Hi everyone,
It’s really cool of you guys to share all these data online. I am currently working on the VIsp’s 2P data, here’s my code to download the original nwb files on my server:
from allensdk.core.brain_observatory_cache import BrainObservatoryCache
import pprint
from pathlib import Path
output_dir = '.'
boc = BrainObservatoryCache(
manifest_file=str(Path(output_dir) / 'brain_observatory_manifest.json'))
data_set = boc.get_ophys_experiment_data(502205092)
It work well before, but today I encountered HTTP 403 error over and over again.the traceback goes like below:
{
"name": "HTTPError",
"message": "HTTP Error 403: Forbidden",
"stack": "---------------------------------------------------------------------------
HTTPError Traceback (most recent call last)
Cell In[19], line 1
----> 1 exp = boc.get_ophys_experiments(experiment_container_ids=[595263152],
2 session_types = ['three_session_A'])[0]
3 pprint.pprint(exp)
File ~/anaconda3/envs/pytorch/lib/python3.11/site-packages/allensdk/core/brain_observatory_cache.py:367, in BrainObservatoryCache.get_ophys_experiments(self, file_name, ids, experiment_container_ids, targeted_structures, imaging_depths, cre_lines, reporter_lines, transgenic_lines, stimuli, session_types, cell_specimen_ids, include_failed, require_eye_tracking, simple)
359 exps = self.api.get_ophys_experiments(
360 path=file_name, strategy=\"lazy\", **Cache.cache_json()
361 )
363 # NOTE: Ugly hack to update the 'fail_eye_tracking' field
364 # which is using True/False values for the previous eye mapping
365 # implementation. This will also need to be fixed in warehouse.
366 # ----- Start of ugly hack -----
--> 367 response = self.api.template_query(
368 \"brain_observatory_queries\", \"all_eye_mapping_files\"
369 )
371 session_ids_with_eye_tracking: set = {
372 entry[\"attachable_id\"]
373 for entry in response
374 if entry[\"attachable_type\"] == \"OphysSession\"
375 }
377 for indx, exp in enumerate(exps):
File ~/anaconda3/envs/pytorch/lib/python3.11/site-packages/allensdk/api/queries/rma_template.py:132, in RmaTemplate.template_query(self, template_name, entry_name, **kwargs)
128 query_args['order'] = template['order']
130 query_args.update(kwargs)
--> 132 data = self.model_query(**query_args)
134 return data
File ~/anaconda3/envs/pytorch/lib/python3.11/site-packages/allensdk/api/queries/rma_api.py:257, in RmaApi.model_query(self, *args, **kwargs)
217 def model_query(self, *args, **kwargs):
218 '''Construct and execute a model stage of an RMA query string.
219
220 Parameters
(...)
255 response, including the normalized query.
256 '''
--> 257 return self.json_msg_query(
258 self.build_query_url(
259 self.model_stage(*args, **kwargs)))
File ~/anaconda3/envs/pytorch/lib/python3.11/site-packages/allensdk/api/api.py:164, in Api.json_msg_query(self, url, dataframe)
147 def json_msg_query(self, url, dataframe=False):
148 ''' Common case where the url is fully constructed
149 and the response data is stored in the 'msg' field.
150
(...)
161 returned data; type depends on dataframe option
162 '''
--> 164 data = self.do_query(lambda *a, **k: url,
165 self.read_data)
167 if dataframe is True:
168 warnings.warn(\"dataframe argument is deprecated\", DeprecationWarning)
File ~/anaconda3/envs/pytorch/lib/python3.11/site-packages/allensdk/api/api.py:204, in Api.do_query(self, url_builder_fn, json_traversal_fn, *args, **kwargs)
200 api_url = url_builder_fn(*args, **kwargs)
202 post = kwargs.get('post', False)
--> 204 json_parsed_data = self.retrieve_parsed_json_over_http(api_url, post)
206 return json_traversal_fn(json_parsed_data)
File ~/anaconda3/envs/pytorch/lib/python3.11/site-packages/allensdk/api/api.py:369, in Api.retrieve_parsed_json_over_http(self, url, post)
366 self._log.info(\"Downloading URL: %s\", url)
368 if post is False:
--> 369 data = json_utilities.read_url_get(
370 requests.utils.quote(url,
371 ';/?:@&=+$,'))
372 else:
373 data = json_utilities.read_url_post(url)
File ~/anaconda3/envs/pytorch/lib/python3.11/site-packages/allensdk/core/json_utilities.py:115, in read_url_get(url)
98 def read_url_get(url):
99 \"\"\"Transform a JSON contained in a file into an equivalent
100 nested python dict.
101
(...)
113 the output will be of the corresponding type.
114 \"\"\"
--> 115 response = urllib_request.urlopen(url)
116 json_string = response.read().decode(\"utf-8\")
118 return json.loads(json_string)
File ~/anaconda3/envs/pytorch/lib/python3.11/urllib/request.py:216, in urlopen(url, data, timeout, cafile, capath, cadefault, context)
214 else:
215 opener = _opener
--> 216 return opener.open(url, data, timeout)
File ~/anaconda3/envs/pytorch/lib/python3.11/urllib/request.py:525, in OpenerDirector.open(self, fullurl, data, timeout)
523 for processor in self.process_response.get(protocol, []):
524 meth = getattr(processor, meth_name)
--> 525 response = meth(req, response)
527 return response
File ~/anaconda3/envs/pytorch/lib/python3.11/urllib/request.py:634, in HTTPErrorProcessor.http_response(self, request, response)
631 # According to RFC 2616, \"2xx\" code indicates that the client's
632 # request was successfully received, understood, and accepted.
633 if not (200 <= code < 300):
--> 634 response = self.parent.error(
635 'http', request, response, code, msg, hdrs)
637 return response
File ~/anaconda3/envs/pytorch/lib/python3.11/urllib/request.py:563, in OpenerDirector.error(self, proto, *args)
561 if http_err:
562 args = (dict, 'default', 'http_error_default') + orig_args
--> 563 return self._call_chain(*args)
File ~/anaconda3/envs/pytorch/lib/python3.11/urllib/request.py:496, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args)
494 for handler in handlers:
495 func = getattr(handler, meth_name)
--> 496 result = func(*args)
497 if result is not None:
498 return result
File ~/anaconda3/envs/pytorch/lib/python3.11/urllib/request.py:643, in HTTPDefaultErrorHandler.http_error_default(self, req, fp, code, msg, hdrs)
642 def http_error_default(self, req, fp, code, msg, hdrs):
--> 643 raise HTTPError(req.full_url, code, msg, hdrs, fp)
HTTPError: HTTP Error 403: Forbidden"
}
However, to double check, I tried the VisualBehaviorOphysProjectCache as well:
from pathlib import Path
import matplotlib.pyplot as plt
import allensdk
from allensdk.brain_observatory.behavior.behavior_project_cache import VisualBehaviorOphysProjectCache
output_dir = "/local1/visual_behavior_ophys_cache_dir"
output_dir = Path(output_dir)
cache = VisualBehaviorOphysProjectCache.from_s3_cache(cache_dir=output_dir)
behavior_session = cache.get_behavior_session(behavior_session_id=870987812)
This time it works well. and I also notice that the Brain Map website is currently down, so I am wondering if this issue is related to the website being temporarily closed or if there are other access restrictions in place? Additionally, could you let me know when the website or data download functionality will be re-enabled?THX a lot 
