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CMIP(6) exclude_dirs #62
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@aaronspring, thank you for pointing this out. This is something missing from the CMIP implementation. The |
@andersy005, are there further opportunities for consolidation/code reuse across CMIP and CESM? |
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I think we should consider generalizing |
Sounds good. If you are not busy this coming week, let's discuss more about what these changes will look like |
With #63 You will be able to add name: cmip5_test_collection
collection_type: cmip5
data_sources:
root_dir:
name: GLADE
loc_type: posix
direct_access: True
urlpath: ./tests/sample_data/cmip/cmip5
exclude_dirs: ['files', 'latest'] |
Re-installed. YAML file: (I think this should work) name: cmip6_collection_mistral
collection_type: cmip6
data_sources:
root_dir:
name: MISTRAL
loc_type: posix
direct_access: True
urlpath: /work/kd0956/CMIP6
exclude_dirs: ['test_data/CMIP6','dc_repli/*','dc_test_data/*'] col = intake.open_esm_metadatastore(collection_input_definition=collection_input_definition, overwrite_existing=True)
Getting list of directories
---------------------------------------------------------------------------
PermissionError Traceback (most recent call last)
<ipython-input-15-554feb33ee30> in <module>
----> 1 col = intake.open_esm_metadatastore(collection_input_definition=collection_input_definition, overwrite_existing=True)
/work/mh0727/m300524/anaconda3/envs/xr/lib/python3.7/site-packages/intake_esm-2019.4.26.1.post15-py3.7.egg/intake_esm/core.py in __init__(self, collection_input_definition, collection_name, overwrite_existing, metadata)
64 collection_input_definition
65 )
---> 66 self.build_collection(overwrite_existing)
67
68 else:
/work/mh0727/m300524/anaconda3/envs/xr/lib/python3.7/site-packages/intake_esm-2019.4.26.1.post15-py3.7.egg/intake_esm/core.py in build_collection(self, overwrite_existing)
97 cc = ESMMetadataStoreCatalog.collection_types[ctype]
98 cc = cc(self.input_collection)
---> 99 cc.build()
100 self.get_built_collections()
101 self.open_collection(name)
/work/mh0727/m300524/anaconda3/envs/xr/lib/python3.7/site-packages/intake_esm-2019.4.26.1.post15-py3.7.egg/intake_esm/cmip.py in build(self)
145 Reference: CMIP6 DRS: http://goo.gl/v1drZl
146 """
--> 147 self.build_cmip(depth=9)
148
149 def _get_entry(self, directory):
/work/mh0727/m300524/anaconda3/envs/xr/lib/python3.7/site-packages/intake_esm-2019.4.26.1.post15-py3.7.egg/intake_esm/common.py in build_cmip(self, depth)
102 if not os.path.exists(self.root_dir):
103 raise NotADirectoryError(f'{os.path.abspath(self.root_dir)} does not exist')
--> 104 dirs = self.get_directories(root_dir=self.root_dir, depth=depth)
105 dfs = [self._parse_directory(directory, self.columns) for directory in dirs]
106 df = dd.from_delayed(dfs).compute()
/work/mh0727/m300524/anaconda3/envs/xr/lib/python3.7/site-packages/intake_esm-2019.4.26.1.post15-py3.7.egg/intake_esm/common.py in get_directories(self, root_dir, depth)
80
81 print('Getting list of directories')
---> 82 y = [x[0] for x in self.walk(root_dir, depth)]
83 diff = depth - 1
84 base = len(root_dir.split('/'))
/work/mh0727/m300524/anaconda3/envs/xr/lib/python3.7/site-packages/intake_esm-2019.4.26.1.post15-py3.7.egg/intake_esm/common.py in <listcomp>(.0)
80
81 print('Getting list of directories')
---> 82 y = [x[0] for x in self.walk(root_dir, depth)]
83 diff = depth - 1
84 base = len(root_dir.split('/'))
/work/mh0727/m300524/anaconda3/envs/xr/lib/python3.7/site-packages/intake_esm-2019.4.26.1.post15-py3.7.egg/intake_esm/common.py in walk(self, top, maxdepth)
69 if maxdepth > 1:
70 for path in dirs:
---> 71 for x in self.walk(path, maxdepth - 1):
72 yield x
73
/work/mh0727/m300524/anaconda3/envs/xr/lib/python3.7/site-packages/intake_esm-2019.4.26.1.post15-py3.7.egg/intake_esm/common.py in walk(self, top, maxdepth)
69 if maxdepth > 1:
70 for path in dirs:
---> 71 for x in self.walk(path, maxdepth - 1):
72 yield x
73
/work/mh0727/m300524/anaconda3/envs/xr/lib/python3.7/site-packages/intake_esm-2019.4.26.1.post15-py3.7.egg/intake_esm/common.py in walk(self, top, maxdepth)
64
65 dirs, nondirs = [], []
---> 66 for entry in os.scandir(top):
67 (dirs if entry.is_dir() else nondirs).append(entry.path)
68 yield top, dirs, nondirs
PermissionError: [Errno 13] Permission denied: '/work/kd0956/CMIP6/test_data/CMIP6' The error comes form
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Looked into the code and dont see the problem.
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I’m wondering why we can’t just wrap the directory scanning in a try block
and only include accessible files in the catalog.
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When you get time, can you confirm that #64 works?
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Closing this as it's been fixed in #64 |
Great job for the CMIP class!
Is it possible to add exclude_dirs for CMIP catalogs? The base directory contains other folders
which I don't have access too and therefore catalog building fails.
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