The astromon.h5 file is being opened in r+ mode. This fails if the user does not have write permission for the file, which is generally the case on HEAD / GRETA machines.
Example:
In [1]: from astromon import get_cross_matches
In [2]: xc = get_cross_matches()
In [3]: !chmod -w /Users/aldcroft/ska/data/astromon/astromon.h5
In [4]: xc = get_cross_matches()
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
<ipython-input-4-98008cb846f8> in <module>
----> 1 xc = get_cross_matches()
~/git/astromon/astromon/db.py in get_cross_matches(name, dbfile, **kwargs)
572 from astromon.cross_match import filter_matches
573
--> 574 matches = get_table('astromon_xcorr', dbfile)
575 matches = matches[matches['select_name'] == name]
576 astromon_cat_src = get_table('astromon_cat_src', dbfile)
~/git/astromon/astromon/db.py in get_table(table_name, dbfile)
176 # raise RuntimeError(f'Astromon DB file does not exist {dbfile}')
177
--> 178 with connect(dbfile) as con:
179 if type(con) is sqlite3.Connection:
180 try:
~/miniconda3/envs/ska3/lib/python3.8/contextlib.py in __enter__(self)
111 del self.args, self.kwds, self.func
112 try:
--> 113 return next(self.gen)
114 except StopIteration:
115 raise RuntimeError("generator didn't yield") from None
~/git/astromon/astromon/db.py in connect(dbfile)
332 mode = 'r+' if dbfile.exists() else 'w'
333 logger.debug(f'{dbfile} open')
--> 334 h5 = tables_open_file(dbfile, mode)
335 if not h5.is_undo_enabled():
336 h5.enable_undo()
~/miniconda3/envs/ska3/lib/python3.8/site-packages/ska_helpers/retry/api.py in tables_open_file(*args, **kwargs)
149 import tables.exceptions
150
--> 151 h5 = ska_helpers.retry.retry_call(
152 tables.open_file, args=args, kwargs=kwargs,
153 exceptions=tables.exceptions.HDF5ExtError,
~/miniconda3/envs/ska3/lib/python3.8/site-packages/ska_helpers/retry/api.py in retry_call(f, args, kwargs, exceptions, tries, delay, max_delay, backoff, jitter, logger)
131 kwargs = {}
132
--> 133 return __retry_internal(f, exceptions, tries, delay, max_delay,
134 backoff, jitter, logger, args=args, kwargs=kwargs)
135
~/miniconda3/envs/ska3/lib/python3.8/site-packages/ska_helpers/retry/api.py in __retry_internal(f, exceptions, tries, delay, max_delay, backoff, jitter, logger, args, kwargs)
43 while _tries:
44 try:
---> 45 return f(*args, **kwargs)
46 except exceptions as e:
47 exc_type, exc_value, exc_traceback = sys.exc_info()
~/miniconda3/envs/ska3/lib/python3.8/site-packages/tables/file.py in open_file(filename, mode, title, root_uep, filters, **kwargs)
313
314 # Finally, create the File instance, and return it
--> 315 return File(filename, mode, title, root_uep, filters, **kwargs)
316
317
~/miniconda3/envs/ska3/lib/python3.8/site-packages/tables/file.py in __init__(self, filename, mode, title, root_uep, filters, **kwargs)
776
777 # Now, it is time to initialize the File extension
--> 778 self._g_new(filename, mode, **params)
779
780 # Check filters and set PyTables format version for new files.
tables/hdf5extension.pyx in tables.hdf5extension.File._g_new()
~/miniconda3/envs/ska3/lib/python3.8/site-packages/tables/utils.py in check_file_access(filename, mode)
184 check_file_access(filename, 'r')
185 if not os.access(filename, os.W_OK):
--> 186 raise IOError("file ``%s`` exists but it can not be written"
187 % (filename,))
188 else:
OSError: file ``/Users/aldcroft/ska/data/astromon/astromon.h5`` exists but it can not be written
The
astromon.h5file is being opened in r+ mode. This fails if the user does not have write permission for the file, which is generally the case on HEAD / GRETA machines.Example: