86 lines
5.5 KiB
Markdown
86 lines
5.5 KiB
Markdown
- [ ] Appending of qPCR results to WW not saving. Find out why.
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- Possibly due to immutable JSON? But... it's worked before... Right?
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- Based on research, if a top-level JSON field is not changed, SQLalchemy will not detect changes.
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- May have to use a special class: [link](https://docs.sqlalchemy.org/en/14/orm/extensions/mutable.html#establishing-mutability-on-scalar-column-values)
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- [ ] Add Bead basher and Assit to DB.
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- [x] Artic not creating right plate name.
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- [ ] Merge BasicSubmission.find_subclasses and BasicSubmission.find_polymorphic_subclass
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- [x] Fix updating of Extraction Kit in submission form widget.
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- [x] Fix cropping of gel image.
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- [ ] Create Tips ... *sigh*.
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- [x] Create platemap image from html for export to pdf.
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- [x] Move plate map maker to submission.
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- [x] Finish Equipment Parser (add in regex to id asset_number)
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- [ ] Complete info_map in the SubmissionTypeCreator widget.
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- [x] Update Artic and add in equipment listings... *sigh*.
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- [x] Fix WastewaterAssociations not in Session error.
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- Done... I think?
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- [x] Fix submitted date always being today.
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- this is an issue with the way client is filling in form with =TODAY()
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- [x] SubmissionReagentAssociation.query
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- [x] Move as much from db.functions to objects as possible.
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- [x] Clean up DB objects after failed test fix.
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- [x] Fix tests.
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- [x] Fix pydant.PydSample.handle_duplicate_samples?
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- [x] See if the number of queries in BasicSubmission functions (and others) can be trimmed down.
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- [x] Document code
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- [x] Create a result object to facilitate returning function results.
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- [x] Refactor main_window_functions into as many objects (forms, etc.) as possible to clean it up.
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- [x] Integrate 'Construct First Strand' into the Artic import.
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- [x] Clear out any unnecessary ctx passes now that queries are improved.
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- [x] Make a 'query or create' method in all db objects to go with new query.
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- Due to necessity of user input this has only been implemented for BasicSubmission, BasicSample and SubmissionSampleAssociation.
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- [x] Ensure Bacterial plates end up with RSL_YY_###_{submitterName}_{submitterPlateID}.xlsx format.
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- [x] Move lookup functions into class methods of db objects?
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- Not sure if will work for associations.
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- [x] Update artic submission type database entry to add more technicians.
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- [x] Rewrite tests... again.
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- [x] Have InfoItem change status self.missing to True if value changed.
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- [x] Make the kit verifier make more sense.
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- [x] Slim down the Import and Submit functions in main_window_functions.
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- [x] Create custom store methods for submission, reagent and sample.
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- [x] Make pydantic models for other things that use constructors.
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- [x] Move backend.db.functions.constructor functions into Pydantic models.
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- This will allow for better data validation.
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- Parser(client input) -> Pydantic(validation) -> Form(user input) -> Pydantic(validation) -> SQL
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- [x] Rebuild RSLNamer and fix circular imports
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- Should be used when coming in to parser and when leaving form. NO OTHER PLACES.
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- [x] Change 'check_is_power_user' to decorator.
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- [x] Drag and drop files into submission form area?
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- [x] Get info for controls into their sample hitpicks.
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- [x] Move submission-type specific parser functions into class methods in their respective models.
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- [x] Improve function results reporting.
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- Maybe make it a list until it gets to the reporter?
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- [x] Increase robustness of form parsers by adding custom procedures for each.
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- [x] Rerun Kit integrity if extraction kit changed in the form.
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- [x] Clean up db.functions.
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- [x] Make kits easier to add.
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- [x] Clean up & document code... again.
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- Including paring down the logging.debugs
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- Also including reducing number of functions in db.functions
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- [x] Fix Tests... again.
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- [x] Rebuild database
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- [x] Provide more generic names for reagenttypes in kits and move specific names to reagents.
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- ex. Instead of "omega_e-z_96_disruptor_plate_c_plus" in reagent types, have "omega_plate" and have "omega_e-z_96_disruptor_plate_c_plus" in reagent name.
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- Maybe rename to "ReagentRoles"?
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- If I'm doing this, since the forms have a different layout for each submission type I should rewrite the parser to use the locations given in database... Which I should do anyway
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- [x] Fix Wastewater/Artic double submission problem
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- [x] Fix tests.
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- [x] Reorganize wastewater artic parser.
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- [x] Streamline addition of new kits by moving as much into DB as possible.
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- [x] Large scale refactor (2023-07-24).
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- [x] Make plate details from html, same as export.
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- [x] Put in SN controls I guess.
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- [x] Code clean-up and refactor (2023-07).
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- [x] Migrate context settings to pydantic-settings model.
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- [x] Insert column into reagent type to indicate if reagent is required for kit.
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- Needed to keep interchangeable bead plates from being forced into forms.
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- [x] Migrate the parser.sub dictionary to pydantic models.
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- [x] Move type_decider to metadata based method rather than excel map.
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- [x] Solve bug for plate mapping when two samples of same name are in different rows.
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- Try importing "L:\Robotics Laboratory Support\Submissions\Wastewater\2023\2023-06-21\RSL-WW-20230621-1.xlsx" for example.
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- [x] Improve plate mapping by using layout in submission forms rather than PCR.
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- [x] Create a method for creation of hitpicking .csvs because of reasons that may or may not exist.
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- [x] Create a method for commenting submissions.
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- [x] Create barcode generator, because of reasons that may or may not exist.
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- [x] Move bulk of functions from frontend.__init__ to frontend.functions as __init__ is getting bloated. |