backward compatible with nixio 1.5.0b3?

[dizcza]

Hello nixio community,

a file, saved with nixio 1.5.0b3, cannot be loaded with 1.5.0b4. Is this a known issue?

wget -N https://web.gin.g-node.org/INM-6/elephant-data/raw/master/dataset-2/asset_showcase_500.nix

with neo.NixIO('asset_showcase_500.nix', 'ro') as f:
    block = f.read_block()

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-4-c2dd4bfdbe67> in <module>
----> 1 with neo.NixIO('asset_showcase_500.nix', 'ro') as f:
      2     block = f.read_block()
      3 segment = block.segments[0]
      4 spiketrains = segment.spiketrains

~/anaconda3/envs/elephant/lib/python3.7/site-packages/neo/io/nixio.py in __init__(self, filename, mode)
    162             self._file_version = '0.5.2'
    163             if "neo" in self.nix_file.sections:
--> 164                 self._file_version = self.nix_file.sections["neo"]["version"]
    165         elif self.nix_file.mode == nix.FileMode.ReadWrite:
    166             if "neo" in self.nix_file.sections:

~/anaconda3/envs/elephant/lib/python3.7/site-packages/nixio/section.py in __getitem__(self, key)
    456 
    457         prop = self.props[key]
--> 458         values = list(prop.values)
    459         if len(values) == 1:
    460             values = values[0]

~/anaconda3/envs/elephant/lib/python3.7/site-packages/nixio/property.py in values(self)
    241         x, y, z = dataset._parent.file.attrs["version"]
    242         if x < 1 or (x == 1 and y < 1) or (x == 1 and y == 1 and z < 1):
--> 243             v = self._read_old_values()
    244             return v
    245         if not sum(dataset.shape):

~/anaconda3/envs/elephant/lib/python3.7/site-packages/nixio/property.py in _read_old_values(self)
    232         val_tu = tuple()
    233         for v in val:
--> 234             v = v["value"]
    235             val_tu += (v,)
    236         return val_tu

TypeError: string indices must be integers

[achilleas-k]

This is a known issue and part of it is a bug in the b3 release that changed the way metadata values are stored but the file version header wasn't updated to reflect this. The next release will include a script to upgrade older files to new formats and fix such inconsistencies.

For now, the best way to work with the file would be to install v1.5.0b3. Alternatively, you could try the master branch and use the upgrade script on the file to test the unrealeased up to date version of the library, but of course for that I would strongly recommend you keep backups of all files and data you work with.

[dizcza]

Thank you.
I'll wait for the next release and try upgrading the file.

[achilleas-k]

The latest beta release (v1.5.0b6) includes the script I mentioned, which upgrades older files to newer formats.

Keep in mind this is a beta release and, while we do our best to test any changes thoroughly, there is always the possibility of bugs. If you plan to use the upgrade script on your files, make sure to run it on copies of the primary files and keep backups.

[dizcza]

You're right. I better wait for a stable release, convert the file, and fix the requirement version.
I think this issue should no longer be open.
I'll open an issue if I encounter a problem while converting the file.