lab-grid / flow Goto Github PK

It would be fine if this is manual for now, rather than a separate admin console (e.g. how about OSS users manage their own auth via auth0, and hosted users send us a list of emails?)

Should affect the previous blocks (up to the nearest signature/witness block)

Alternatively, make "sections" for protocols that get optionally signed/witnessed.

The third way to do this would be to provide a way to link protocols/runs

Robert, if you could pick a framework for this and put in an example, I can work on writing tests as well. My plan is to try to make it as complete as possible, with a focus on our specific protocol and tracking barcodes end-to-end.

These tests will serve as the "validation" suite for regulated labs who need to certify that their LIMS behave as expected.

Currently the server does not properly store data that it has been passed. The server_test.py file should also validate that this basic functionality is working.

• Fix run CRUD endpoints
• Fix protocol CRUD endpoints
• Fix server_test.py

This could use an upload modal that:

• shows a preview of the uploaded file
• allows re-mapping of columns if necessary (this can be made "smarter" in the future)

Could have a way to configure the required/default file format at the protocol block level

We should be keeping track of all edits made to all entities in the system.

Add a _version table for each existing entity that stores actual data. Non _version suffixed tables should not contain actual data and instead contain a reference to the current version.

A run or a protocol should be able to be "signed" (and optionally, "witnessed" or "reviewed and signed" by a second person). A "signed" run or protocol can't be edited. (Unless it is later "unsigned" and then edited...) For each user who "signs", it needs to record the user's name and the date/time of signing, and then change status to "signed".

This could be implemented as a new block type, or all runs could be presumed to have a special "results" block type (are intermediate result blocks needed?).

Results section should have a table with the following columns:

• sample barcode/id
• sequencing result
• plate label per step*

This table should also have a button on each row that can "invalidate" that sample. (or make all fields editable)

To reproduce, try to edit the notes section on a run.

This should:

• Record the thermocycler ID
• Record the start time

In short term, everyone on the team can see each others' runs/protocols

Noticed this in these widgets:

• Run plate sampler
• Add reagent to plate
• Options question (the options are linked)

The goal here is to add some variety to the frontend, to demonstrate that it's flexible.

• Textbox (done example: Run title)
• Textbox should record date/time that text was entered.
• Checkbox that records the date/time it was checked.
• Upload a file (and the file is just stored as part of the "run")
• Different type of file upload, where the file is stored AND the backend parses that file to produce... how about it just displays the file contents as text for now?
• Click then scan a barcode into that field (and again, save date/time the field was populated)
• At the bottom of a "run", a button "sign" that saves the whole run (including the logged-in user) and doesn't let the run change after that.

https://github.com/casbin/casbin-dashboard

By default casbin-dashboard is setup to read/write casbin policies to mysql. Since it uses XORM for db access, we should be able to configure it to talk to the flow postgres db.

This should only return runs that have the specified status.

This should:

• Record the end time

Could consider adding an export modal that allows customization of columns/do this at the protocol level.

There should be at least 1 restricted user type, who can run protocols but can't edit protocols. Open to naming ideas for these admin/not user roles... "admin" and "operator"?

• Add an administrators policy editor UI

We need interfaces allowing us to DI a auth provider type into the:

• web react frontend
• server api service
• native client

On the front page, besides protocol ID, Name, Last modified, let's also add:

• Owner i.e. the user who created it
• Status example statuses = ["" (default), "signed", "witnessed"].
• Created date/time similar to "Last modified".

Also need to add:

• An editable field in <ProtocolEditorPage>

To reproduce:

• Create a new run
• Navigate to the "edit run" page
• Refresh the page

Support the following cell formats:

• checkbox
• switch
• text input
• text readonly
• numeric input
• timestamp
• user/select

TBD, Kubernetes?

This should be a new entity that runs/protocols can be shared with just like users.

The "formula" for the calculation can be configured at the protocol block level using an excel-macro like language.

The run block should show the calculation as one of the following:

• A mad-lib style fill-in-the-blank
• The formula followed by a list of variable inputs

Perhaps start with the following ways to do this:

• From the protocol itself
• From the home page

• Give me a report of all protocols and runs that have happened, with all user/date/signature details. This could be a db dump to .csv plus the ERD or schema. i.e. all tables. (This dump would satisfy the CLIA requirement for audit trail.)
• Give me all runs with status todo/in-progress or signed-but-not-witnessed. (This query is run by the supervisor to track work, and also witness as needed.) (ok for v1 if technicians have this same level of read access.)
• I have 1 run ID and want to get all sample barcodes and all sequencing results for that run. (This is the query for the data that gets returned to patient-facing portal.)

Also useful:

• I have 1 sample and want to get the results for its sequencing
• I have 1 sample and want to get all data from all runs associated with it (useful for debugging why a result is not as expected)
• I have a reagent ID and want to get the runs associated with it (useful for debugging bad reagent batches)

See: https://brendancleary.com/2013/03/08/including-a-github-wiki-in-a-repository-as-a-submodule/

Identified by sample ID/barcode.

Results should include:

• Run(s)
• Protocol(s)
• Sequencing Result(s)
• Signer
• Witness

Use a toast perhaps?

This should populate the new user's profile data using the POST /user endpoint.

Need to:

• Wire up run form component's disabled attributes to API permission endpoints.
• Wire up protocol form component's disabled attributes to API permission endpoints.

Looks like some other package may be preventing it from being upgraded

This should be a new entity that runs/protocols can be shared with just like users.

We'd like to have the following product areas be fully customizable:

• Home-page/dashboard widgets
• Protocol/run steps
• User authentication/authorization

Lets do a second pass of the UI once we have basic functionality in place

The reason for this is that some tasks take 5+ hours (like sequencing), so there will be one protocol for "start the task", and a different protocol for "complete the task", and those will very likely be run by techs in different shifts. And info from the "start the task" run will be needed to complete the report for "complete the task".

This may necessitate moving to react-native fully.

Make sure page is up and alert us if not.
Add to terraform later.

On the front page, besides run ID, Name, Last modified, let's also add:

• Owner i.e. the user who created it
• Status example statuses = ["in progress" (default), "signed", "witnessed"].
• Created date/time similar to "Last modified".

Also need to add:

• An editable field in <RunEditorPage>