get_annotation_count throws error for reference tables
Opened this issue · 0 comments
schlegelp commented
Hi!
I ran into this error when trying to get the annotation count for a reference table:
>>> client = CAVEclient('flywire_fafb_production')
>>> client.annotation.get_annotation_count('fly_synapses_neuropil_v5')
---------------------------------------------------------------------------
HTTPError Traceback (most recent call last)
Cell In[133], line 1
----> 1 client.annotation.get_annotation_count('fly_synapses_neuropil_v5')
File ~/.pyenv/versions/3.9.9/lib/python3.9/site-packages/caveclient/annotationengine.py:190, in AnnotationClientV2.get_annotation_count(self, table_name, aligned_volume_name)
187 url = self._endpoints["table_count"].format_map(endpoint_mapping)
189 response = self.session.get(url)
--> 190 return handle_response(response)
File ~/.pyenv/versions/3.9.9/lib/python3.9/site-packages/caveclient/base.py:88, in handle_response(response, as_json, log_warning)
86 def handle_response(response, as_json=True, log_warning=True):
87 """Deal with potential errors in endpoint response and return json for default case"""
---> 88 _raise_for_status(response, log_warning=log_warning)
89 _check_authorization_redirect(response)
90 if as_json:
File ~/.pyenv/versions/3.9.9/lib/python3.9/site-packages/caveclient/base.py:79, in _raise_for_status(r, log_warning)
71 http_error_msg = "%s Server Error: %s for url: %s content:%s" % (
72 r.status_code,
73 reason,
74 r.url,
75 r.content,
76 )
78 if http_error_msg:
---> 79 raise requests.HTTPError(http_error_msg, response=r)
80 if log_warning:
81 warning = r.headers.get("Warning")
HTTPError: 500 Server Error: Foreign key associated with column 'fly_synapses_neuropil_v5.target_id' could not find table 'synapses_nt_v1' with which to generate a foreign key to target column 'id' for url: https://prod.flywire-daf.com/annotation/api/v2/aligned_volume/fafb_seung_alignment_v0/table/fly_synapses_neuropil_v5/count content:b'{"code": 500, "message": "Foreign key associated with column \'fly_synapses_neuropil_v5.target_id\' could not find table \'synapses_nt_v1\' with which to generate a foreign key to target column \'id\'", "traceback": ["Traceback (most recent call last):\\n", " File \\"/usr/local/lib/python3.9/site-packages/flask/app.py\\", line 1950, in full_dispatch_request\\n rv = self.dispatch_request()\\n", " File \\"/usr/local/lib/python3.9/site-packages/flask/app.py\\", line 1936, in dispatch_request\\n return self.view_functions[rule.endpoint](**req.view_args)\\n", " File \\"/usr/local/lib/python3.9/site-packages/flask_restx/api.py\\", line 403, in wrapper\\n resp = resource(*args, **kwargs)\\n", " File \\"/usr/local/lib/python3.9/site-packages/flask/views.py\\", line 89, in view\\n return self.dispatch_request(*args, **kwargs)\\n", " File \\"/usr/local/lib/python3.9/site-packages/flask_restx/resource.py\\", line 49, in dispatch_request\\n resp = meth(*args, **kwargs)\\n", " File \\"/usr/local/lib/python3.9/site-packages/middle_auth_client/decorators.py\\", line 265, in decorated_function\\n return f(*args, **kwargs)\\n", " File \\"/usr/local/lib/python3.9/site-packages/middle_auth_client/decorators.py\\", line 397, in decorated_function\\n return f(*args, **kwargs)\\n", " File \\"/app/./annotationengine/api.py\\", line 282, in get\\n return db.database.get_annotation_table_size(table_name), 200\\n", " File \\"/usr/local/lib/python3.9/site-packages/dynamicannotationdb/database.py\\", line 165, in get_annotation_table_size\\n return session.query(Model).count()\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 3803, in count\\n return self.from_self(col).scalar()\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 3523, in scalar\\n ret = self.one()\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 3490, in one\\n ret = self.one_or_none()\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 3459, in one_or_none\\n ret = list(self)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 3531, in __iter__\\n context = self._compile_context()\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 4085, in _compile_context\\n entity.setup_context(self, context)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 4853, in setup_context\\n column = query._adapt_clause(self.column, False, True)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 394, in _adapt_clause\\n return visitors.replacement_traverse(clause, {}, replace)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/visitors.py\\", line 484, in replacement_traverse\\n obj = clone(obj, **opts)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/visitors.py\\", line 473, in clone\\n newelem = replace(elem)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/orm/query.py\\", line 390, in replace\\n e = adapter(elem)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/util.py\\", line 848, in replace\\n return self._corresponding_column(col, True)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/util.py\\", line 820, in _corresponding_column\\n newcol = self.selectable.corresponding_column(\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/selectable.py\\", line 560, in corresponding_column\\n if self.c.contains_column(column):\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/util/langhelpers.py\\", line 893, in __get__\\n obj.__dict__[self.__name__] = result = self.fget(obj)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/selectable.py\\", line 647, in columns\\n self._populate_column_collection()\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/selectable.py\\", line 1395, in _populate_column_collection\\n for col in self.element.columns._all_columns:\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/util/langhelpers.py\\", line 893, in __get__\\n obj.__dict__[self.__name__] = result = self.fget(obj)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/selectable.py\\", line 647, in columns\\n self._populate_column_collection()\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/selectable.py\\", line 3906, in _populate_column_collection\\n c._make_proxy(self, key=key, name=name, name_is_truncatable=True)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/schema.py\\", line 1791, in _make_proxy\\n fk = [\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/schema.py\\", line 1792, in <listcomp>\\n ForeignKey(f.column, _constraint=f.constraint)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/util/langhelpers.py\\", line 893, in __get__\\n obj.__dict__[self.__name__] = result = self.fget(obj)\\n", " File \\"/usr/local/lib/python3.9/site-packages/sqlalchemy/sql/schema.py\\", line 2247, in column\\n raise exc.NoReferencedTableError(\\n", "sqlalchemy.exc.NoReferencedTableError: Foreign key associated with column \'fly_synapses_neuropil_v5.target_id\' could not find table \'synapses_nt_v1\' with which to generate a foreign key to target column \'id\'\\n"]}\n'This is with caveclient 5.13.0