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Support legacy namespace names #403

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merged 2 commits into from
Jul 24, 2023

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lawrence-mbf
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Fixes #398

Currently throws a weird save cache error. Now suggests generating
an extension or something.
@lawrence-mbf
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@mpompolas Does this pass your tests?

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codecov bot commented Feb 17, 2022

Codecov Report

Merging #403 (8c3991f) into master (a4fc5c6) will decrease coverage by 0.02%.
The diff coverage is 60.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #403      +/-   ##
==========================================
- Coverage   85.70%   85.67%   -0.03%     
==========================================
  Files         125      125              
  Lines        4735     4740       +5     
==========================================
+ Hits         4058     4061       +3     
- Misses        677      679       +2     
Impacted Files Coverage Δ
nwbRead.m 76.47% <60.00%> (-1.03%) ⬇️

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@mpompolas
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mpompolas commented Feb 25, 2022

Hi @lawrence-mbf ,

I get a different error now:

Error using types.util.dynamictable.checkConfig (line 45)
Invalid table detected: column heights (vector lengths or number of matrix columns) must be the same.

Error in types.core.Units (line 51)
            types.util.dynamictable.checkConfig(obj);

Error in io.parseGroup (line 85)
    parsed = eval([Type.typename '(kwargs{:})']);

Error in io.parseGroup (line 38)
    subg = io.parseGroup(filename, group, Blacklist);

Error in nwbRead (line 59)
nwb = io.parseGroup(filename, h5info(filename), Blacklist);

The values I have for tableHeight and columnHeightsis:

K>> columnHeights

columnHeights =

     0
     5
     0
     5
     0
     5

K>> tableHeight

tableHeight =

     0
     5

and the dynamicTable:

DynamicTable = 

  Units with properties:

        electrode_group: [1×1 types.hdmf_common.VectorData]
             electrodes: [1×1 types.hdmf_common.DynamicTableRegion]
       electrodes_index: [1×1 types.hdmf_common.VectorIndex]
          obs_intervals: []
    obs_intervals_index: []
            spike_times: [1×1 types.hdmf_common.VectorData]
      spike_times_index: [1×1 types.hdmf_common.VectorIndex]
          waveform_mean: [1×1 types.hdmf_common.VectorData]
            waveform_sd: []
               colnames: {6×1 cell}
            description: 'Generated from addUnitsInfo_Neuroscope'
                     id: [1×1 types.hdmf_common.ElementIdentifiers]
             vectordata: [2×1 types.untyped.Set]
            vectorindex: [0×1 types.untyped.Set]
K>> DynamicTable.colnames

ans =

  6×1 cell array

    {'shank_id'       }
    {'spike_times'    }
    {'electrode_group'}
    {'cell_type'      }
    {'global_id'      }
    {'max_electrode'  }

@lawrence-mbf lawrence-mbf self-assigned this Jul 24, 2023
@lawrence-mbf
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This should have been forked out into its own issue. Unsure if the error mentioned here is still present.

@lawrence-mbf lawrence-mbf merged commit 12f1996 into master Jul 24, 2023
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Namespace label inconsistency
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