. Must be defined. "
+ "Set on : match to null if you wish to keep the rule but make it inactive."
+ )
+
+ if self.triggers["match"] is None:
+ self.parent.active = False
+
+ for key, value in self.triggers.items():
+ if value == "rename" and "rename" not in rule_dict.keys():
+ raise ValueError(
+ f"Trigger {key} in rule {rule_name} was defined with action rename, "
+ "but rename rules are not defined"
+ )
+ if key not in self.allowed_triggers:
+ raise ValueError(
+ f"Trigger {key} in rule {rule_name} is invalid. Valid keys are {','.join(self.allowed_triggers)}"
+ )
+ if value not in self.allowed_actions:
+ raise ValueError(
+ f"Action {value} in trigger {key} in rule {rule_name} is invalid. Valid keys are"
+ f" {','.join(self.allowed_actions)}"
+ )
+
+ self.rename_rule: dict[Element, str | dict] = rule_dict.get("rename", {})
+ for key, value in self.rename_rule.items():
+ if isinstance(value, dict):
+ pattern_name = value.get("pattern", None)
+ if pattern_name and pattern_name not in self.patterns.keys():
+ raise KeyError(
+ f"Pattern {pattern_name} was specified in rename action of rule : {self.rule_name} but that "
+ "pattern was not defined in re_patterns."
+ )
+ elif not isinstance(value, str):
+ raise ValueError(
+ f"{rule_name} rule errror in 'rename' with {key}. The content of a renaming the rule must be either"
+ " a constant string or a dictionnary. See documentation for more details."
+ )
+
+ @property
+ def patterns(self):
+ return self.parent.patterns
+
+ def actions_cascade(self, file_record: FileRecord):
+ if not file_record.match:
+ return file_record
+
+ match_action = self.triggers.get("match", None)
+ if match_action is None:
+ return file_record
+
+ if not self.is_matching_rule(file_record):
+ return file_record
+
+ file_record.used_rule += self.rule_name + " "
+
+ self.get_action_function_for("match", default="abort")(file_record, "match")
+
+ if not file_record.destination_file.is_dataset_type_valid:
+ self.get_action_function_for("invalid_alf_format", default="abort")(file_record, "invalid_alf_format")
+
+ return file_record
+
+ def is_matching_rule(self, file_record: FileRecord):
+ matching_rules = file_record.matching_rules
+
+ # no conflict between two matched rules, return the only matching rule
+ if len(matching_rules) == 1:
+ return self.rule_name == matching_rules[0]
+
+ # get a dict of "rule" : "list of overriding rules"
+ overrides_dict = {rule_name: self.parent.parent.rules[rule_name].overrides for rule_name in matching_rules}
+
+ overriden_rules = set()
+ for rule_name, overrides in overrides_dict.items():
+ for overriden_name in overrides:
+ if overriden_name in matching_rules:
+ overriden_rules.add(overriden_name)
+
+ remaining_rules = set(matching_rules).difference(overriden_rules)
+ if len(remaining_rules) == 0:
+ raise ValueError(
+ f"{','.join(set(matching_rules))} rules may be mutually overriding. Please double check your rules set."
+ )
+ if len(remaining_rules) > 1:
+ raise ValueError(
+ f"{','.join(set(remaining_rules))} rules are matched together for one file and overridings are not"
+ " defined for such cases. Please double check."
+ )
+
+ if self.rule_name == list(remaining_rules)[0]:
+ return True
+ return False
+
+ def rename_element(
+ self, file_record: FileRecord, element: Element, rule: RenameElementRule
+ ) -> Tuple[str | None, bool]:
+ """Return a renamed element of the source file based on the element name an content.
+
+ Args:
+ file_record (FileRecord): The file to perform renaming on
+ element (str): the elemnt to rename (ocject, attribute, etc.)
+ rule (str | dict): _description_
+
+ Raises:
+ ValueError: _description_
+
+ Returns:
+ _type_: _description_
+ """
+ if isinstance(rule, str): # constant replacement
+ return rule, True
+ # then, it must be a dictionnary with pattern defined
+ pattern_name = rule["pattern"]
+ search_on = rule.get("search_on", "source_path")
+ if search_on == "source_path":
+ searched_string = str(file_record.source_path)
+ elif search_on == "source_filename":
+ searched_string = str(file_record.source_path.name)
+ else:
+ searched_string = file_record.source_file[search_on] # TODO make a list check in __init__ for that
+
+ match = self.patterns[pattern_name].search(searched_string)
+
+ # we make objects that we can use in case there is a matching or evaluation error.
+ # action_if_error is a bound method instance of the current class,
+ # that corresponds by name to what the user entered in "rename_error" : "" in rule in the json file.
+ # defaults to the abort method.
+ action_if_error = self.get_action_function_for("rename_error", default="abort")
+ message_error_prefix = (
+ f"{element} matching error. Searched on {search_on}, with pattern {pattern_name}, matched {match}."
+ )
+
+ if eval_string := rule.get("eval", None):
+ try:
+ return eval(eval_string), True
+ # this occurs when there is most likely not match.
+ # Examples : NoneType is not supscriptable if match = None (TypeError)
+ # or match[3] does not exist because match contains only two elements (IndexError)
+ except (IndexError, TypeError) as e:
+ action_if_error(
+ file_record,
+ "no_match",
+ message=message_error_prefix
+ + f" Error : {e}. No match have been found. Test on https://regex101.com/",
+ )
+ return "", False
+
+ # this occurs when there is probably an error with the eval statement of the rule.
+ except Exception as e:
+ action_if_error(
+ file_record,
+ "evaluation_string_invalid",
+ message=message_error_prefix + f" Error : {e}. Evaluation string is probably invalid.",
+ )
+ return "", False
+ else: # eval is not specified. We then expect to use the first element of match as rename
+ try:
+ return match[0], True
+ # this occurs when there is most likely not match.
+ except (IndexError, TypeError) as e:
+ action_if_error(
+ file_record,
+ "no_match_first_element",
+ message=message_error_prefix
+ + f" Error : {e}. No match have been found for first element. Test on https://regex101.com/",
+ )
+ return "", False # we backtrack and don't change the element's value
+
+ # actions :
+ def rename(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.rename = True
+ file_record.executed_actions.append(f"{source} -> rename")
+ rename_status = True # will be set to false in the for loop after if any element renaming fails
+ for element, rule in self.rename_rule.items():
+ file_record.destination_file[element], element_status = self.rename_element(file_record, element, rule)
+ rename_status = rename_status and element_status
+
+ if not rename_status: # if we got a rename_error above, we skip the next steps
+ return file_record
+
+ if file_record.destination_file.fullpath == file_record.source_path:
+ file_record.rename = False
+ self.get_action_function_for("rename_unchanged", default="include")(file_record, "rename_unchanged")
+ else:
+ self.get_action_function_for("rename_successfull", default="include")(file_record, "rename_successfull")
+
+ return file_record
+
+ def exclude(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.include = False
+ file_record.executed_actions.append(f"{source} -> exclude")
+ return file_record
+
+ def include(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.include = True
+ file_record.executed_actions.append(f"{source} -> include")
+ return file_record
+
+ def delete(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.delete = True
+ file_record.executed_actions.append(f"{source} -> delete")
+ return file_record
+
+ def abort(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.abort.append(message)
+ file_record.executed_actions.append(f"{source} -> abort")
+ return file_record
+
+ def get_action_function_for(self, trigger_name: Triggers, *, default: Actions) -> ActionFunction:
+ return getattr(self, self.triggers.get(trigger_name, default))
+
+ def __str__(self):
+ spacer = "\n - "
+ triggers_str = spacer + spacer.join([str(key) + " : " + str(value) for key, value in self.triggers.items()])
+ rename_rule = spacer.join([str(key) + " : " + str(value) for key, value in self.rename_rule.items()])
+ if rename_rule:
+ rename_rule = "\n Rename Rule :" + spacer + rename_rule
+ override_rule = spacer.join(self.parent.overrides)
+ if override_rule:
+ override_rule = "\n Overrides :" + spacer + override_rule
+ return f" Actions triggers :{triggers_str}{rename_rule}{override_rule}"
+
+
+class Rule:
+ def __init__(self, rule_dict: dict, rule_name: str, parent: "Config"):
+ if "if" not in rule_dict.keys():
+ raise ValueError(f"An if field must be defined in the rule {rule_name}")
+ self.rule_name = rule_name
+ self.parent = parent
+ self.rule_conditions = RuleConditions(rule_dict["if"], self, rule_name=rule_name)
+ self.rule_actions = RuleActions(rule_dict, rule_name, self)
+ overrides = rule_dict.get("overrides", [])
+ self.overrides = overrides if isinstance(overrides, list) else [overrides]
+ self.active = True
+
+ @property
+ def patterns(self):
+ return self.parent.patterns
+
+ def evaluate(self, file_record):
+ return self.rule_conditions.evaluate(file_record) if self.active else file_record
+
+ def actions_cascade(self, file_record) -> FileRecord:
+ return self.rule_actions.actions_cascade(file_record) if self.active else file_record
+
+ def __str__(self):
+ return f"Rule : {self.rule_name}" + "\n" + str(self.rule_actions) + "\n" + str(self.rule_conditions)
diff --git a/src/alyx_connector/files/registration/__init__.py b/src/alyx_connector/files/registration/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/alyx_connector/files/registration/files.py b/src/alyx_connector/files/registration/files.py
new file mode 100644
index 0000000000000000000000000000000000000000..f297d29baa3edc85086daafa84190dae6e665b94
--- /dev/null
+++ b/src/alyx_connector/files/registration/files.py
@@ -0,0 +1,198 @@
+from dataclasses import dataclass, field
+from pathlib import Path
+from pandas import Series, DataFrame
+from ...files.parsing.files import File
+
+
+@dataclass
+class ActionRequests:
+
+ rename = False
+ delete = False
+ include = False
+ abort = False
+
+
+@dataclass
+class Issues:
+
+ path_conflicts = False
+ parseable = False
+ dataset_type_exists = False
+
+ sources: list[str] = field(default_factory=list)
+
+
+class FileStatus:
+
+ def __init__(self):
+ self.issues = Issues()
+ self.requests = ActionRequests()
+
+
+class FileRecordSeries(Series):
+
+ def __init__(self, source_path: str | Path):
+ data = {}
+ data["source_path"] = Path(source_path)
+ data["matching_rules"] = []
+ data["used_rule"] = None
+ super().__init__(data)
+
+
+@dataclass
+class FileRecord:
+ # source_path is the original path from disk scan. will never change
+ source_path: Path
+
+ match: bool = False
+ matching_rules: list = field(default_factory=list)
+ used_rule: str = ""
+
+ valid_alf: bool = False
+ path_conflicts: bool = False
+ dataset_type_exists: bool = False
+ rename: bool = False
+ delete: bool = False
+ include: bool = False
+ abort: list = field(default_factory=list)
+
+ frozen = False
+
+ executed_actions = []
+
+ # source file
+ @property
+ def source_file(self) -> File:
+ source_file = getattr("self", "_source_file", None)
+ if source_file is None:
+ try:
+ source_file = File.from_path(self.source_path)
+ except Exception as e:
+ raise ValueError(f"File from {self.source_path} was not parseable ! {type(e)}:{e}")
+ self._source_file = source_file
+ return source_file
+
+ # was alf_info
+ @property
+ def destination_file(self) -> File:
+ destination_file = getattr("self", "_destination_file", None)
+ if destination_file is None:
+ destination_file = self.source_file.copy()
+ self._destination_file = destination_file
+ return destination_file
+
+ @property
+ def final_path(self) -> Path:
+ if not hasattr("self", "_final_path"):
+ self._final_path = self.destination_file.fullpath if self.rename else self.source_path
+ return self._final_path
+
+ @property
+ def final_file(self) -> "File":
+ if not hasattr("self", "_final_file"):
+ self._final_file = self.destination_file if self.rename else self.source_file
+ return self._final_file
+
+ @property
+ def final_pathstring(self):
+ if not hasattr("self", "_final_pathstring"):
+ self._final_pathstring = str(self.final_path)
+ return self._final_pathstring
+
+ def actions_cascade(self, config: "Config"):
+ for rule in config.rules.values():
+ rule.actions_cascade(self)
+
+ def finish_cascade(self, config: "Config"):
+ # change the values of the filre record after all other actions have been resolved.
+ # finish actions include calculating ,
+
+ self.valid_alf = self.destination_file.is_dataset_type_valid
+
+ if self.valid_alf and self.destination_file.dataset_type in config.dataset_types:
+ self.dataset_type_exists = True
+
+ @property
+ def inclusion_accepted(self):
+ if (
+ self.include
+ and self.valid_alf
+ and self.dataset_type_exists
+ and not self.path_conflicts
+ and not self.abort
+ and not self.delete
+ ):
+ return True
+ return False
+
+ @property
+ def rename_accepted(self):
+ if self.rename and self.valid_alf and not self.path_conflicts and not self.abort and not self.delete:
+ return True
+ return False
+
+ def apply_changes(self, do_deletes=True, do_renames=True): # apply changes to file_record
+ if self.delete and self.rename:
+ raise ValueError("Cannot rename AND delete the same entry.")
+
+ if self.rename_accepted and do_renames:
+ file_directory = self.destination_file.fullpath.parent
+ file_directory.mkdir(parents=True, exist_ok=True)
+ self.source_file.fullpath.rename(self.destination_file.fullpath)
+
+ elif self.delete and do_deletes:
+ self.source_file.fullpath.unlink()
+ self.include = False
+
+ def to_user_dict(self):
+ return {
+ "source_path": self.source_path,
+ "dest_path": str(self.destination_file.fullpath) if self.rename_accepted else "",
+ "info": self.info_message,
+ }
+
+ @property
+ def info_message(
+ self,
+ ): # message to make from action booleans to help the use understand what happened
+ message = ""
+ if self.inclusion_accepted and not self.rename_accepted:
+ message = " included without change"
+
+ if self.inclusion_accepted and self.rename_accepted:
+ message = " renamed and included"
+
+ if not self.inclusion_accepted and self.rename_accepted:
+ message = " renamed and excluded"
+
+ if not self.inclusion_accepted and not self.rename_accepted:
+ message = " excluded without change"
+
+ if not self.valid_alf:
+ message = message + " dataset_type doesn't follow alyx format"
+
+ if not self.dataset_type_exists:
+ message = message + f" dataset_type:{self.destination_file.dataset_type} not existing"
+
+ if self.delete:
+ message = " auto deleted"
+
+ if self.abort:
+ message_prefix = " Aborting due to errors : "
+ abort_messages = []
+ for ab_msg in self.abort:
+ if ab_msg == " filepath_conflicts":
+ ab_msg = " File name conflicts with a current file or another file that will be renamed identically"
+ abort_messages.append(ab_msg)
+
+ message = (
+ message_prefix
+ + ", ".join(abort_messages)
+ # + " --- Without Abort, would have been "
+ # + message
+ )
+ else:
+ message = "Will be " + message
+
+ return str(message)
diff --git a/src/alyx_connector/files/registration/manage.py b/src/alyx_connector/files/registration/manage.py
new file mode 100644
index 0000000000000000000000000000000000000000..7105d2ad0149242e556ca2642eedd6961b5b1b1c
--- /dev/null
+++ b/src/alyx_connector/files/registration/manage.py
@@ -0,0 +1,21 @@
+
+
+
+class RegistrationClient:
+
+ def add_files(self, files_list):
+
+ connector.web_client.create(
+ endpoint="datasets",
+ data={
+ "session_pk": "dc5a61db-cbb6-48dc-bcb9-310211c8512c",
+ "dataset_type": "trials.choice",
+ "collection": "DELETE_LATER_JUST_A_TEST",
+ "data_format": ".txt",
+ "set_file_records": [
+ {"extra": "001", "exists": True},
+ {"extra": "002", "exists": True},
+ {"extra": "003", "exists": True},
+ ],
+ },
+ )
diff --git a/src/alyx_connector/files/registration/rules.json b/src/alyx_connector/files/registration/rules.json
new file mode 100644
index 0000000000000000000000000000000000000000..8845409e3c3b858b4ba6ea6ff0b2ed1bd3c79d54
--- /dev/null
+++ b/src/alyx_connector/files/registration/rules.json
@@ -0,0 +1,466 @@
+{
+ "re_patterns": {
+ "VGAT_MOUSE_NO": "Vgat.*?(\\d{1,3}).*jRGECO",
+ "TIFF_FRAME_NO": ".*(\\d{5})\\.tiff?$",
+ "TDMS_TRIALS_TABLE_TIME": "(\\d{4}_\\d{2}_\\d{2}_\\d{2}_\\d{2})\\.tdms$",
+ "TDMS_VIDEO_TRIAL_NO": ".*?(\\d+)\\.tdms$",
+ "FOV_NO": "^.*(?:(?:FOV)|(?:fieldOfView))[-_ \\.]*?(\\d+).*$",
+ "CONDENSED_DATE": ".*?(20\\d{4,6}).*?",
+ "SESSION_NO": ".*?20\\d{4,6}_(\\d).*?",
+ "ALYX_PATH_EID": "\\w+(?:\\|\/)\\d{4}\\-\\d{2}\\-\\d{2}(?:\\|\/)\\d{3}",
+ "IOI_WHISKER": "^([a-zA-Z0-9]+)",
+ "IOI_WITH_VERSIONS": "^(?:stim.*?_)?([a-zA-Z0-9]+)(?:(?:_|.)((?:[vV]\\d+)|(?:crash)))?(?:stim)?.*$"
+ },
+ "rules": {
+ "imaging_data_rule1": {
+ "if": {
+ "extension": {
+ "exact": [
+ "tif",
+ "tiff"
+ ]
+ },
+ "collection": {
+ "contain": "imaging_data"
+ }
+ },
+ "on": {
+ "match": "rename",
+ "destination_exists": "abort",
+ "rename_unchanged": "exclude"
+ },
+ "rename": {
+ "object": "imaging",
+ "attribute": "frames",
+ "extra": {
+ "pattern": "TIFF_FRAME_NO",
+ "eval": "match[1].zfill(5)"
+ }
+ }
+ },
+ "imaging_data_rule2": {
+ "if": {
+ "object": "imaging",
+ "attribute": "frames",
+ "extra": {
+ "exact_not": ""
+ }
+ },
+ "on": {
+ "match": "include"
+ },
+ "overrides": [
+ "imaging_data_rule1"
+ ]
+ },
+ "behavior_pupil_rule1": {
+ "if": {
+ "extension": "tdms",
+ "collection": {
+ "contain": [
+ "pupil"
+ ]
+ }
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "behaviour",
+ "attribute": "video",
+ "collection": "behaviour_imaging\\pupil",
+ "extra": {
+ "pattern": "TDMS_VIDEO_TRIAL_NO",
+ "eval": "'pupil.' + match[1].zfill(5)"
+ }
+ }
+ },
+ "behavior_whiskers_rule1": {
+ "if": {
+ "extension": "tdms",
+ "collection": {
+ "contain": [
+ "whiskers",
+ "whisker"
+ ]
+ }
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "behaviour",
+ "attribute": "video",
+ "collection": "behaviour_imaging\\whiskers",
+ "extra": {
+ "pattern": "TDMS_VIDEO_TRIAL_NO",
+ "eval": "'whiskers.' + match[1].zfill(5)"
+ }
+ }
+ },
+ "field_of_view_png_rule1": {
+ "if": {
+ "extension": [
+ "png",
+ "PNG"
+ ],
+ "collection": [
+ "",
+ "imaging_data"
+ ],
+ "object": {
+ "contain": [
+ "FOV",
+ "imaging"
+ ]
+ }
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "imaging",
+ "attribute": "fieldOfView",
+ "collection": "imaging_data",
+ "extra": {
+ "pattern": "FOV_NO",
+ "eval": "match[1].zfill(2) if match is not None and match.lastindex > 0 else ''"
+ }
+ }
+ },
+ "behavior_timeline_tdms_rule1": {
+ "if": {
+ "extension": "tdms",
+ "collection": ""
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "trials",
+ "attribute": "eventTimeline",
+ "extra": ""
+ }
+ },
+ "behavior_timeline_tdms_rule2": {
+ "if": {
+ "extension": "tdms",
+ "collection": "imaging_data",
+ "object": {
+ "contain": [
+ "VGAT",
+ "EGFP"
+ ]
+ }
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "trials",
+ "attribute": "eventTimeline",
+ "collection": "",
+ "extra": ""
+ },
+ "overrides": [
+ "behavior_timeline_tdms_rule1"
+ ]
+ },
+ "intrinsic_imaging_tdms_rule1": {
+ "if": {
+ "extension": "tdms",
+ "collection": {
+ "exact": [
+ "intrinsic_optical_imaging",
+ "IOI"
+ ]
+ }
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "imaging_intrinsic",
+ "attribute": "delta_stim_images",
+ "extra": {
+ "search_on": "source_filename",
+ "pattern": "IOI_WITH_VERSIONS",
+ "eval": "match[1] + ('.' + match[2] if match.lastindex > 1 else '')"
+ },
+ "collection": "intrinsic_optical_imaging"
+ }
+ },
+ "intrinsic_imaging_vessels_rule1": {
+ "if": {
+ "extension": [
+ "",
+ "tiff"
+ ],
+ "collection": {
+ "exact": [
+ "intrinsic_optical_imaging",
+ "IOI"
+ ]
+ },
+ "object": {
+ "contain": [
+ "reference",
+ "green",
+ "Green",
+ "FOV",
+ "fov"
+ ]
+ }
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "imaging_intrinsic",
+ "attribute": "vessels_reference",
+ "extension": "tiff",
+ "collection": "intrinsic_optical_imaging"
+ }
+ },
+ "intrinsic_imaging_binaries_rule1": {
+ "if": {
+ "extension": [
+ ""
+ ],
+ "collection": {
+ "exact": [
+ "intrinsic_optical_imaging",
+ "IOI"
+ ]
+ },
+ "object": {
+ "contain_not": [
+ "reference",
+ "green",
+ "Green"
+ ]
+ }
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "imaging_intrinsic",
+ "attribute": "bin_delta_stim_images",
+ "extension": "binlv",
+ "collection": "intrinsic_optical_imaging",
+ "extra": {
+ "search_on": "source_filename",
+ "pattern": "IOI_WITH_VERSIONS",
+ "eval": "match[1] + ('.' + match[2] if match.lastindex > 1 else '')"
+ }
+ }
+ },
+ "intrinsic_imaging_alredy_renamed_versions_rule1": {
+ "if": {
+ "collection": {
+ "exact": [
+ "intrinsic_optical_imaging"
+ ]
+ },
+ "object": {
+ "exact": "imaging_intrinsic"
+ },
+ "attribute": {
+ "exact": [
+ "delta_stim_images",
+ "bin_delta_stim_images",
+ "vessels_reference"
+ ]
+ },
+ "extension": {
+ "exact": [
+ "binlv",
+ "tdms",
+ "tiff"
+ ]
+ }
+ },
+ "on": {
+ "match": "include"
+ },
+ "overrides": [
+ "intrinsic_imaging_binaries_rule1",
+ "intrinsic_imaging_vessels_rule1",
+ "intrinsic_imaging_tdms_rule1"
+ ]
+ },
+ "behavior_trigger_text_pupil_rule1": {
+ "if": {
+ "extension": "txt",
+ "collection": {
+ "contain": [
+ "pupil"
+ ]
+ },
+ "object": "Trigger"
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "behaviour",
+ "attribute": "video_triggers",
+ "collection": "behaviour_imaging\\pupil",
+ "extra": "pupil"
+ }
+ },
+ "behavior_trigger_text_whiskers_rule1": {
+ "if": {
+ "extension": "txt",
+ "collection": {
+ "contain": [
+ "whiskers",
+ "whisker"
+ ]
+ },
+ "object": "Trigger"
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "behaviour",
+ "attribute": "video_triggers",
+ "collection": "behaviour_imaging\\whiskers",
+ "extra": "whiskers"
+ }
+ },
+ "behavior_cam_settings_text_pupil_rule1": {
+ "if": {
+ "extension": "txt",
+ "collection": {
+ "contain": [
+ "pupil"
+ ]
+ },
+ "object": "CameraSettings"
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "behaviour",
+ "attribute": "camera_settings",
+ "collection": "behaviour_imaging\\pupil",
+ "extra": "pupil"
+ }
+ },
+ "behavior_cam_settings_text_whiskers_rule1": {
+ "if": {
+ "extension": "txt",
+ "collection": {
+ "contain": [
+ "whiskers",
+ "whisker"
+ ]
+ },
+ "object": "CameraSettings"
+ },
+ "on": {
+ "match": "rename"
+ },
+ "rename": {
+ "object": "behaviour",
+ "attribute": "camera_settings",
+ "collection": "behaviour_imaging\\whiskers",
+ "extra": "whiskers"
+ }
+ },
+ "behavior_cam_sessings_include_rule": {
+ "if": {
+ "extension": "txt",
+ "collection": {
+ "exact": [
+ "behaviour_imaging\\whiskers",
+ "behaviour_imaging\\pupil"
+ ]
+ },
+ "object": "behaviour",
+ "attribute": "camera_settings",
+ "extra": {
+ "exact": [
+ "whiskers",
+ "pupil"
+ ]
+ }
+ },
+ "on": {
+ "match": "include"
+ },
+ "overrides": [
+ "behavior_cam_settings_text_whiskers_rule1",
+ "behavior_cam_settings_text_pupil_rule1"
+ ]
+ },
+ "delete_tdms_index_rule1": {
+ "if": {
+ "extension": "tdms_index"
+ },
+ "on": {
+ "match": "delete"
+ },
+ "overrides": [
+ "intrinsic_imaging_exclude_versions_rule1"
+ ]
+ },
+ "exclude_Thumbs_rule1": {
+ "if": {
+ "extension": "db",
+ "object": "Thumbs"
+ },
+ "on": {
+ "match": "exclude"
+ }
+ },
+ "exclude_svg_files_rule1": {
+ "if": {
+ "extension": [
+ "svg",
+ "SVG"
+ ]
+ },
+ "on": {
+ "match": "exclude"
+ }
+ },
+ "include_test_data_rule": {
+ "if": {
+ "collection": "DELETE_LATER_JUST_A_TEST"
+ },
+ "on": {
+ "match": "include"
+ }
+ }
+ },
+ "excluded_folders": [
+ "figures",
+ "preprocessing_saves",
+ "screen_captures",
+ "suite2p",
+ "screenshots",
+ "trash",
+ "draft",
+ "scratch",
+ "Fiji_analysis",
+ "fiji_analysis",
+ "fijianalysis",
+ "Fiji_Analysis",
+ "FijiAnalysis",
+ "fijiAnalysis"
+ ],
+ "excluded_filenames": [
+ "session_meta.json",
+ "pipelines_arguments.json"
+ ],
+ "cleanup_folders": [
+ "pupil",
+ "whiskers",
+ "whisker"
+ ]
+}
\ No newline at end of file
diff --git a/src/alyx_connector/files/registration/rules_config.py b/src/alyx_connector/files/registration/rules_config.py
new file mode 100644
index 0000000000000000000000000000000000000000..b8bde7fa30406290dc39c029d0d1fe7abb09b95a
--- /dev/null
+++ b/src/alyx_connector/files/registration/rules_config.py
@@ -0,0 +1,900 @@
+from dataclasses import dataclass, field
+from logging import getLogger
+import os, shutil, re, json, pkgutil
+from pandas import Series, DataFrame
+from pathlib import Path
+from re import Pattern
+
+from .utils import get_existing_datasets, find_files
+from ...files.parsing.files import File
+
+from typing import Literal, List, Dict, Tuple, Optional, Union, Callable, Protocol, Iterator, cast, TYPE_CHECKING
+
+if TYPE_CHECKING:
+ from ...connector import Connector
+
+Element = Literal[
+ "source_path",
+ "subject",
+ "date",
+ "number",
+ "root",
+ "object",
+ "attribute",
+ "extension",
+ "extra",
+ "collection",
+ "revision",
+]
+
+Triggers = Literal[
+ "match",
+ "destination_exists",
+ "invalid_alf_format",
+ "rename_unchanged",
+ "rename_error",
+ "rename_successfull",
+]
+
+
+Actions = Literal["rename", "include", "delete", "exclude", "abort"]
+
+CheckFullOperation = Literal["exact", "contain", "match", "exact_not", "contain_not", "match_not"]
+CheckOperation = Literal["exact", "contain", "match"]
+
+RulesConfig = Dict[
+ Literal["re_patterns", "rules", "excluded_folders", "excluded_filenames", "cleanup_folders"], str | dict
+]
+
+Rules = Dict[Literal["if", "on", "overrides", Actions], dict | list]
+
+RenameElementRule = Union[str, Dict[Literal["pattern", "eval", "search_on"], str]]
+
+Patterns = Dict[str, str]
+
+
+class FilesRecordList:
+ def __init__(self, records: List["FileRecord"], session: Optional[Series] = None):
+ self.records = records
+ self.session = session
+
+ def to_dataframe(self, details=True) -> DataFrame:
+ dicts = []
+
+ if details:
+ for file_record in self.records:
+ dico = file_record.__dict__
+ dico["info"] = file_record.info_message
+ dicts.append(dico)
+ else:
+
+ for file_record in self.records:
+ dicts.append(file_record.to_user_dict())
+
+ return DataFrame(dicts)
+
+ def actions_cascade(self, config: "Config"):
+
+ for record in self.records:
+ record.source_file # verify we can pase the path as a valid file system compatible item
+ record.actions_cascade(config)
+
+ def finish_cascade(self, config: "Config"):
+ for record in self.records:
+ record.finish_cascade(config)
+
+ def check_duplicate_final_paths(self):
+ # checking if destination_file conflicts with a file already existing
+ # of other file's destination_file.fullpath.
+ paths = Series([fr.final_pathstring for fr in self.records if not fr.delete])
+ duplicates = paths[paths.duplicated(keep=False)].unique()
+
+ for file_record in self.records:
+ if file_record.final_pathstring in duplicates:
+ file_record.abort.append("filepath_conflicts")
+ file_record.path_conflicts = True
+
+ def __repr__(self):
+ return repr(self.to_dataframe(details=True))
+
+ def _repr_mimebundle_(self, include=None, exclude=None):
+ from IPython.core.getipython import get_ipython
+ from IPython.core.formatters import DisplayFormatter
+
+ df = self.to_dataframe(details=True)
+ ipython = get_ipython()
+ if ipython is None or ipython.display_formatter is None:
+ return None
+ formatter = cast(DisplayFormatter, ipython.display_formatter).format
+ return formatter(df, include=include, exclude=exclude)
+
+ # Delegate list methods explicitly
+ def __getitem__(self, index: int) -> "FileRecord":
+ return self.records[index]
+
+ def __len__(self):
+ return len(self.records)
+
+ def __iter__(self) -> Iterator["FileRecord"]:
+ return iter(self.records)
+
+ def append(self, item: "FileRecord"):
+ self.records.append(item)
+
+ def extend(self, items: List["FileRecord"]):
+ self.records.extend(items)
+
+ def stats(self):
+ return self.to_dataframe().groupby(["used_rule", "info"]).size()
+
+
+class ActionFunction(Protocol):
+ def __call__(self, file_record: "FileRecord", source: str, *, message: str = "") -> "FileRecord": ...
+
+
+class OperationFunction(Protocol):
+ def __call__(
+ self,
+ value: str,
+ ) -> bool: ...
+
+
+@dataclass
+class FileRecord:
+ # source_path is the original path from disk scan. will never change
+ source_path: Path
+
+ match: bool = False
+ matching_rules: list = field(default_factory=list)
+ used_rule: str = ""
+
+ valid_alf: bool = False
+ path_conflicts: bool = False
+ dataset_type_exists: bool = False
+ rename: bool = False
+ delete: bool = False
+ include: bool = False
+ abort: list = field(default_factory=list)
+
+ executed_actions: list = field(default_factory=list)
+
+ # source file
+ @property
+ def source_file(self) -> File:
+ source_file = getattr(self, "_source_file", None)
+ if source_file is None:
+ try:
+ source_file = File.from_path(self.source_path)
+ except Exception as e:
+ raise ValueError(f"File from {self.source_path} was not parseable ! {type(e)}:{e}")
+ self._source_file = source_file
+ return source_file
+
+ # was alf_info
+ @property
+ def destination_file(self) -> File:
+ if not hasattr(self, "_destination_file"):
+ self._destination_file = self.source_file.copy()
+ return self._destination_file
+
+ @property
+ def final_path(self) -> Path:
+ if not hasattr(self, "_final_path"):
+ self._final_path = self.destination_file.fullpath if self.rename else self.source_path
+ return self._final_path
+
+ @property
+ def final_file(self) -> "File":
+ if not hasattr(self, "_final_file"):
+ self._final_file = self.destination_file if self.rename else self.source_file
+ return self._final_file
+
+ @property
+ def final_pathstring(self):
+ if not hasattr(self, "_final_pathstring"):
+ self._final_pathstring = str(self.final_path)
+ return self._final_pathstring
+
+ def actions_cascade(self, config: "Config"):
+ for rule in config.rules.values():
+ rule.actions_cascade(self)
+
+ def finish_cascade(self, config: "Config"):
+ # change the values of the file record after all other actions have been resolved.
+ # finish actions include calculating ,
+
+ self.valid_alf = self.destination_file.is_dataset_type_valid
+
+ if self.valid_alf and self.destination_file.dataset_type in config.dataset_types:
+ self.dataset_type_exists = True
+
+ @property
+ def inclusion_accepted(self):
+ if (
+ self.include
+ and self.valid_alf
+ and self.dataset_type_exists
+ and not self.path_conflicts
+ and not self.abort
+ and not self.delete
+ ):
+ return True
+ return False
+
+ @property
+ def rename_accepted(self):
+ if self.rename and self.valid_alf and not self.path_conflicts and not self.abort and not self.delete:
+ return True
+ return False
+
+ def apply_changes(self, do_deletes=True, do_renames=True): # apply changes to file_record
+ if self.delete and self.rename:
+ raise ValueError("Cannot rename AND delete the same entry.")
+
+ if self.rename_accepted and do_renames:
+ file_directory = self.destination_file.fullpath.parent
+ file_directory.mkdir(parents=True, exist_ok=True)
+ self.source_file.fullpath.rename(self.destination_file.fullpath)
+
+ elif self.delete and do_deletes:
+ self.source_file.fullpath.unlink()
+ self.include = False
+
+ def to_user_dict(self):
+ return {
+ "source_path": self.source_path,
+ "dest_path": str(self.destination_file.fullpath) if self.rename_accepted else "",
+ "info": self.info_message,
+ }
+
+ @property
+ def info_message(
+ self,
+ ): # message to make from action booleans to help the use understand what happened
+ message = ""
+ if self.inclusion_accepted and not self.rename_accepted:
+ message = " included without change"
+
+ if self.inclusion_accepted and self.rename_accepted:
+ message = " renamed and included"
+
+ if not self.inclusion_accepted and self.rename_accepted:
+ message = " renamed and excluded"
+
+ if not self.inclusion_accepted and not self.rename_accepted:
+ message = " excluded without change"
+
+ if not self.valid_alf:
+ message = message + " dataset_type doesn't follow alyx format"
+
+ if not self.dataset_type_exists:
+ message = message + f" dataset_type:{self.destination_file.dataset_type} not existing"
+
+ if self.delete:
+ message = " auto deleted"
+
+ if self.abort:
+ message_prefix = " Aborting due to errors : "
+ abort_messages = []
+ for ab_msg in self.abort:
+ if ab_msg == " filepath_conflicts":
+ ab_msg = " File name conflicts with a current file or another file that will be renamed identically"
+ abort_messages.append(ab_msg)
+
+ message = (
+ message_prefix
+ + ", ".join(abort_messages)
+ # + " --- Without Abort, would have been "
+ # + message
+ )
+ else:
+ message = "Will be " + message
+
+ return str(message)
+
+
+class Statement:
+ allowed_operations: List[CheckOperation] = ["exact", "contain", "match"]
+ allowed_elements = [
+ "source_path",
+ "subject",
+ "date",
+ "number",
+ "root",
+ "object",
+ "attribute",
+ "extension",
+ "extra",
+ "collection",
+ "revision",
+ ]
+ conditions: List[str] | List[Pattern]
+ operation: CheckOperation
+ operation_method: OperationFunction
+
+ def __init__(
+ self, element: Element, operation_detail: str | List[str] | Dict[CheckFullOperation, str | list[str]], parent
+ ):
+ self.inverted = False
+ self.parent = parent
+
+ for el in self.allowed_elements:
+ if element == el:
+ self.tested_element = element
+ break
+ else:
+ raise ValueError(
+ f"Tested element is {self.tested_element} wich is invalid value. "
+ f"If must be one of :({''.join(self.allowed_elements)})"
+ )
+
+ if isinstance(operation_detail, dict):
+ # if the operation detail is a dict, if should contain a single key, wich is the check operation type
+ if len(operation_detail) != 1:
+ raise ValueError(
+ f"Content of tested element {self.tested_element} is a dict. "
+ "Then it must contain only one key ({''.join(self.allowed_operations)})"
+ )
+
+ operation = list(operation_detail.keys())[0]
+ conditions = operation_detail[operation]
+
+ for op in self.allowed_operations:
+ if op in operation:
+ self.inverted = True if "_not" in operation else False
+ self.operation = op
+ break
+ else:
+ raise ValueError(
+ f"Content of tested element {self.tested_element} is a dict and the key present was : {operation}. "
+ "It must contain one of : ({''.join(self.allowed_operations)}). "
+ )
+ else:
+ # If the operation detail is not a dict, then we asume that the check operation
+ # is : "exact" matching of the string or strings
+ self.operation = "exact"
+ conditions = operation_detail
+
+ if not isinstance(conditions, list):
+ conditions = [conditions]
+
+ if self.operation == "match":
+ existing_patterns = self.patterns
+ patterns = []
+ for pattern_name in conditions:
+ try:
+ patterns.append(existing_patterns[pattern_name])
+ except KeyError:
+ raise ValueError(
+ f"Pattern {pattern_name} was asked in condition statement {self.tested_element} "
+ "but was not defined in re_patterns."
+ )
+ conditions = patterns
+
+ # self.operation is a string name of a method of the class that handles boolean matchong a condition.
+ # self.operation_method is the actual bound method object that corresponds to that string
+ self.operation_method = getattr(self, self.operation)
+ self.conditions = conditions
+
+ @property
+ def patterns(self):
+ return self.parent.patterns
+
+ def evaluate(self, file_record: FileRecord):
+ if self.tested_element == "source_path":
+ value = str(file_record.source_path)
+ else:
+ value = file_record.source_file[self.tested_element]
+ if value is None:
+ return False
+ value = str(value)
+ # we invert the result of the boolean check if Statement.inverted is True, or not if not inverted
+ return self.operation_method(value) != self.inverted
+
+ def exact(self, value):
+ return value in self.conditions
+
+ def contain(self, value):
+ for item in self.conditions:
+ if item in value:
+ return True
+ return False
+
+ def match(self, value):
+ for pattern in self.conditions:
+ if pattern.search(value):
+ return True
+ return False
+
+ def __str__(self):
+ return (
+ f"{self.tested_element} {'~' if self.inverted else ''}{self.operation} -> "
+ f"{', '.join([str(value) for value in self.conditions])}"
+ )
+
+
+class RuleConditions:
+ def __init__(
+ self,
+ rule_dict: dict,
+ parent: "Rule | RuleConditions",
+ rule_name: Optional[str] = None,
+ rule_type: Literal["all", "any"] = "all",
+ inverted: bool = False,
+ ):
+ allowed_types: List[Literal["all", "any"]] = ["all", "any"]
+ rule_methods = [all, any]
+ if rule_type not in allowed_types:
+ raise ValueError(f"rule_type must be one of : {','. join(allowed_types)}")
+
+ self.parent = parent
+ self.rule_name = rule_name
+ self.rule_type = rule_type
+ self.rule_method = rule_methods[
+ allowed_types.index(self.rule_type)
+ ] # get the actual python object corresponding to the rule type
+ self.inverted = inverted
+ self.sub_rules: List[RuleConditions | Statement] = []
+
+ for key, value in rule_dict.items():
+ allowed_types = ["all", "any"]
+ for ty in allowed_types:
+ if ty in key:
+ _rule_type = ty
+ _inverted = True if "_not" in key else False
+ sub_rule = RuleConditions(value, self, rule_type=_rule_type, inverted=_inverted)
+ break
+ else:
+ sub_rule = Statement(key, value, self)
+
+ self.sub_rules.append(sub_rule)
+
+ @property
+ def patterns(self):
+ return self.parent.patterns
+
+ def evaluate(self, file_record: FileRecord | str | Path) -> FileRecord | bool:
+ if isinstance(file_record, (str, Path)):
+ file_record = FileRecord(Path(file_record))
+ evaluations = []
+ for condition in self.sub_rules:
+ boolean_return = condition.evaluate(file_record)
+ evaluations.append(boolean_return)
+ boolean_return = self.rule_method(evaluations)
+
+ boolean_return = not boolean_return if self.inverted else boolean_return
+ if self.rule_name is None:
+ return boolean_return
+
+ file_record.match |= boolean_return
+ if boolean_return:
+ file_record.matching_rules.append(self.rule_name)
+ return file_record
+
+ def __str__(self):
+ spacer = "\n - "
+ line_return = "\n"
+ sub_rules_str = spacer + spacer.join(str(value) for value in self.sub_rules)
+ type_str = self.rule_type
+ type_str += "~" if self.inverted else ""
+ return f"{' Conditions :' if self.rule_name else ' ' + type_str}{sub_rules_str}"
+
+
+class RuleActions:
+ allowed_actions = ["rename", "include", "delete", "exclude", "abort"]
+ allowed_triggers = ["match", "destination_exists", "rename_unchanged", "rename_error", "rename_successfull"]
+ triggers: Dict[Triggers, Actions]
+
+ def __init__(self, rule_dict: dict, rule_name: str, parent: "Rule"):
+ self.rule_name = rule_name
+ self.parent = parent
+ if "on" not in rule_dict.keys():
+ raise ValueError(f'The rule {rule_name} defined no "on" triggers !')
+
+ self.triggers = rule_dict["on"]
+
+ if "match" not in self.triggers.keys():
+ raise ValueError(
+ f"match action was not defined in rule {rule_name}. Must be defined. "
+ "Set on : match to null if you wish to keep the rule but make it inactive."
+ )
+
+ if self.triggers["match"] is None:
+ self.parent.active = False
+
+ for key, value in self.triggers.items():
+ if value == "rename" and "rename" not in rule_dict.keys():
+ raise ValueError(
+ f"Trigger {key} in rule {rule_name} was defined with action rename, "
+ "but rename rules are not defined"
+ )
+ if key not in self.allowed_triggers:
+ raise ValueError(
+ f"Trigger {key} in rule {rule_name} is invalid. Valid keys are {','.join(self.allowed_triggers)}"
+ )
+ if value not in self.allowed_actions:
+ raise ValueError(
+ f"Action {value} in trigger {key} in rule {rule_name} is invalid. Valid keys are"
+ f" {','.join(self.allowed_actions)}"
+ )
+
+ self.rename_rule: dict[Element, str | dict] = rule_dict.get("rename", {})
+ for key, value in self.rename_rule.items():
+ if isinstance(value, dict):
+ pattern_name = value.get("pattern", None)
+ if pattern_name and pattern_name not in self.patterns.keys():
+ raise KeyError(
+ f"Pattern {pattern_name} was specified in rename action of rule : {self.rule_name} but that "
+ "pattern was not defined in re_patterns."
+ )
+ elif not isinstance(value, str):
+ raise ValueError(
+ f"{rule_name} rule errror in 'rename' with {key}. The content of a renaming the rule must be either"
+ " a constant string or a dictionnary. See documentation for more details."
+ )
+
+ @property
+ def patterns(self):
+ return self.parent.patterns
+
+ def actions_cascade(self, file_record: FileRecord):
+ if not file_record.match:
+ return file_record
+
+ match_action = self.triggers.get("match", None)
+ if match_action is None:
+ return file_record
+
+ if not self.is_matching_rule(file_record):
+ return file_record
+
+ file_record.used_rule += self.rule_name + " "
+
+ self.get_action_function_for("match", default="abort")(file_record, "match")
+
+ if not file_record.destination_file.is_dataset_type_valid:
+ self.get_action_function_for("invalid_alf_format", default="abort")(file_record, "invalid_alf_format")
+
+ return file_record
+
+ def is_matching_rule(self, file_record: FileRecord):
+ matching_rules = file_record.matching_rules
+
+ # no conflict between two matched rules, return the only matching rule
+ if len(matching_rules) == 1:
+ return self.rule_name == matching_rules[0]
+
+ # get a dict of "rule" : "list of overriding rules"
+ overrides_dict = {rule_name: self.parent.parent.rules[rule_name].overrides for rule_name in matching_rules}
+
+ overriden_rules = set()
+ for rule_name, overrides in overrides_dict.items():
+ for overriden_name in overrides:
+ if overriden_name in matching_rules:
+ overriden_rules.add(overriden_name)
+
+ remaining_rules = set(matching_rules).difference(overriden_rules)
+ if len(remaining_rules) == 0:
+ raise ValueError(
+ f"{','.join(set(matching_rules))} rules may be mutually overriding. Please double check your rules set."
+ )
+ if len(remaining_rules) > 1:
+ raise ValueError(
+ f"{','.join(set(remaining_rules))} rules are matched together for one file and overridings are not"
+ " defined for such cases. Please double check."
+ )
+
+ if self.rule_name == list(remaining_rules)[0]:
+ return True
+ return False
+
+ def rename_element(
+ self, file_record: FileRecord, element: Element, rule: RenameElementRule
+ ) -> Tuple[str | None, bool]:
+ """Return a renamed element of the source file based on the element name an content.
+
+ Args:
+ file_record (FileRecord): The file to perform renaming on
+ element (str): the elemnt to rename (ocject, attribute, etc.)
+ rule (str | dict): _description_
+
+ Raises:
+ ValueError: _description_
+
+ Returns:
+ _type_: _description_
+ """
+ if isinstance(rule, str): # constant replacement
+ return rule, True
+ # then, it must be a dictionnary with pattern defined
+ pattern_name = rule["pattern"]
+ search_on = rule.get("search_on", "source_path")
+ if search_on == "source_path":
+ searched_string = str(file_record.source_path)
+ elif search_on == "source_filename":
+ searched_string = str(file_record.source_path.name)
+ else:
+ searched_string = file_record.source_file[search_on] # TODO make a list check in __init__ for that
+
+ match = self.patterns[pattern_name].search(searched_string)
+
+ # we make objects that we can use in case there is a matching or evaluation error.
+ # action_if_error is a bound method instance of the current class,
+ # that corresponds by name to what the user entered in "rename_error" : "" in rule in the json file.
+ # defaults to the abort method.
+ action_if_error = self.get_action_function_for("rename_error", default="abort")
+ message_error_prefix = (
+ f"{element} matching error. Searched on {search_on}, with pattern {pattern_name}, matched {match}."
+ )
+
+ if eval_string := rule.get("eval", None):
+ try:
+ return eval(eval_string), True
+ # this occurs when there is most likely not match.
+ # Examples : NoneType is not supscriptable if match = None (TypeError)
+ # or match[3] does not exist because match contains only two elements (IndexError)
+ except (IndexError, TypeError) as e:
+ action_if_error(
+ file_record,
+ "no_match",
+ message=message_error_prefix
+ + f" Error : {e}. No match have been found. Test on https://regex101.com/",
+ )
+ return "", False
+
+ # this occurs when there is probably an error with the eval statement of the rule.
+ except Exception as e:
+ action_if_error(
+ file_record,
+ "evaluation_string_invalid",
+ message=message_error_prefix + f" Error : {e}. Evaluation string is probably invalid.",
+ )
+ return "", False
+ else: # eval is not specified. We then expect to use the first element of match as rename
+ try:
+ return match[0], True
+ # this occurs when there is most likely not match.
+ except (IndexError, TypeError) as e:
+ action_if_error(
+ file_record,
+ "no_match_first_element",
+ message=message_error_prefix
+ + f" Error : {e}. No match have been found for first element. Test on https://regex101.com/",
+ )
+ return "", False # we backtrack and don't change the element's value
+
+ # actions :
+ def rename(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.rename = True
+ file_record.executed_actions.append(f"{source} -> rename")
+ rename_status = True # will be set to false in the for loop after if any element renaming fails
+ for element, rule in self.rename_rule.items():
+ file_record.destination_file[element], element_status = self.rename_element(file_record, element, rule)
+ rename_status = rename_status and element_status
+
+ if not rename_status: # if we got a rename_error above, we skip the next steps
+ return file_record
+
+ if file_record.destination_file.fullpath == file_record.source_path:
+ file_record.rename = False
+ self.get_action_function_for("rename_unchanged", default="include")(file_record, "rename_unchanged")
+ else:
+ self.get_action_function_for("rename_successfull", default="include")(file_record, "rename_successfull")
+
+ return file_record
+
+ def exclude(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.include = False
+ file_record.executed_actions.append(f"{source} -> exclude")
+ return file_record
+
+ def include(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.include = True
+ file_record.executed_actions.append(f"{source} -> include")
+ return file_record
+
+ def delete(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.delete = True
+ file_record.executed_actions.append(f"{source} -> delete")
+ return file_record
+
+ def abort(self, file_record: FileRecord, source: str, *, message: str = "") -> FileRecord:
+ file_record.abort.append(message)
+ file_record.executed_actions.append(f"{source} -> abort")
+ return file_record
+
+ def get_action_function_for(self, trigger_name: Triggers, *, default: Actions) -> ActionFunction:
+ return getattr(self, self.triggers.get(trigger_name, default))
+
+ def __str__(self):
+ spacer = "\n - "
+ triggers_str = spacer + spacer.join([str(key) + " : " + str(value) for key, value in self.triggers.items()])
+ rename_rule = spacer.join([str(key) + " : " + str(value) for key, value in self.rename_rule.items()])
+ if rename_rule:
+ rename_rule = "\n Rename Rule :" + spacer + rename_rule
+ override_rule = spacer.join(self.parent.overrides)
+ if override_rule:
+ override_rule = "\n Overrides :" + spacer + override_rule
+ return f" Actions triggers :{triggers_str}{rename_rule}{override_rule}"
+
+
+class Rule:
+ def __init__(self, rule_dict: dict, rule_name: str, parent: "Config"):
+ if "if" not in rule_dict.keys():
+ raise ValueError(f"An if field must be defined in the rule {rule_name}")
+ self.rule_name = rule_name
+ self.parent = parent
+ self.rule_conditions = RuleConditions(rule_dict["if"], self, rule_name=rule_name)
+ self.rule_actions = RuleActions(rule_dict, rule_name, self)
+ overrides = rule_dict.get("overrides", [])
+ self.overrides = overrides if isinstance(overrides, list) else [overrides]
+ self.active = True
+
+ @property
+ def patterns(self):
+ return self.parent.patterns
+
+ def evaluate(self, file_record):
+ return self.rule_conditions.evaluate(file_record) if self.active else file_record
+
+ def actions_cascade(self, file_record) -> FileRecord:
+ return self.rule_actions.actions_cascade(file_record) if self.active else file_record
+
+ def __str__(self):
+ return f"Rule : {self.rule_name}" + "\n" + str(self.rule_actions) + "\n" + str(self.rule_conditions)
+
+
+class Config:
+ patterns: Dict[str, Pattern]
+ rules: Dict[str, Rule]
+
+ def __init__(
+ self,
+ rules_path: Optional[str | Path] = None,
+ connector: "Optional[Connector]" = None,
+ session: Optional[Series] = None,
+ ):
+ from alyx_connector import Connector
+
+ if session is not None and connector and not rules_path:
+ # TODO
+ if session["projects"].iloc[0]:
+ pass
+
+ if rules_path is None:
+ data = pkgutil.get_data(__name__, "./rules.json")
+ if data is None:
+ raise ValueError("Could not find a rules.json file !")
+ rules_config: RulesConfig = json.loads(data.decode("utf-8"))
+ else:
+ rules_config: RulesConfig = json.load(open(rules_path, "r"))
+
+ self.connector = connector if connector else Connector()
+
+ patterns: Patterns = rules_config.get("re_patterns", {}) # type: ignore
+ compiled_paterns = {}
+ for pattern_name, pattern in patterns.items():
+ compiled_paterns[pattern_name] = re.compile(pattern)
+ self.patterns = compiled_paterns
+
+ rules: Dict[str, Rules] = rules_config["rules"] # type: ignore
+
+ self.rules = {rule_name: Rule(rule_dict, rule_name, self) for rule_name, rule_dict in rules.items()}
+
+ self.excluded_folders = rules_config.get("excluded_folders", [])
+
+ self.excluded_filenames = rules_config.get("excluded_filenames", [])
+
+ self.cleanup_folders = rules_config.get("cleanup_folders", [])
+
+ self.dataset_types = get_existing_datasets(self.connector)
+ if len(self.dataset_types) == 0:
+ raise ValueError(
+ "dataset_types is empty. Cannot register any dataset if no dataset type exists. Maybe one's connector"
+ " has a problem ?"
+ )
+
+ def registration_pipeline(self, session):
+ file_records = self.evaluate_session(session)
+ if not self.is_applicable(file_records):
+ print("Some conflicts are present, cannot continue.")
+ return file_records
+ selected_records = self.apply_to_files(file_records)
+ records_groups = self.apply_to_alyx(selected_records, session)
+ return records_groups
+
+ def evaluate_session(self, session: Series | str) -> FilesRecordList:
+
+ if isinstance(session, Series):
+ search_folder = session["path"]
+ else: # session is a string, not a Series
+ session = cast(Series, self.connector.search(id=session, no_cache=True, details=True)["path"])
+ search_folder = session["path"]
+
+ files_list = find_files(search_folder, relative=False, levels=-1, get="files")
+
+ file_records = self.evaluate(files_list)
+ file_records.session = session
+ return file_records
+
+ def evaluate(self, file_list: List[str] | List[Path]) -> FilesRecordList:
+ file_records = FilesRecordList([FileRecord(Path(file_path)) for file_path in file_list])
+
+ for file_record in file_records:
+ skip = (
+ False # If we find that a find is in the excluded folders, we just discard it (not even try to match)
+ )
+ if file_record.destination_file.collection:
+ if any(
+ [
+ collection in self.excluded_folders
+ for collection in file_record.destination_file.collection.parts
+ ]
+ ):
+ skip = True
+ if file_record.source_path.name in self.excluded_filenames: # same for filenames
+ skip = True
+ if skip:
+ continue
+
+ for rule in self.rules.values():
+ rule.evaluate(file_record)
+ self.actions_cascade(file_records)
+ return file_records
+
+ def actions_cascade(self, file_records: FilesRecordList):
+ file_records.actions_cascade(self)
+ file_records.finish_cascade(self)
+ file_records.check_duplicate_final_paths()
+ return file_records
+
+ def is_applicable(self, file_records):
+ status = [len(file_record.abort) >= 1 for file_record in file_records]
+ return not (any(status))
+
+ def apply_to_files(self, file_records: FilesRecordList, do_deletes=True, do_renames=True, do_cleanup=True):
+ # DELETING and RENAMING
+
+ for file_record in file_records:
+ file_record.apply_changes(do_deletes, do_renames)
+
+ # just cleaning up empty folders after renaming.
+ # could be improved to do recursive search.
+ # this implementation may miss nested empty folders
+ if do_cleanup:
+ session_path = file_records[0].source_file.session_path
+ folders_list = find_files(session_path, relative=True, levels=-1, get="folders")
+ for folder in folders_list:
+ if folder in self.cleanup_folders:
+ _folder_path = os.path.join(session_path, folder)
+ files_in_dir = find_files(_folder_path, relative=True, levels=-1, get="files")
+ if len(files_in_dir):
+ continue # folder is not empty, we cannot clean it up
+ shutil.rmtree(_folder_path, ignore_errors=True)
+
+ return file_records
+
+ def apply_to_alyx(self, file_records: FilesRecordList, session: Optional[Series] = None):
+
+ if session is None:
+ session = file_records.session
+
+ if session is None:
+ raise ValueError("A session must be provided")
+
+ selected_records: List[FileRecord] = []
+ for file_record in file_records:
+ if file_record.inclusion_accepted:
+ selected_records.append(file_record)
+
+ files_list = [
+ file_record.destination_file.fullpath if file_record.rename else file_record.source_path
+ for file_record in selected_records
+ ]
+
+ self.connector.register.files(session, files_list)
+
+ def __str__(self):
+ spacer = "\n- "
+ rules_str = spacer + spacer.join([str(rule) + "\n" for rule in self.rules.values()])
+ return f"One-Registrator with configured rules : \n{rules_str}"
diff --git a/src/alyx_connector/files/registration/utils.py b/src/alyx_connector/files/registration/utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..6cc2582ce01a4d51e70d0e010aa31648f914fa42
--- /dev/null
+++ b/src/alyx_connector/files/registration/utils.py
@@ -0,0 +1,68 @@
+import os, re, pandas as pd
+
+from typing import List, TYPE_CHECKING
+
+if TYPE_CHECKING:
+ from alyx_connector import Connector
+
+
+def get_existing_datasets(one_connector: "Connector"):
+ existing_dst = one_connector.search("dataset-types", details=False)
+ existing_types = [dst["name"] for _, dst in existing_dst.iterrows() if dst["attribute"]]
+ return existing_types
+
+
+def find_files(
+ input_path, re_pattern=None, relative=False, levels=-1, get="files", parts="all", sort=True
+) -> List[str]:
+ """
+ Get full path of files from all folders under the ``input_path`` (including itself).
+ Can return specific files with optionnal conditions
+ Args:
+ input_path (str): A valid path to a folder.
+ This folder is used as the root to return files found
+ (possible condition selection by giving to re_callback a function taking a regexp
+ pattern and a string as argument, an returning a boolean).
+ Returns:
+ list: List of the file fullpaths found under ``input_path`` folder and subfolders.
+ """
+ # if levels = -1, we get everything whatever the depth
+ # (at least up to 32767 subfolders, but this should be fine...)
+
+ if levels == -1:
+ levels = 32767
+ current_level = 0
+ output_list = []
+
+ if re_pattern is not None:
+ re_pattern = re.compile(re_pattern)
+
+ def _recursive_search(_input_path):
+ nonlocal current_level
+ for subdir in os.listdir(_input_path):
+ fullpath = os.path.join(_input_path, subdir)
+ if os.path.isfile(fullpath):
+ if (get == "all" or get == "files") and (re_pattern is None or re_pattern.match(fullpath)):
+ output_list.append(os.path.normpath(fullpath))
+
+ else:
+ if (get == "all" or get == "dirs" or get == "folders") and (
+ re_pattern is None or re_pattern.match(fullpath)
+ ):
+ output_list.append(os.path.normpath(fullpath))
+ if current_level < levels:
+ current_level += 1
+ _recursive_search(fullpath)
+ current_level -= 1
+
+ if os.path.isfile(input_path):
+ raise ValueError(f"Can only list files in a directory. A file was given : {input_path}")
+
+ _recursive_search(input_path)
+
+ if relative:
+ output_list = [os.path.relpath(file, start=input_path) for file in output_list]
+ if parts == "name":
+ output_list = [os.path.basename(file) for file in output_list]
+
+ return output_list
diff --git a/src/alyx_connector/files/transfers.py b/src/alyx_connector/files/transfers/transfers.py
similarity index 95%
rename from src/alyx_connector/files/transfers.py
rename to src/alyx_connector/files/transfers/transfers.py
index 30534082283acf1a0c3f609850f662eda19bb873..61295e9d47f8f38338ff6a5b6402910876e26a5e 100644
--- a/src/alyx_connector/files/transfers.py
+++ b/src/alyx_connector/files/transfers/transfers.py
@@ -19,6 +19,17 @@ from pandas import DataFrame, Series
from typing import Optional
+from typing import TypedDict, Literal
+
+
+class Policies(TypedDict, total=False):
+ close_dates: Literal["conflict", "overwrite", "transfer", "ignore"]
+ destination_older: Literal["conflict", "overwrite", "transfer", "ignore"]
+ no_file_exists: Literal["conflict", "overwrite", "transfer", "ignore"]
+ destination_younger: Literal["conflict", "overwrite", "transfer", "ignore"]
+ close_dates_threshold: int
+
+
class FileTransferManager:
results: DataFrame
@@ -51,7 +62,7 @@ class FileTransferManager:
conflicts = results[results["decision"] == "conflict"]
accepted_decisions = ["transfer", "overwrite", "ignore", "conflict"]
- def conflict_pannel(conflict=None):
+ def conflict_pannel(conflict: Optional[Series] = None):
if conflict is None:
return Panel("", title="❗ Handling Conflict :", border_style="dark_blue")
@@ -424,25 +435,32 @@ class FileTransferManager:
)
return DataFrame(copy_results)
- def fetch(self, policies=None, show_status=True):
+ def fetch(self, policies: Optional[Policies] = None, show_status=True):
results = self.check_files(source="remote_path", destination="local_path", policies=policies)
new_file_namager = FileTransferManager(self.sessions, results, direction="pull")
if show_status:
new_file_namager.status()
return new_file_namager
- def push_request(self, policies=None, show_status=True):
+ def push_request(self, policies: Optional[Policies] = None, show_status=True):
results = self.check_files(source="local_path", destination="remote_path", policies=policies)
new_file_namager = FileTransferManager(self.sessions, results, direction="push")
if show_status:
new_file_namager.status()
return new_file_namager
- def check_files(self, source="remote_path", destination="local_path", policies=None):
+ def pull_request(self, policies: Optional[Policies] = None, show_status=True):
+ results = self.check_files(source="remote_path", destination="local_path", policies=policies)
+ new_file_namager = FileTransferManager(self.sessions, results, direction="push")
+ if show_status:
+ new_file_namager.status()
+ return new_file_namager
+
+ def check_files(self, source="remote_path", destination="local_path", policies: Optional[Policies] = None):
console = Console()
- default_policies = {
+ default_policies: Policies = {
"close_dates": "conflict",
"destination_older": "overwrite",
"no_file_exists": "transfer",
diff --git a/src/alyx_connector/web/api.py b/src/alyx_connector/web/api.py
index 026157696314536f8c7daf08a22270384fcd4071..4a2c8a92c1fe5d0ae7cb480764078c37bca1aec9 100644
--- a/src/alyx_connector/web/api.py
+++ b/src/alyx_connector/web/api.py
@@ -1,10 +1,9 @@
from openapi_parser.specification import Operation, Specification, Path as OpenAPIPath
from openapi_parser import parse as parse_openapi_schema
from openapi_parser.errors import ParserError
-import requests
+import json, re, requests
from requests.models import Response
-import json
-import re
+from urllib.parse import urlencode
from logging import getLogger
from abc import ABC
@@ -111,7 +110,7 @@ class EndpointUrl(str):
protocol=self.client.protocol, # http or https
netloc=self.client.netloc, # netloc = host+port
path=self.finalized_path(**requirements_dict), # path
- query_string=self.make_query_string(query_dict), # querystring example : ?thing=truc
+ query_string=urlencode(query_dict), # querystring example : ?thing=truc
fragment=fragment, # basically an anchor, fragment example : #title1
)
return url
@@ -135,11 +134,11 @@ class EndpointUrl(str):
query_dict = {k: v for k, v in kwargs.items() if k not in self.requirements}
return query_dict, requirements
- def make_query_string(self, query_dict: dict) -> str:
- query_list = []
- for key, value in query_dict.items():
- query_list.append(f"{key}={value}")
- return "&".join(query_list)
+ # def make_query_string(self, query_dict: dict) -> str:
+ # query_list = []
+ # for key, value in query_dict.items():
+ # query_list.append(f"{key}={value}")
+ # return "&".join(query_list)
@property
def endpoint(self):
diff --git a/src/alyx_connector/web/clients.py b/src/alyx_connector/web/clients.py
index abd4261417dce01d7915259a29bb86a98dd2c9ca..9067a46f4907baaf4b128792cdff1dd58d7a7c70 100644
--- a/src/alyx_connector/web/clients.py
+++ b/src/alyx_connector/web/clients.py
@@ -12,7 +12,7 @@ from ..configuration import Configuration
from .urls import UrlValidator
from .api import EndpointUrl, Endpoint, APISpecification, OpenAPISpecification, Request, Operateur
-from typing import Optional, Type, TypeVar, Generic, Literal, List, Dict
+from typing import Optional, Type, TypeVar, Generic, Literal, List, Dict, Any, cast
Specification = TypeVar("Specification", bound=APISpecification)
@@ -218,7 +218,7 @@ class Client(ABC, Generic[Specification]):
for result in tqdm(
search_result, total=len(search_result), delay=2, desc=f"Loading {endpoint} details", file=stdout
):
- retrieve_params = {name: result[name] for name in required_params}
+ retrieve_params = cast(Dict[str, Any], {name: result[name] for name in required_params})
detailed_results.append(self.rest(endpoint, "retrieve", **retrieve_params))
return detailed_results
@@ -443,3 +443,9 @@ class ClientWithConfig(ClientWithAuth):
class WebClient(ClientWithConfig):
specification_class = OpenAPISpecification
+
+
+class CreationClient:
+
+ def __init__(self) -> None:
+ pass
diff --git a/src/alyx_connector/web/responses.py b/src/alyx_connector/web/responses.py
deleted file mode 100644
index 675097af053cc64970e1676060fa36c2bbcc97a7..0000000000000000000000000000000000000000
--- a/src/alyx_connector/web/responses.py
+++ /dev/null
@@ -1,196 +0,0 @@
-import math
-import urllib, requests
-from logging import getLogger
-from collections.abc import Mapping
-
-from .urls import UrlValidator
-
-from typing import TYPE_CHECKING
-
-if TYPE_CHECKING:
- from .clients import Client
-
-
-logger = getLogger("alyx_conntector.web.responses")
-
-
-class ResponseManager:
-
- def __init__(self, client: Client):
- self.client = client
-
- def __getitem__(self, value):
- return getattr(self, value)
-
- def list(self, json_response: dict, original_url: str, **kwargs):
-
- if isinstance(json_response, dict) and list(json_response.keys()) == [
- "count",
- "next",
- "previous",
- "results",
- ]:
- if len(json_response["results"]) < json_response["count"]:
- cache_args = {k: v for k, v in kwargs.items() if k in ("clobber", "expires")}
- logger.debug(f"Creating a paginated response for a large Alyx request. Query : {original_url}")
- json_response = _PaginatedResponse(self, json_response, cache_args, callbacks=self.fix_url)
- logger.debug(
- f"Paginated response total size is : {json_response.count}. "
- f"Limit size is : {json_response.limit}. Query is : {json_response.query}"
- )
- else:
- json_response = json_response["results"]
- return self.fix_url(json_response)
-
- def fix_url(self, response_data, fixed_keys=["admin_url"], do_fix=False):
-
- if isinstance(response_data, list):
- return [self.fix_url(item, do_fix=False) for item in response_data]
- elif isinstance(response_data, dict):
- return {
- key: (self.fix_url(item, do_fix=True) if key in fixed_keys else self.fix_url(item, do_fix=False))
- for key, item in response_data.items()
- }
- elif isinstance(response_data, _PaginatedResponse):
- response_data.add_finishing_callback(self.fix_url)
- return response_data
- elif do_fix:
- baseurl = UrlValidator.urlsplit(self.client.url)
- return UrlValidator.urlsplit(response_data)._replace(scheme=baseurl.scheme, netloc=baseurl.netloc).geturl()
- else:
- return response_data
-
-
-class _PaginatedResponse(Mapping):
- """
- This class allows to emulate a list from a paginated response.
- Provides cache functionality.
-
- Examples
- --------
- >>> r = _PaginatedResponse(client, response)
- """
-
- def __init__(self, alyx, rep, cache_args=None, callbacks=[]):
- """
- A paginated response cache object
-
- Parameters
- ----------
- alyx : AlyxClient
- An instance of an AlyxClient associated with the REST response
- rep : dict
- A paginated REST response JSON dictionary
- cache_args : dict
- A dict of kwargs to pass to _cache_response decorator upon subsequent requests
- """
-
- self.alyx = alyx
- self.base_url = self.alyx.base_url
- self.count = rep["count"]
- self.limit = len(rep["results"])
- self._cache_args = cache_args or {}
- # store URL without pagination query params
- self.query = rep["next"]
- # init the cache, list with None with count size
- self._cache = [None] * self.count
-
- if not isinstance(callbacks, list):
- callbacks = [callbacks]
-
- self.finishing_callbacks = callbacks
-
- # fill the cache with results of the query
- self.store_results(rep, 0)
-
- def __len__(self):
- return self.count
-
- def __getitem__(self, item):
- """Returns an item from cache if the indices locations are already loaded,
- or populates the cache chunk by chunk if some locations are empty.
- """
- if isinstance(item, slice):
- while None in self._cache[item]:
- # .index(None) finds the first location where the cache is none,
- # and populate stores a new chunk starting from here
- self.populate(self._cache[item].index(None))
- elif item > self.count:
- raise IndexError(
- f"The paginated response has no item at position {item} : " f"it contains only {self.count} items"
- )
- elif self._cache[item] is None:
- self.populate(item)
- return self._cache[item]
-
- def populate(self, idx):
- """Populate a chunk of size self.limit, from an offset query depending on the value of the index required."""
- offset = self.limit * math.floor(idx / self.limit)
- query = update_url_params(self.query, {"limit": self.limit, "offset": offset})
- res = self.alyx._generic_request(requests.get, query, **self._cache_args)
- if self.count != res["count"]:
- logger.warning(
- f"remote results for {UrlValidator.urlsplit(query).path} endpoint changed; results may be inconsistent",
- RuntimeWarning,
- )
- self.store_results(res, offset)
-
- def store_results(self, res, offset):
- for i, r in enumerate(res["results"][: self.count - offset]):
- self._cache[i + offset] = self.finish_result(r)
-
- def finish_result(self, result):
- """Method that should be overridden in child classes"""
- for callback in self.finishing_callbacks:
- result = callback(result)
- return result
-
- def add_finishing_callback(self, callback):
- if callback not in self.finishing_callbacks:
- self.finishing_callbacks.append(callback)
-
- def __iter__(self):
- for i in range(self.count):
- try:
- yield self.__getitem__(i)
- except requests.HTTPError as e:
- logger.error(
- f"{e.response.status_code} error while trying to access " f"PaginatedResponse data at position {i}"
- )
- raise e
-
-
-def update_url_params(url: str, params: dict) -> str:
- """Add/update the query parameters of a URL and make url safe
-
- Parameters
- ----------
- url : str
- A URL string with which to update the query parameters
- params : dict
- A dict of new parameters. For multiple values for the same query, use a list (see example)
-
- Returns
- -------
- str
- A new URL with said parameters updated
-
- Examples
- -------
- >>> update_url_params('website.com/?q=', {'pg': 5})
- 'website.com/?pg=5'
-
- >>> update_url_params('website.com?q=xxx', {'pg': 5, 'foo': ['bar', 'baz']})
- 'website.com?q=xxx&pg=5&foo=bar&foo=baz'
- """
- # Remove percent-encoding
- url = urllib.parse.unquote(url)
- parsed_url = urllib.parse.urlsplit(url)
- # Extract URL query arguments and convert to dict
- parsed_get_args = urllib.parse.parse_qs(parsed_url.query, keep_blank_values=False)
- # Merge URL arguments dict with new params
- parsed_get_args.update(params)
- # Convert back to query string
- encoded_get_args = urllib.parse.urlencode(parsed_get_args, doseq=True)
- # Update parser and convert to full URL str
- return parsed_url._replace(query=encoded_get_args).geturl()