Unify activity status

[eleftherioszisis]

Activity status moved to activity table and unified with ActivityStatus:

class ActivityStatus(StrEnum):
    created = auto()
    pending = auto()
    running = auto()
    done = auto()
    error = auto()
    cancelled = auto()

Issue: #511

Activities the status of which moved to activity parent table:

• circuit_extraction_execution
• skeletonization_execution
• ion_channel_modeling_execution
• simulation_execution

Columns that remapped to ActivityStatus

• memodel.validation_status
• single_neuron_simulation.status
• single_neuron_synaptome_simulation.status

Activities without prior status column set to "done" because activity parent table has a status now

• analysis_notebook_execution
• calibration
• circuit_extraction_config_generation
• ion_channel_modeling_config_generation
• simulation_generation
• skeletonization_config_generation
• validation

Given that this is a breaking change, fyi @james-isbister @chr-pok @AurelienJaquier @ilkilic

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Flag	Coverage Δ
pytest	97.62% <100.00%> (-0.02%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
app/db/model.py	99.08% <100.00%> (-0.01%)	⬇️
app/db/types.py	99.40% <100.00%> (-0.05%)	⬇️
app/filters/activity.py	100.00% <100.00%> (ø)
app/filters/analysis_notebook_execution.py	100.00% <ø> (ø)
app/filters/circuit_extraction_execution.py	100.00% <ø> (ø)
app/filters/ion_channel_modeling_execution.py	100.00% <ø> (ø)
app/filters/memodel.py	100.00% <100.00%> (ø)
app/filters/simulation_execution.py	100.00% <ø> (ø)
app/filters/single_neuron_simulation.py	100.00% <100.00%> (ø)
app/filters/single_neuron_synaptome_simulation.py	100.00% <100.00%> (ø)
... and 8 more

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[GianlucaFicarelli]

validation_status is an attribute of me_model, and not the status of an activity, so it seems strange to define it on the entity and use the same enum.
Where is validation_status used and how is it updated?
Should it be replaced with ValidationResult?

[eleftherioszisis]

If it's the status of the validation process, it seems to me it should be an activity status. Not sure this is the case however. @jdcourcol wdyt?

[jdcourcol]

We will have to ask @pgetta . I don't see a place in the code where that flag is being updated.

[pgetta]

Indeed, there seems to be a certain disconnect with respect to this property.

In the UI it's used in the ME-model list view as a separate column with binary value (Validated: true/false) as well as in the detailed and mini detailed view.

In Bluenaas, when the ME-model is getting created - the property is set to created but the validation process doesn't update that.

From what I see only a subset of public models have this property set to done.

At the moment we have a single validation job, but it has a set of different tasks each producing and registering it's own ValidationResult entity.

If the idea for the validation_status property is to track the validation job - I'll have to update the logic in Bluenaas. @jdcourcol could you please confirm.

[jdcourcol]

this validated property should come from the ValidationResult entity. and we should get rid of the validation_status property.

[chr-pok]

Thanks @eleftherioszisis, nice work!