Merge pull request #542 from AllenInstitute/fix-nwb-files-failing-dandi-validate

Stop IPFX from caching its NWB Schemas when writing/modifying NWB files

Author: njmei

.circleci/config.yml

@@ -36,6 +36,7 @@ jobs:
           command: |
             python3 -m venv venv
             . venv/bin/activate
+            pip install -U pip
             pip install -U -r requirements.txt
             pip install codecov
 

ipfx/attach_metadata/sink/nwb2_sink.py

@@ -94,7 +94,11 @@ def _commit_nwb_changes(self):
 
         set_container_sources(self.nwbfile, self._h5_file.filename)
         self.nwbfile.set_modified(True)
-        self._nwb_io.write(self.nwbfile)
+        # Because the NWB schema versions of NWB data produced by MIES are older
+        # we do not want to cache the newer schema versions that IPFX is currently using
+        # WARNING: Doing this may introduce fragility down the road though if IPFX writes NWB fields
+        #          that require the newer schema versions...
+        self._nwb_io.write(self.nwbfile, cache_spec=False)
         self._nwb_io.close()
         self._h5_file.close()
 

ipfx/nwb_append.py

@@ -63,7 +63,11 @@ def append_spike_times(input_nwb_path: PathLike,
 
         nwbfile.add_processing_module(spike_module)
 
-        nwb_io.write(nwbfile)
+        # Because the NWB schema versions of NWB data produced by MIES are older
+        # we do not want to cache the newer schema versions that IPFX is currently using
+        # WARNING: Doing this may introduce fragility down the road though if IPFX writes NWB fields
+        #          that require the newer schema versions...
+        nwb_io.write(nwbfile, cache_spec=False)
     else:
         raise ValueError("Cannot add spikes times to the nwb file: "
                          "spikes times already exist!")

ipfx/version.txt

@@ -1 +1 @@
-1.0.5
+1.0.6