Errors submitting manifest

[andrewelamb]

Describe the bug I'm getting the two errors below submitting a manifest schematic model -c ../schematic/config.yml submit -mp synapse_storage_manifest.csv -d syn50896918 -vc Genes schema

Expected behavior The manifest should submit.

• row 3 the attribute hgnc_id is A2MP1, I'm not sure how that is not a string
• syn50896918 is definitely in this asset view

Priority (select one)

• [ ] Minor ⬇️
• [x] Major 📢
• [ ] Critical 🆘

schematic model -c ../schematic/config.yml submit -mp synapse_storage_manifest.csv -d syn50896918 -vc Genes
Starting schematic...
The (model > input > location) argument with value '../iAtlasSchema/iatlas_schema.jsonld' is being read from the config file.
The (model > input > file_type) argument with value 'local' is being read from the config file.
 [####################]100.00%   1/1   Done...
Downloading  [####################]100.00%   55.7kB/55.7kB (675.8kB/s) SYNAPSE_TABLE_QUERY_121331300.csv Done...
    JSON schema successfully generated from schema.org schema!
JSON schema file log stored as ../iAtlasSchema/iatlas_schema.Genes.schema.json
FileDataContext loading zep config
GxConfig.parse_yaml() failed with errors - [{'loc': ('xdatasources',), 'msg': 'field required', 'type': 'value_error.missing'}]
GxConfig.parse_yaml() returning empty `xdatasources`
Loading 'datasources' ->
{}
Loaded 'datasources' ->
{}
EphemeralDataContext has not implemented `_load_zep_config()` returning empty `GxConfig`
Loading 'datasources' ->
{}
Loaded 'datasources' ->
{}
[WARNING] /home/alamb/.cache/pypoetry/virtualenvs/schematicpy-gKAjXOOq-py3.9/lib/python3.9/site-packages/jinja2/environment.py:1088: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.
  return concat(self.root_render_func(self.new_context(vars)))

warning: /home/alamb/.cache/pypoetry/virtualenvs/schematicpy-gKAjXOOq-py3.9/lib/python3.9/site-packages/jinja2/environment.py:1088: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.
warning:   return concat(self.root_render_func(self.new_context(vars)))
    10 expectation(s) included in expectation_suite.
Calculating Metrics: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 66/66 [00:00<00:00, 639.39it/s]
[WARNING] /home/alamb/.cache/pypoetry/virtualenvs/schematicpy-gKAjXOOq-py3.9/lib/python3.9/site-packages/jinja2/environment.py:1088: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.
  return concat(self.root_render_func(self.new_context(vars)))

warning: /home/alamb/.cache/pypoetry/virtualenvs/schematicpy-gKAjXOOq-py3.9/lib/python3.9/site-packages/jinja2/environment.py:1088: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.
warning:   return concat(self.root_render_func(self.new_context(vars)))
[WARNING] /home/alamb/.cache/pypoetry/virtualenvs/schematicpy-gKAjXOOq-py3.9/lib/python3.9/site-packages/jinja2/environment.py:1088: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.
  return concat(self.root_render_func(self.new_context(vars)))

warning: /home/alamb/.cache/pypoetry/virtualenvs/schematicpy-gKAjXOOq-py3.9/lib/python3.9/site-packages/jinja2/environment.py:1088: DeprecationWarning: 'soft_unicode' has been renamed to 'soft_str'. The old name will be removed in MarkupSafe 2.1.
warning:   return concat(self.root_render_func(self.new_context(vars)))
error: On row 3 the attribute hgnc_id does not contain the proper value type str.
error: 'syn50896918' could not be found in the asset view (or file view for Synapse user)

[andrewelamb]

manifest: synapse_storage_manifest.csv

[milen-sage]

Related to #1097

[milen-sage]

@andrewelamb to test with updates to develop branch.

[andrewelamb]

@milen-sage, @GiaJordan I'm still seeing this error with the latest version of schematic

[andrewelamb]

@milen-sage, @GiaJordan Never mind, it was an issue with my schematic config!