Document procedure to run Data Browser locally (#7643) #7698

dsotirho-ucsc · 2026-01-15T18:33:50Z

Linked issues: #7643

Checklist

Author

¹ when the issue title describes a problem, the corresponding PR
title is Fix: followed by the issue title

Author (partiality)

Added p tag to titles of partial commits
This PR is labeled partial _{or completely resolves all linked issues}
This PR partially resolves each of the linked issues _{or does not have the partial label}

Author (reindex)

Added r tag to commit title _{or the changes introduced by this PR will not require reindexing of any deployment}
This PR is labeled reindex:dev _{or the changes introduced by it will not require reindexing of dev}
This PR is labeled reindex:anvildev _{or the changes introduced by it will not require reindexing of anvildev}
This PR is labeled reindex:anvilprod _{or the changes introduced by it will not require reindexing of anvilprod}
This PR is labeled reindex:prod _{or the changes introduced by it will not require reindexing of prod}
This PR is labeled reindex:partial and its description documents the specific reindexing procedure for dev, anvildev, anvilprod and prod _{or requires a full reindex or carries none of the labels reindex:dev, reindex:anvildev, reindex:anvilprod and reindex:prod}

Author (API changes)

This PR and its linked issues are labeled API _{or this PR does not modify a REST API}
Added a (A) tag to commit title for backwards (in)compatible changes _{or this PR does not modify a REST API}
Updated REST API version number in app.py _{or this PR does not modify a REST API}

Author (upgrading deployments)

Ran make docker_images.json and committed the resulting changes _{or this PR does not modify azul_docker_images, or any other variables referenced in the definition of that variable}
Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading deployments}
Added u tag to commit title _{or this PR does not require upgrading deployments}
This PR is labeled upgrade _{or does not require upgrading deployments}
This PR is labeled deploy:shared _{or does not modify docker_images.json, and does not require deploying the shared component for any other reason}
This PR is labeled deploy:gitlab _{or does not require deploying the gitlab component}
This PR is labeled deploy:runner _{or does not require deploying the runner image}

Author (hotfixes)

Added F tag to main commit title _{or this PR does not include permanent fix for a temporary hotfix}
Reverted the temporary hotfixes for any linked issues _{or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues linked to this PR}

Author (before every review)

Rebased PR branch on develop, squashed fixups from prior reviews
Ran make requirements_update _{or this PR does not modify Dockerfile, environment, requirements*.txt, common.mk, Makefile or environment.boot}
Added R tag to commit title _{or this PR does not modify requirements*.txt}
This PR is labeled reqs _{or does not modify requirements*.txt}
make integration_test passes in personal deployment _{or this PR does not modify functionality that could affect the IT outcome}
PR is awaiting requested review from a peer
Status of PR is Review requested
PR is assigned to only the peer and the author

Peer reviewer (after approval)

Note that after requesting changes, the PR must be assigned to only the author.

Actually approved the PR
PR is not a draft
PR is awaiting requested review from system administrator
Status of PR is Review requested
PR is assigned to only the system administrator and the author

System administrator (after approval)

Actually approved the PR
Labeled linked issues as demo or no demo
Commented on linked issues about demo expectations _{or all linked issues are labeled no demo}
Decided if PR can be labeled no sandbox
A comment to this PR details the completed security design review
PR title is appropriate as title of merge commit
N reviews label is accurate
Status of PR is Approved
PR is assigned to only the operator and the author

Operator

Checked reindex:… labels and r commit title tag
Checked that demo expectations are clear _{or all linked issues are labeled no demo}
Squashed PR branch and rebased onto develop
Sanity-checked history
Pushed PR branch to GitHub

Operator (deploy `.shared` and `.gitlab` components)

Ran _select dev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select dev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply _{or this PR is not labeled deploy:gitlab}
Ran _select anvildev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select anvildev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply _{or this PR is not labeled deploy:gitlab}
Checked the items in the next section _{or this PR is labeled deploy:gitlab}
PR is assigned to only the system administrator and the author _{or this PR is not labeled deploy:gitlab}

System administrator (post-deploy of `.gitlab` component)

Background migrations for dev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
Background migrations for anvildev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
PR is assigned to only the operator and the author

Operator (deploy runner image)

Ran _select dev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}
Ran _select anvildev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}

Operator (sandbox build)

Operator (merge the branch)

All status checks passed and the PR is mergeable
The title of the merge commit starts with the title of this PR
Added PR # reference to merge commit title
Collected commit title tags in merge commit title _{but only included p if the PR is also labeled partial}
Pushed merge commit to GitHub
Status of PR is Merged lower
Status of blocked issues is Triage _{or no issues are blocked on the linked issues}

Operator (main build)

Operator (reindex)

Operator (mirroring)

Started mirroring in dev _{or this PR does not require mirroring dev}
Started mirroring in anvildev _{or this PR does not require mirroring anvildev}
Checked for, triaged and possibly requeued messages in mirror fail queue in dev _{or this PR does not require mirroring dev}
Checked for, triaged and possibly requeued messages in mirror fail queue in anvildev _{or this PR does not require mirroring anvildev}
Emptied mirror fail queue in dev _{or this PR does not require mirroring dev}
Emptied mirror fail queue in anvildev _{or this PR does not require mirroring anvildev}

Operator

Propagated the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels to the next promotion PRs _{or this PR carries none of these labels}
Propagated any specific instructions related to the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels, from the description of this PR to that of the next promotion PRs _{or this PR carries none of these labels}
PR is assigned to no one

Shorthand for review comments

L line is too long
W line wrapping is wrong
Q bad quotes
F other formatting problem

coveralls · 2026-01-15T18:50:28Z

coverage: 85.108%. remained the same
when pulling 2501a3b on issues/dsotirho-ucsc/7643-data-browser-documentation
into b6ab56b on develop.

codecov · 2026-01-15T18:57:17Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.88%. Comparing base (b6ab56b) to head (2501a3b).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #7698   +/-   ##
========================================
  Coverage    84.88%   84.88%           
========================================
  Files          157      157           
  Lines        22943    22943           
========================================
  Hits         19476    19476           
  Misses        3467     3467

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

dsotirho-ucsc · 2026-01-15T19:11:44Z

7698_IT_2026-01-16.txt

achave11-ucsc

For the section regarding prerequisites, maybe you can provide a quick overview but reference the DB README-prerequisites to 1) prevent duplication and 2) reduce the likeliness of having stale information on the DB.

achave11-ucsc · 2026-01-15T23:37:18Z

README.md



-# 4. Running indexer or service locally
+# 4. Running local instances


Suggested change

# 4. Running local instances

# 4. Run system component(s) locally

Perhaps? Or something like it. For us 'instance' may involve a machine (EC2, GitLab) and maybe even AWS accounts which isn't the intent of this section.

achave11-ucsc · 2026-01-15T23:51:50Z

README.md


+## 4.2 Running the Data Browser locally
+
+In order to run the Data Browser locally, you will need:


Suggested change

In order to run the Data Browser locally, you will need:

The following prerequisites must be satisfied:

achave11-ucsc · 2026-01-15T23:54:13Z

README.md

+
+In order to run the Data Browser locally, you will need:
+
+- Node.js, on macOS this can be installed with `brew install node`


From the DB prerequisites

Node.js 22.12.0 is required to run the app

It seems a specific version of Node.js is required.

achave11-ucsc · 2026-01-15T23:54:46Z

README.md

+In order to run the Data Browser locally, you will need:
+
+- Node.js, on macOS this can be installed with `brew install node`
+- A clone of the Data Browser repo: https://github.com/DataBiosphere/data-browser


This is also part of the DB prereqs…

achave11-ucsc · 2026-01-15T23:58:07Z

README.md

+Follow the steps in the [Data Browser's README] to install the client-side
+dependencies, and launch the development server.


This is the last step in the prereqs.

dsotirho-ucsc · 2026-01-16T19:33:35Z

7698_IT_2026-01-16.txt

achave11-ucsc

LGTM ✅

dsotirho-ucsc linked an issue Jan 15, 2026 that may be closed by this pull request

Document procedure to run Data Browser locally #7643

Open

dsotirho-ucsc self-assigned this Jan 15, 2026

Document procedure to run Data Browser locally (#7643)

706fd57

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7643-data-browser-documentation branch from d02523d to 706fd57 Compare January 15, 2026 18:42

dsotirho-ucsc requested a review from achave11-ucsc January 15, 2026 19:13

dsotirho-ucsc assigned achave11-ucsc Jan 15, 2026

achave11-ucsc requested changes Jan 16, 2026

View reviewed changes

achave11-ucsc removed their assignment Jan 16, 2026

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7643-data-browser-documentation branch from 3cd0943 to 1ff94d3 Compare January 16, 2026 18:51

fixup! Document procedure to run Data Browser locally (#7643)

2501a3b

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7643-data-browser-documentation branch from 1ff94d3 to 2501a3b Compare January 16, 2026 19:06

dsotirho-ucsc assigned achave11-ucsc Jan 16, 2026

dsotirho-ucsc requested a review from achave11-ucsc January 16, 2026 19:33

achave11-ucsc approved these changes Jan 16, 2026

View reviewed changes

achave11-ucsc marked this pull request as ready for review January 16, 2026 20:13

achave11-ucsc requested a review from hannes-ucsc as a code owner January 16, 2026 20:13

achave11-ucsc assigned hannes-ucsc and unassigned achave11-ucsc Jan 16, 2026

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Document procedure to run Data Browser locally (#7643) #7698

Document procedure to run Data Browser locally (#7643) #7698

Uh oh!

dsotirho-ucsc commented Jan 15, 2026 •

edited by achave11-ucsc

Loading

Uh oh!

coveralls commented Jan 15, 2026 •

edited

Loading

Uh oh!

codecov bot commented Jan 15, 2026 •

edited

Loading

Uh oh!

dsotirho-ucsc commented Jan 15, 2026

Uh oh!

achave11-ucsc left a comment

Uh oh!

achave11-ucsc Jan 15, 2026

Uh oh!

achave11-ucsc Jan 15, 2026

Uh oh!

achave11-ucsc Jan 15, 2026

Uh oh!

achave11-ucsc Jan 15, 2026

Uh oh!

achave11-ucsc Jan 15, 2026

Uh oh!

dsotirho-ucsc commented Jan 16, 2026

Uh oh!

achave11-ucsc left a comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants



		# 4. Running indexer or service locally
		# 4. Running local instances

	# 4. Running local instances
	# 4. Run system component(s) locally


		## 4.2 Running the Data Browser locally

		In order to run the Data Browser locally, you will need:

	In order to run the Data Browser locally, you will need:
	The following prerequisites must be satisfied:


		In order to run the Data Browser locally, you will need:

		- Node.js, on macOS this can be installed with `brew install node`

		Follow the steps in the [Data Browser's README] to install the client-side
		dependencies, and launch the development server.

Document procedure to run Data Browser locally (#7643) #7698

Are you sure you want to change the base?

Document procedure to run Data Browser locally (#7643) #7698

Uh oh!

Conversation

dsotirho-ucsc commented Jan 15, 2026 • edited by achave11-ucsc Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Checklist

Author

Author (partiality)

Author (reindex)

Author (API changes)

Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

Peer reviewer (after approval)

System administrator (after approval)

Operator

Operator (deploy .shared and .gitlab components)

System administrator (post-deploy of .gitlab component)

Operator (deploy runner image)

Operator (sandbox build)

Operator (merge the branch)

Operator (main build)

Operator (reindex)

Operator (mirroring)

Operator

Shorthand for review comments

Uh oh!

coveralls commented Jan 15, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

codecov bot commented Jan 15, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

dsotirho-ucsc commented Jan 15, 2026

Uh oh!

achave11-ucsc left a comment

Choose a reason for hiding this comment

Uh oh!

achave11-ucsc Jan 15, 2026

Choose a reason for hiding this comment

Uh oh!

achave11-ucsc Jan 15, 2026

Choose a reason for hiding this comment

Uh oh!

achave11-ucsc Jan 15, 2026

Choose a reason for hiding this comment

Uh oh!

achave11-ucsc Jan 15, 2026

Choose a reason for hiding this comment

Uh oh!

achave11-ucsc Jan 15, 2026

Choose a reason for hiding this comment

Uh oh!

dsotirho-ucsc commented Jan 16, 2026

Uh oh!

achave11-ucsc left a comment

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

dsotirho-ucsc commented Jan 15, 2026 •

edited by achave11-ucsc

Loading

Operator (deploy `.shared` and `.gitlab` components)

System administrator (post-deploy of `.gitlab` component)

coveralls commented Jan 15, 2026 •

edited

Loading

codecov bot commented Jan 15, 2026 •

edited

Loading