Submissions-App/TODO.md

• Put "Not applicable" reagents in to_dict() method.
  • Currently in to_pydantic().
• Critical: Convert Json lits to dicts so I can have them update properly without using crashy Sqlalchemy-json
  • Was actually not necessary.
• Fix Parsed/Missing mix ups.
• Have sample parser check for controls and add to reagents?
• Update controls to NestedMutableJson
• Appending of qPCR results to WW not saving. Find out why.
  • Possibly due to immutable JSON? But... it's worked before... Right?
  • Based on research, if a top-level JSON field is not changed, SQLalchemy will not detect changes.
  • Using sqlalchemy-json module seems to have helped.
• Add Bead basher and Assist to DB.
• Artic not creating right plate name.
• Merge BasicSubmission.find_subclasses and BasicSubmission.find_polymorphic_subclass
• Fix updating of Extraction Kit in submission form widget.
• Fix cropping of gel image.
• Create Tips ... sigh.
• Create platemap image from html for export to pdf.
• Move plate map maker to submission.
• Finish Equipment Parser (add in regex to id asset_number)
• Complete info_map in the SubmissionTypeCreator widget.
• Update Artic and add in equipment listings... sigh.
• Fix WastewaterAssociations not in Session error.
  • Done... I think?
• Fix submitted date always being today.
  • this is an issue with the way client is filling in form with =TODAY()
• SubmissionReagentAssociation.query
• Move as much from db.functions to objects as possible.
• Clean up DB objects after failed test fix.
• Fix tests.
• Fix pydant.PydSample.handle_duplicate_samples?
• See if the number of queries in BasicSubmission functions (and others) can be trimmed down.
• Document code
• Create a result object to facilitate returning function results.
• Refactor main_window_functions into as many objects (forms, etc.) as possible to clean it up.
• Integrate 'Construct First Strand' into the Artic import.
• Clear out any unnecessary ctx passes now that queries are improved.
• Make a 'query or create' method in all db objects to go with new query.
  • Due to necessity of user input this has only been implemented for BasicSubmission, BasicSample and SubmissionSampleAssociation.
• Ensure Bacterial plates end up with RSL_YY_###{submitterName}{submitterPlateID}.xlsx format.
• Move lookup functions into class methods of db objects?
  • Not sure if will work for associations.
• Update artic submission type database entry to add more technicians.
• Rewrite tests... again.
• Have InfoItem change status self.missing to True if value changed.
• Make the kit verifier make more sense.
• Slim down the Import and Submit functions in main_window_functions.
• Create custom store methods for submission, reagent and sample.
• Make pydantic models for other things that use constructors.
• Move backend.db.functions.constructor functions into Pydantic models.
  • This will allow for better data validation.
  • Parser(client input) -> Pydantic(validation) -> Form(user input) -> Pydantic(validation) -> SQL
• Rebuild RSLNamer and fix circular imports
  • Should be used when coming in to parser and when leaving form. NO OTHER PLACES.
• Change 'check_is_power_user' to decorator.
• Drag and drop files into submission form area?
• Get info for controls into their sample hitpicks.
• Move submission-type specific parser functions into class methods in their respective models.
• Improve function results reporting.
  • Maybe make it a list until it gets to the reporter?
• Increase robustness of form parsers by adding custom procedures for each.
• Rerun Kit integrity if extraction kit changed in the form.
• Clean up db.functions.
• Make kits easier to add.
• Clean up & document code... again.
  • Including paring down the logging.debugs
  • Also including reducing number of functions in db.functions
• Fix Tests... again.
• Rebuild database
• Provide more generic names for reagenttypes in kits and move specific names to reagents.
  • 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.
  • Maybe rename to "ReagentRoles"?
  • 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
• Fix Wastewater/Artic double submission problem
• Fix tests.
• Reorganize wastewater artic parser.
• Streamline addition of new kits by moving as much into DB as possible.
• Large scale refactor (2023-07-24).
• Make plate details from html, same as export.
• Put in SN controls I guess.
• Code clean-up and refactor (2023-07).
• Migrate context settings to pydantic-settings model.
• Insert column into reagent type to indicate if reagent is required for kit.
  • Needed to keep interchangeable bead plates from being forced into forms.
• Migrate the parser.sub dictionary to pydantic models.
• Move type_decider to metadata based method rather than excel map.
• Solve bug for plate mapping when two samples of same name are in different rows.
  • Try importing "L:\Robotics Laboratory Support\Submissions\Wastewater\2023\2023-06-21\RSL-WW-20230621-1.xlsx" for example.
• Improve plate mapping by using layout in submission forms rather than PCR.
• Create a method for creation of hitpicking .csvs because of reasons that may or may not exist.
• Create a method for commenting submissions.
• Create barcode generator, because of reasons that may or may not exist.
• Move bulk of functions from frontend.init to frontend.functions as init is getting bloated.