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Dataset hot fix #1109
Dataset hot fix #1109
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Pandas compatibility issues resolved
Fixed broken links for notebooks
Update load_Allen_Visual_Behavior_from_SDK.ipynb
we are getting some odd errors while trying to process your changes. ------------------
data_storage_directory = "/temp" # Note: this path must exist on your local drive
cache = VisualBehaviorOphysProjectCache.from_s3_cache(cache_dir=data_storage_directory)
============================== Failure ==============================
------------------
---------------------------------------------------------------------------
PermissionError Traceback (most recent call last)
Cell In[3], line 2
1 data_storage_directory = "/temp" # Note: this path must exist on your local drive
----> 2 cache = VisualBehaviorOphysProjectCache.from_s3_cache(cache_dir=data_storage_directory)
File /opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/allensdk/brain_observatory/behavior/behavior_project_cache/project_cache_base.py:77, in ProjectCacheBase.from_s3_cache(cls, cache_dir, bucket_name_override)
50 @classmethod
51 def from_s3_cache(
52 cls,
53 cache_dir: Union[str, Path],
54 bucket_name_override: Optional[str] = None
55 ) -> "ProjectCacheBase":
56 """instantiates this object with a connection to an s3 bucket and/or
57 a local cache related to that bucket.
58
(...)
74
75 """
---> 77 fetch_api = cls.cloud_api_class().from_s3_cache(
78 cache_dir,
79 bucket_name=(
80 bucket_name_overrideifbucket_name_overrideisnotNone
81 elsecls.BUCKET_NAME),
82 project_name=cls.PROJECT_NAME,
83 ui_class_name=cls.__name__)
85 return cls(fetch_api=fetch_api)
File /opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/allensdk/brain_observatory/behavior/behavior_project_cache/project_apis/data_io/project_cloud_api_base.py:108, in ProjectCloudApiBase.from_s3_cache(cls, cache_dir, bucket_name, project_name, ui_class_name)
78 @classmethod
79 def from_s3_cache(cls, cache_dir: Union[str, Path],
80 bucket_name: str,
81 project_name: str,
82 ui_class_name: str) -> "ProjectCloudApiBase":
83 """instantiates this object with a connection to an s3 bucket and/or
84 a local cache related to that bucket.
85
(...)
106
107 """
--> 108 cache = S3CloudCache(cache_dir,
109 bucket_name,
110 project_name,
111 ui_class_name=ui_class_name)
112 return cls(cache)
File /opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/allensdk/api/cloud_cache/cloud_cache.py:1066, in S3CloudCache.__init__(self, cache_dir, bucket_name, project_name, ui_class_name)
1063 self._manifest = None
1064 self._bucket_name = bucket_name
-> 1066 super().__init__(cache_dir=cache_dir,project_name=project_name,
1067 ui_class_name=ui_class_name)
File /opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/allensdk/api/cloud_cache/cloud_cache.py:391, in CloudCacheBase.__init__(self, cache_dir, project_name, ui_class_name)
390 def __init__(self, cache_dir, project_name, ui_class_name=None):
--> 391 super().__init__(cache_dir=cache_dir,project_name=project_name,
392 ui_class_name=ui_class_name)
394 # what latest_manifest was the last time an OutdatedManifestWarning
395 # was emitted
396 self._manifest_last_warned_on = None
File /opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/site-packages/allensdk/api/cloud_cache/cloud_cache.py:63, in BasicLocalCache.__init__(self, cache_dir, project_name, ui_class_name)
57 def __init__(
58 self,
59 cache_dir: Union[str, Path],
60 project_name: str,
61 ui_class_name: Optional[str] = None
62 ):
---> 63 os.makedirs(cache_dir,exist_ok=True)
65 # the class users are actually interacting with
66 # (for warning message purposes)
67 if ui_class_name is None:
File /opt/hostedtoolcache/Python/3.9.19/x64/lib/python3.9/os.py:225, in makedirs(name, mode, exist_ok)
223 return
224 try:
--> 225 mkdir(name,mode)
226 except OSError:
227 # Cannot rely on checking for EEXIST, since the operating system
2[28](https://github.com/NeuromatchAcademy/course-content/actions/runs/9813753170/job/27100280023#step:10:29) # could give priority to other errors like EACCES or EROFS
229 if not exist_ok or not path.isdir(name):
PermissionError: [Errno 13] Permission denied: '/temp'
Error: Process completed with exit code 1. I do think this is unrelated to your changes, but it is preventing our pipeline from running. Any ideas? |
Let's wait on this one. The original creator of the notebook is supposed to upload a fixed version very soon... |
@iamzoltan @marius10p @yavorska-iryna, I think that @yavorska-iryna has addressed the issues in her pull request (if she is the original creator of the notebook you mentioned @marius10p). @iamzoltan, do you think we can now accept the pull request? What about the other pull requests ? |
Alright, I will close this PR. |
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