Hi all,
I’m using the AllenSDK (2.16.2 on python 3.11, Windows 11) to download a StructureTree. When I run the following code I get an HTTP error:
from allensdk.api.queries.ontologies_api import OntologiesApi
oapi = OntologiesApi()
structure_graph = oapi.get_structures_with_sets([1])
The error is HTTPError: HTTP Error 503: Service Unavailable. Sometimes when running the same code, I will instead get HTTP Error 504: Gateway Time-out.
I get the same behavior running on an AllenSDK installation on my Ubuntu 18.04 workstation
I suspect this is a server error?
I should note that I have no issue accessing the MouseConnectivityApi to download annotation volumes, so it seems to be just an OntologiesAPI service issue and not all AllenAPI services.
Full error stack follows
---------------------------------------------------------------------------
HTTPError Traceback (most recent call last)
Cell In[11], line 2
1 oapi = OntologiesApi()
----> 2 structure_graph = oapi.get_structures_with_sets([1]) # 1 is the id of the adult mouse structure graph
3 structure_graph = StructureTree.clean_structures(structure_graph)
4 tree = StructureTree(structure_graph)
File C:\ProgramData\anaconda3\Lib\site-packages\allensdk\api\warehouse_cache\cache.py:661, in cacheable.<locals>.decor.<locals>.w(*args, **kwargs)
658 if decor.post and not 'post in kwargs':
659 kwargs['post'] = decor.post
--> 661 result = Cache.cacher(func,
662 *args,
663 **kwargs)
664 return result
File C:\ProgramData\anaconda3\Lib\site-packages\allensdk\api\warehouse_cache\cache.py:378, in Cache.cacher(fn, *args, **kwargs)
375 strategy = 'create'
377 if strategy == 'pass_through':
--> 378 data = fn(*args, **kwargs)
379 elif strategy in ['create']:
380 Manifest.safe_make_parent_dirs(path)
File C:\ProgramData\anaconda3\Lib\site-packages\allensdk\api\queries\ontologies_api.py:235, in OntologiesApi.get_structures_with_sets(self, structure_graph_ids, order, num_rows, count, **kwargs)
214 @cacheable()
215 def get_structures_with_sets(self, structure_graph_ids, order=['structures.graph_order'],
216 num_rows='all', count=False, **kwargs):
217 '''Download structures along with the sets to which they belong.
218
219 Parameters
(...)
232
233 '''
--> 235 return self.template_query('ontology_queries', 'structures_with_sets',
236 graph_ids=structure_graph_ids,
237 order=order, num_rows=num_rows,
238 count=count)
File C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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 C:\ProgramData\anaconda3\Lib\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)