biosimulations / biosimulations Goto Github PK

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/896df2abe3b2ba51129c415572852c83c94f419f/CRBM-Viz/src/app/Pages/data/data.component.spec.ts#L12-L17

This issue was generated by todo based on a TODO comment in 896df2a when #66 was merged. cc @reproducible-biomedical-modeling.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Pages/simulate/simulate.component.spec.ts#L6-L11

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

The first loading of the page address "https://crbm-viz.herokuapp.com/" seems a bit slow, both on mobile network and ethernet connections.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Layout/navigation/navigation.component.spec.ts#L13-L18

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Components/past-simulation/past-simulation.component.spec.ts#L9-L14

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Pages/visualize/visualize.component.spec.ts#L9-L14

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Pages/simulate/simulate.component.spec.ts#L6-L11

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Components/callback/callback.component.spec.ts#L7-L12

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

Sidebar is shorter than topbar

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Components/new-simulation/new-simulation.component.spec.ts#L6-L11

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Pages/files/file-edit/file-edit.component.spec.ts#L11-L16

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

the image use to load, now does not.
Need to look at auth0 conf

Docker file is unable to build due to a vega-lite error at the build step. However, the node CI is able to build the site just fine.

I think this means there is some sort of versioning issue. Both node ci and docker ci use node 12.x and the latest angular/cli. Vega-lite should be the same in both through the package.json file.

The build also started failing without any changes to the codebase, further making me think this is some upstream bug due to versioning

Need to revert the app module to previous organization

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Components/new-simulation/new-simulation.component.spec.ts#L10-L15

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

The footer will extend to the right of the viewport on a small screen, creating a scroll bar. The icons are displayed over a blank background.
This can probably be fixed by enabling wrapping in the flex container but will need to replace the current spacing hack with a better method

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Layout/navigation/navigation.component.spec.ts#L4-L9

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

Currently search page displays a page not found error since it is not yet implemented.
A search service needs to be created to fetch available resources from the server

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Layout/navigation/navigation.component.spec.ts#L4-L9

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Pages/visualize/visualize.component.spec.ts#L9-L14

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

1. Mat-Progress spinner
2. Mat-Progress-bar
3. Store past simulations on first fetch
4. Modify file API for extension filter

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/e1f203460277898763134c1c78aaf9d5eab2c71e/CRBM-Viz/src/app/Layout/nav-icons/nav-icons.component.spec.ts#L6-L11

This issue was generated by todo based on a TODO comment in e1f2034 when #72 was merged. cc @reproducible-biomedical-modeling.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Layout/navigation/navigation.component.spec.ts#L13-L18

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Components/past-simulation/past-simulation.component.spec.ts#L9-L14

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

Change dockerfile to only build once all tests pass
need to resolve #9 first

Convert this to a menu list

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Pages/visualize/visualize.component.spec.ts#L8-L13

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Components/new-simulation/new-simulation.component.spec.ts#L10-L15

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

I'm entering all of my comments into one issue. Feel free to separate this into multiple issues if that's easier for you. The comments aren't in any particular order.

Issues that I've already address are striked out

• Submission: here's two ways I could see organizing the submission of models/simulation and browsing previously submitted models/simulations

  • Under models and under simulations, have pages to submit a model or simulation
  • Make submit a top-level entity in the menu. Nest pages for submitting models and simulations under this.

• Models section

  • To help users find models, perhaps we should allow users to tag models with keywords (e.g., about the physical scale they represent, biological process involved, organism represented, etc.). For well-annotated models, this information could be extracted from the model file.

• Simulations section

  • I think this could focus on metadata about simulations rather than the numerical results. I think a
    long list of data points will be hard for users to make sense of. I think visualizations are better for this. This could include metadata such as

    • Which model was simulated
    • Brief textual description of simulation provided by the user who requested it
    • Parameter values that were changed relative to model (can be parsed from SED-ML)
    • Length of simulation time
    • Which simulator ran the simulation and the version of the simulation.
      • DockerHub image id/tag
    • When the simulation was requested
    • When the simulation was run
    • Which user requested it
    • How long the took (wall time)
    • Public/private status

  • When users first navigate to the simulations section, I suggest showing a (paginated) list of all of the simulations they have access to. Then a search bar or faceted search could be provided to help users drill down to specific simulations.

  • Two additional things that would make sense to me are

    • (a) a table of the predicted species concentrations and reaction fluxes (ids and names) and buttons to open a visualization of the dynamics of their dynamics in the selected simulation and
    • (b) link to download the data.

  • Submenu elements: (a) browse completed simulations, (b) browse simulations in progress, (c) submit simulation

• Visualizations section

  • Maybe this menu section should have two sections: (a) exploratory visualizations with standard statistical chars, and (b) "expert"-designed visualizations.

• Top-right menu:

  • this should probably have the same sub-menus as the left menu
  • use same icons as in left menu (i.e. for account sub-menu)

• User section

  • User profile: to polish the demo, format the name and picture with HTML
  • User notifications: for now, this icon could be hidden. Do you intend for this to enable users to control how they get notifications (e.g., email of completion of simulation requests)?
  • User settings page what settings are you thinking of?
  • It would be nice to capture some additional information about users (see #112 )

• Left menu design

  • I think the menu should have 1 background color for the whole menu to distinguish it from the top bar and content section. The background should contrast the blue of the top bar and the grey of the content. The icon could be moved up to where "Menu" is currently located.
  • Rename "BioSimulations" to "About" or "About " so users don't confuse this with the simulations themselves.
  • Add right padding to the icons in the menu (e.g., "BioSimulations", "Account", etc.)
  • Move "BioSimulations" and "Account" to the bottom of the menu

• Icons

  • Some of the icons Nicola has made would be good for models (model structure), simulations (WC-SimDB), and visualizations (WC-Viz)
  • Since its hard to find visually consistent icons that include icons for models and simulations, we can have Nicola design visually consistent icons for users, about, etc.
    

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Components/new-simulation/new-simulation.component.spec.ts#L12-L17

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/706415da132959c28467a0085e5bf6923fd3ef2b/CRBM-Viz/src/app/app.component.ts#L11-L16

This issue was generated by todo based on a TODO comment in 706415d when #26 was merged. cc @reproducible-biomedical-modeling.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Components/callback/callback.component.spec.ts#L7-L12

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

The window property relies on the browser, preventing this from being usable with server-side rendering. Might be worth switching the window property to use Angular's Route or ActivatedRoute

The route changes, but component does not reload.

Top bar needs to remove buttons when viewport shrinks
Menu bar does not auto/open close
Button to open/close menu is laggy,

Menu button is not aligned to end of bar

Using *ngIf in the parent element of a table prevents pagination and sort/filter from working properly. This is preventing proper use of a spinner during data loading.
Potential solutions:

https://stackoverflow.com/questions/50767580/mat-filtering-mat-sort-not-work-correctly-when-use-ngif-in-mat-table-parent

angular/components#10205

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Components/new-simulation/new-simulation.component.spec.ts#L6-L11

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

Need to write tests for each component

Favicon is not showing up on final build

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Pages/files/file-edit/file-edit.component.spec.ts#L11-L16

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

At https://crbm-viz.herokuapp.com/visualize/7 the image does not go below 100% vh

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/9990812697ca6b0d1c64faa445e907e7e1b21055/CRBM-Viz/src/app/Components/new-simulation/new-simulation.component.spec.ts#L12-L17

This issue was generated by todo based on a TODO comment in 9990812 when #35 was merged. cc @reproducible-biomedical-modeling.

https://github.com/reproducible-biomedical-modeling/CRBM-Viz/blob/1b71baf50c90d234805e9c76d1c1347742c9816e/CRBM-Viz/src/app/Pages/visualize/visualize.component.spec.ts#L8-L13

This issue was generated by todo based on a TODO comment in 1b71baf. It's been assigned to @bilalshaikh42 because they committed the code.

to display simulation data, available simulations, search results etc.
Perhaps have it as its own components, feed in search data etc