The results are not appearing for some of the base experiments in bulk

[ke4]

Example experiment in staging: https://wwwdev.ebi.ac.uk/gxa/experiments/E-MTAB-6592/Results

Here is the error log from the JS Console:

The above error occurred in the <AnatomogramSvg> component:
    in AnatomogramSvg (created by Anatomogram)
    in div (created by Anatomogram)
    in Anatomogram (created by mapProps(Anatomogram))
    in mapProps(Anatomogram) (created by defaultProps(mapProps(Anatomogram)))
    in defaultProps(mapProps(Anatomogram)) (created by defaultProps(defaultProps(mapProps(Anatomogram))))
    in defaultProps(defaultProps(mapProps(Anatomogram))) (created by onlyUpdateForPropTypes(defaultProps(defaultProps(mapProps(Anatomogram)))))
    in onlyUpdateForPropTypes(defaultProps(defaultProps(mapProps(Anatomogram)))) (created by withPropsOnChange(onlyUpdateForPropTypes(defaultProps(defaultProps(mapProps(Anatomogram))))))
    in withPropsOnChange(onlyUpdateForPropTypes(defaultProps(defaultProps(mapProps(Anatomogram))))) (created by defaultProps(withPropsOnChange(onlyUpdateForPropTypes(defaultProps(defaultProps(mapProps(Anatomogram)))))))
    in defaultProps(withPropsOnChange(onlyUpdateForPropTypes(defaultProps(defaultProps(mapProps(Anatomogram)))))) (created by DebouncedContainer)
    in DebouncedContainer (created by _HeatmapWithControls)
    in div (created by _HeatmapWithControls)
    in div (created by _HeatmapWithControls)
    in div (created by _HeatmapWithControls)
    in _HeatmapWithControls (created by Uncontrolled(_HeatmapWithControls))
    in Uncontrolled(_HeatmapWithControls) (at uncontrollable.js:128)
    in ForwardRef (created by HeatmapWithControlsContainer)
    in HeatmapWithControlsContainer (created by ChartContainer)
    in div (created by ChartContainer)
    in div (created by ChartContainer)
    in ChartContainer (created by Container)
    in div (created by Container)
    in Container (created by ContainerLoader)
    in ContainerLoader (created by Refetch.connect(ContainerLoader))
    in Refetch.connect(ContainerLoader) (created by ExpressionAtlasHeatmap)
    in div (created by ExpressionAtlasHeatmap)
    in ExpressionAtlasHeatmap (created by Main)
    in div (created by Main)
    in div (created by Main)
    in Main (created by Context.Consumer)
    in withRouter(Main)
    in Unknown (created by Context.Consumer)
    in Route (created by ExperimentContainerRouter)
    in Switch (created by ExperimentContainerRouter)
    in div (created by ExperimentContainerRouter)
    in Router (created by BrowserRouter)
    in BrowserRouter (created by ExperimentContainerRouter)
    in ExperimentContainerRouter

Consider adding an error boundary to your tree to customize error handling behavior.
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[ke4]

I did some research today. It looks like that we have a repo: atlas-experiment that is published to npm with this name: @ebi-gene-expression-group/expression-atlas-experiment-page. That has the ExperimentContainerRouter component. I still have to dig deeper to find what exactly is the issue with this bug.

[ke4]

The issues were the following:

• atlas-web-core submodule were pointing to a commit that was somewhere halfway in an already merged PR (regarding to the experiment table refactor)
• inside the package.json config file webpack was bumped to version 5.x.x and probably some dependency changes caused some other issues. Still needs to investigate this.

What I have done to enable the bulk release:

• created a hotfix branch: https://github.com/ebi-gene-expression-group/atlas-web-bulk/tree/hotfix/without_exp_design
  • in this branch I reset the branch to the commit before the exp design PR's merge: e03e938e21635f078cd8e889d11cf64480669e92 (git hash)
  • I cherry picked the following commits into that :
  • @upendrakumbham's all commits related the RNA-Seq API reference and publication changes
  • build endpoint changes
  • Added a new commit that fixes all the issues with our docker compose files without changing the webpack and package.json config

This branch of bulk was built on my local successfully with the following manual steps:

1. Manually build the UI: ./compile-front-end-packages.sh -iu
2. Manually build the backend: ./gradlew :app:war
3. Use this script to startup the web app on your local environment: ./build-and-deploy-webapp.sh -n

[ke4]

I also deployed the locally built WAR file into:

• our test server: Bulk test server
• our staging server: Bulk staging server

[ke4]

Next steps:

• [x] Make current develop branch for bulk compatible for our hotfix branch (https://github.com/ebi-gene-expression-group/atlas-web-bulk/tree/hotfix/without_exp_design) to merge
• [x] Create a new ticket for this: Investigate and fix the webpack/dependencies issue to be able to bump into version 5 of webpack -> going to be done in this ticket: Update bulk with the latest webpack and irs dependencies

[ke4]

A compatible develop branch has been created to be able to merge the hot-fix branch (without the experiment design refactor): https://github.com/ebi-gene-expression-group/atlas-web-bulk/tree/hotfix/without_exp_design. This is the new develop branch: adc31c62a20dfa004e7f3c5052808b1b318704e5

[ke4]

I have created another another ticket for the dependency update: Update bulk with the latest webpack and irs dependencies. I am going to close this ticket as the original problem has been solved.