Experiment & Session reports with flags

AllenInstitute / brain_observatory_qc

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Experiment & Session reports with flags #277

Closed shiellac closed 11 months ago

shiellac commented 1 year ago

Experiment QC Report status shows as 'Flag' when there sections of the report that are marked as such.

A status of 'Flag' does not provide guidance to the Operator when selecting a Pass/Fail workflow state in LIMS for individual experiments/planes.

Could the workflow states be Pass/Fail/Incomplete (when the report is not finished) and a separate column or a way to distinguish if the reports include any flags ?

example, session report: http://mouse-seeks/qc/ophys/session/1286805635 w/ experiment http://mouse-seeks/qc/ophys/experiment/1286901204 shows a workflow state of 'Flag' but operator should still change LIMS workflow state to 'Pass' despite a flag on the report.

macarenasa commented 1 year ago

Follow up with Pete and Marina in QC Ops meeting on 8/7. Impacted by transition to CodeOcean.

DowntonCrabby commented 1 year ago

For more context:

there was a decision to move away from passing/flagging/failing whole sessions and instead treat each data stream individually with pass/fail/flag status. We will need to implement that
the move to code ocean will likely change how we designate this pass/fail/flag status since we won't be using LIMS anymore
Having a decision is important for knowing what experiments are included in a container

matchings commented 1 year ago

im not sure if i have a full enough understanding of the back end implications, but it seems to me that we need to separate the "workflow states" (which should correspond to the pass/fail designation that goes into lims, with the limitation that we cant pass/fail individual data streams) and the data stream specific pass/fail/flag state (which we can use later on to filter the data when we are independent of lims).

Once we move to Code Ocean we can implement data stream specific QC state outcomes, but until then we still need to pass/fail entire experiments / sessions / containers as we have been doing in the past.

DowntonCrabby commented 11 months ago

If an experiment or session has any failures then list it as failed in LIMS If has flags and passes only then it passes in LIMS.

Sean, Arielle and myself will work out the details of pass,flag,fail of individual data streams in code ocean when we move to that platform. However, that process will not require any differences in how operators do the qc and will in fact be easier because it will automatically apply the pass/flag/fail to the data streams rather than having to manually submit it after the fact.