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themathmajor

metaprot's Issues

Integrate Howard's data transformation script

  • We will have a script that transforms the pre-processed input file(s) into the expected formats for metabolite analysis and temporal pattern recognition. This will be attached to the last step in the processing stage, wherein the user is given both features as options.

Semantics of reset

It's a good practice to have a reset button whenever there is user input - however because there can be multiple plots on the same page, wherein all interact via highlighting the same data points, it is up to debate as to how the reset would work.

Simply resetting a single plot might not be semantically correct, as this means the corresponding data points in other plots would be "out-of-sync" and unaffected. That is, points referring to the same metabolite/protein in another plot will still be highlighted, while the ones in the resetted plot will be reverted. This would go against the central idea of tracking the same metabolite/protein across plots.

Integrity checker

Create a Java class that will check for correct file formatting. See Howard for more details + examples.

Normalization

Implement necessary functions for handling data normalization.

Drag multi select

Currently there is code in place that highlights based on dragging from left to right, up and down. Need to generalize this in any direction as well as add a bounding box. Enabling multi select has some start code, but is buggy.

zooming is buggy

Mainly in terms of interactions with other events, such as resetting the plot+form

Upload form thresholds

Need to debug threshold input for the front page upload form - can postpone until after Mongo is completely set up, as this could be a potential solution.

Mongo setup for metaprot

Setup complete using spring-boot-starter-data-mongodb. Basic functionality such as storing and retrieving tasks is complete locally, but waiting on #10 to be resolved before pushing to remote.

Restructure data table in results page

We should keep the all-items table to allow exporting to CSV and excel. However, see Howard's sketch of the new UI. Multiple panels, threshold input elements, and multiple plots per result page.

[For demo] Addition to Pattern Recognition

Aim to implement a rough version of strain visualization before the consortium meeting.

Core features:

  • 3 plots, one for each strain of a metabolite
  • one main control panel, where clicking a metabolite name plots the appropriate lines in each plot
  • there will be ~3 replica lines for each metabolite

Research AWS DynamoDB

Perhaps when the time comes to deploy Metaprot, we should migrate from MongoDB to DynamoDB.

Create front-end to accommodate new site structure

After the landing page, the main page will allow the user to upload a file. After this is complete (and all checks succeed), the user will be directed to a page with filtering, etc. options. After the pre-processing is complete, the user is then given the option to use either feature in Metaprot.

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