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9689906
fix manual workflow [CE-314]
eapearson Oct 20, 2023
384a8a9
a little bit of cleanup [CE-314]
eapearson Oct 20, 2023
09afc23
a few updates to work better w/integration tests [CE-314]
eapearson Oct 20, 2023
8fce761
support a base path [CE-315]
eapearson Oct 24, 2023
0400fe4
minor dep update [CE-315]
eapearson Oct 25, 2023
eceeddf
local image, disable base path changes for local proxy [CE-315]
eapearson Oct 25, 2023
587b634
set target for to "_top" for the auto-form-post [URO-183]
eapearson Oct 25, 2023
06824c1
big big set of changes (wip) [CE-314]
eapearson Mar 22, 2024
fb41924
local server run decoupled from proxy [CE-360]
eapearson Mar 25, 2024
c335993
reformatted [CE-360]
eapearson Mar 25, 2024
2e259ee
improve connection status view [CE-360]
eapearson Mar 25, 2024
0cfc676
minor dep updates [CE-360]
eapearson Mar 25, 2024
a945ea9
wip changes to watch out for incorrect authentication message form Eu…
eapearson Mar 25, 2024
6d76717
console.log -> .error [CE-360]
eapearson Mar 25, 2024
a3cbd1c
reformat [CE-360]
eapearson Mar 25, 2024
e6e3a4b
reformat [CE-360]
eapearson Mar 25, 2024
e4bb19e
better filename [CE-360]
eapearson Mar 25, 2024
c9c2920
reformat [CE-360]
eapearson Mar 25, 2024
b9b09a4
add connection and build to about menu (for devs and admins) [CE-360]
eapearson Mar 25, 2024
ad7eea6
reformat [CE-360]
eapearson Mar 25, 2024
e67dfa4
remove proxy from main docker compose [CE-360]
eapearson Mar 25, 2024
9e1a277
remove unused files [CE-360]
eapearson Mar 25, 2024
16aa0cc
add standalone proxy task, refactor local kbase-ui, europa, narrative…
eapearson Mar 25, 2024
86ad3c0
remove console log [CE-360]
eapearson Mar 25, 2024
81e5e2c
add comment to generated env file [CE-360]
eapearson Mar 25, 2024
fba01d1
add docs [CE-360]
eapearson Mar 25, 2024
dbcffd6
argh, still getting extra authentication event [CE-360]
eapearson Mar 25, 2024
e3621f6
use direct domains rather than upstream [CE-360]
eapearson Mar 29, 2024
bf5b9c3
update dependencies [CE-360]
eapearson Mar 29, 2024
2f3f784
add setChannelId method [CE-360]
eapearson Mar 29, 2024
68bafa4
fix login navigation [CE-360]
eapearson Mar 29, 2024
6b2f52f
just reformat [CE-360]
eapearson Mar 29, 2024
2dee292
refactor from "ready" to "connect" design [CE-360]
eapearson Mar 29, 2024
85d6232
wip doc update [CE-360]
eapearson Mar 29, 2024
2bc8951
vsc settings [CE-360]
eapearson Mar 29, 2024
cb2b97c
clean up proxy docker compose [CE-360]
eapearson Mar 29, 2024
10ccba4
test should use ci not install [CE-360]
eapearson Mar 29, 2024
5aa92a2
test improvements [CE-360]
eapearson Mar 29, 2024
b0bf8a5
vscode settings [CE-360]
eapearson Mar 29, 2024
2479fd2
take care of unused params in test file [CE-360]
eapearson Mar 29, 2024
0b23069
minor npm dep updates [CE-360]
eapearson Apr 2, 2024
4ad6a88
navigate to narratives if signed in [CE-360]
eapearson Apr 3, 2024
2ca2e53
navigate to signedout page if no navigation provided [CE-360]
eapearson Apr 3, 2024
f4c8d5b
remove unsupported styles [CE-360]
eapearson Apr 3, 2024
4b15347
fix europa domain for navigation [CE-360]
eapearson Apr 3, 2024
be99437
remove unsupported styles [CE-360]
eapearson Apr 3, 2024
bea05f2
fix typo [CE-360]
eapearson Apr 3, 2024
5ce83d4
don't show linking form if all providers linked [CE-360]
eapearson Apr 3, 2024
23c7d81
remove commented out style [CE-360]
eapearson Apr 3, 2024
7d20335
rename kbase-ui.navigation to kbase-ui.navigated [CE-360]
eapearson Apr 4, 2024
d91bd73
add about kbase-ui back to about view [CE-360]
eapearson Apr 4, 2024
a780583
remove commented out code [CE-360]
eapearson Apr 4, 2024
f036844
minor npm dep updates [CE-360]
eapearson Apr 4, 2024
e63b36b
update to latest npm [CE-360]
eapearson Apr 4, 2024
d904b40
latest vsc settings [CE-360]
eapearson Apr 4, 2024
89efa97
add param to enable message spy [CE-360]
eapearson Apr 4, 2024
4033ff4
Clear timer on dismount [CE-360]
eapearson Apr 5, 2024
d8ab762
update markdownlint config [CE-360]
eapearson Apr 5, 2024
2caafde
add markdown lint as a dependency [CE-360]
eapearson Apr 5, 2024
a76b21f
add Europa integration doc (wip) [CE-360]
eapearson Apr 5, 2024
84e2633
reformatted... [CE-360]
eapearson Apr 5, 2024
b942012
add new remote extensions [CE-360]
eapearson Apr 5, 2024
0371251
improve prop-table styles, optional border [CE-360]
eapearson Apr 5, 2024
f460e41
update devcontainer config, add prettier plugin [CE-360]
eapearson Apr 5, 2024
453b059
improve header [CE-360]
eapearson Apr 5, 2024
c042bda
minor improvements [CE-360]
eapearson Apr 5, 2024
4a20a62
minor doc updates [CE-360]
eapearson Apr 5, 2024
7d4e530
minor format [CE-360]
eapearson Apr 5, 2024
596e896
minor dep update [CE-360]
eapearson Apr 5, 2024
fbbe88b
add ajv (back), and prettier plugin [CE-360]
eapearson Apr 5, 2024
e8866d7
replace eslint config with flat config [CE-360]
eapearson Apr 5, 2024
e8d5594
add eslint to devcontiner config [CE-360]
eapearson Apr 5, 2024
8d96c64
use unique channel per send/receive pair [CE-360]
eapearson Apr 5, 2024
df5a293
more documentation [CE-360]
eapearson Apr 5, 2024
a5e28bf
simplify devcontainer dockerfile [CE-360]
eapearson Apr 6, 2024
df8c8c2
cleanup after linting rule changes [CE-360]
eapearson Apr 7, 2024
7531cfc
big prettification [CE-360]
eapearson Apr 7, 2024
9cd77fc
remove commented-out code [CE-360]
eapearson Apr 10, 2024
7180b10
use replaceState not pushState [CE-360]
eapearson Apr 10, 2024
76effce
refactor to use send and receive channel ids, initially provided in u…
eapearson Apr 10, 2024
18c888e
remove unused parameter [CE-360]
eapearson Apr 10, 2024
5942369
update dependencies [CE-360]
eapearson Apr 10, 2024
f5f0fc4
npm dep update [CE-360]
eapearson Apr 10, 2024
4e13ea3
remove console debugging lines [CE-360]
eapearson Apr 10, 2024
541c60a
modest sign-in ux improvement [CE-360]
eapearson Apr 10, 2024
561380a
update to npm 10.5.2 [CE-260]
eapearson Apr 10, 2024
22f7587
update deps [CE-360]
eapearson Apr 11, 2024
888cf66
remove obsolete "version" property [CE-360]
eapearson Apr 11, 2024
b535e2d
refactor UI_DOMAIN -> KBASE_DOMAIN, remove KBASE_ENDPOINT [CE-360]
eapearson Apr 11, 2024
1d523e5
add jre to devcontainer for plant uml plugin support [CE-360]
eapearson Apr 11, 2024
bf9dc85
document updates [CE-360]
eapearson Apr 11, 2024
239fd07
ensure index page is not cached [CE-360]
eapearson Apr 12, 2024
c8384ab
keep initial search params [CE-360]
eapearson Apr 12, 2024
b0e667d
dep updates [CE-360]
eapearson Apr 12, 2024
f1e2f8d
use latest Alpine Linux [CE-360]
eapearson Apr 12, 2024
311858d
more docs for env vars [CE-360]
eapearson Apr 12, 2024
4683bb6
remove commented-out line [CE-360]
eapearson Apr 12, 2024
3c8f14f
add simple-git-hooks [CE-360]
eapearson Apr 12, 2024
c328f23
more documentation progress [CE-360]
eapearson Apr 12, 2024
1040b2e
remove commented out, remove unnecessary command, use IMAGE variable …
eapearson Apr 15, 2024
a4759ed
support generating env both with and without defaults [CE-360]
eapearson Apr 15, 2024
383a6f7
documentation update [CE-360]
eapearson Apr 15, 2024
4838bc6
minor dep updates [CE-360]
eapearson Apr 16, 2024
4a5736a
move variable into branch that uses it [CE-360]
eapearson Apr 16, 2024
d2bd3ce
fix local url [CE-360]
eapearson Apr 16, 2024
731f98d
prefix manual build with 'manual-' [CE-360]
eapearson Apr 17, 2024
f1d1717
remove similar_genomes feature switch [CE-360]
eapearson Apr 17, 2024
ce2ee4d
remove old ini configs [CE-360]
eapearson Apr 17, 2024
c5824d2
remove similar_genomes from doc [CE-360]
eapearson Apr 17, 2024
608ae62
add a - after pr [CE-360]
eapearson Apr 17, 2024
c89fe3f
remvoe similar_genomes doc references [CE-360]
eapearson Apr 17, 2024
e627cdf
improve deployment quickstart [CE-360]
eapearson Apr 17, 2024
6dd68e2
remove feature switches (none used now), a few plugin url fixes [CE-360]
eapearson Apr 17, 2024
68848b3
simplify config further [CE-360]
eapearson Apr 18, 2024
efd012c
simplify further and align documentation [CE-360]
eapearson Apr 18, 2024
460314e
improve generated comments in configs [CE-360]
eapearson Apr 18, 2024
85c39e2
dataview fix tabs corrupted by minification [CE-360]
eapearson Apr 19, 2024
e71c49b
fix "modules" nginx rule [CE-360]
eapearson Apr 19, 2024
51d707a
improve plugin caching support [CE-360]
eapearson Apr 19, 2024
b03152d
switch build scripts to python from deno [CE-360]
eapearson Apr 21, 2024
46ce02b
minor dep updates [CE-360]
eapearson Apr 21, 2024
1aac35d
minor dep update [CE-360]
eapearson Apr 24, 2024
7d3d730
just a reformat [CE-360]
eapearson Apr 24, 2024
37b758f
update all outdated actions [CE-360]
eapearson Apr 24, 2024
012b0ed
improve git and build info scripts [CE-360]
eapearson Apr 24, 2024
0f77e85
hmm, git-info still not working [CE-360]
eapearson Apr 24, 2024
a85c9c3
restore manifest to plugins [CE-360]
eapearson Apr 25, 2024
342e3f1
make directory optional [CE-360]
eapearson Apr 25, 2024
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8 changes: 4 additions & 4 deletions .devcontainer/Dockerfile-devcontainer
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
FROM node:18
FROM node:20

RUN apt-get update && \
apt-get install -y npm python3 git make bash && \
npm install --location=global npm@10.2.0
RUN apt-get update && apt-get install -y default-jre

RUN npm install --location=global npm@10.5.2
10 changes: 0 additions & 10 deletions .devcontainer/custom.env

This file was deleted.

1 change: 0 additions & 1 deletion .devcontainer/devcontainer.env

This file was deleted.

19 changes: 13 additions & 6 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
Expand Up @@ -14,12 +14,19 @@
// The optional 'workspaceFolder' property is the path VS Code should open by default when
// connected. This is typically a file mount in .devcontainer/docker-compose.yml
"workspaceFolder": "/workspace",
// Set *default* container specific settings.json values on container create.
"settings": {},
// Add the IDs of extensions you want installed when the container is created.
"extensions": [
"DavidAnson.vscode-markdownlint"
],
"customizations": {
"vscode": {
"extensions": [
"DavidAnson.vscode-markdownlint",
"jebbs.plantuml",
"srmeyers.git-prefix",
"esbenp.prettier-vscode",
"dbaeumer.vscode-eslint",
"darkriszty.markdown-table-prettify"
],
"settings": {}
}
},
// "containerEnv": {
// "DEPLOY_ENV": "narrative-dev"
// }
Expand Down
167 changes: 62 additions & 105 deletions .devcontainer/docker-compose.yml
Original file line number Diff line number Diff line change
@@ -1,107 +1,64 @@
version: '3.6'
name: kbase-dev
networks:
kbase-dev:
name: kbase-dev
kbase-dev:
name: kbase-dev
services:
kbase-ui:
build:
context: .
dockerfile: Dockerfile-devcontainer
# just use dev for the image tag so we can easily clean
# up afterwards.

image: kbase/kbase-ui:dev

container_name: kbase-ui
dns: 8.8.8.8
volumes:
# Update this to wherever you want VS Code to mount the folder of your project
- ..:/workspace:cached
# Uncomment the next line to use Docker from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker-compose for details.
# - /var/run/docker.sock:/var/run/docker.sock

# Uncomment the next four lines if you will use a ptrace-based debugger like C++, Go, and Rust.
# cap_add:
# - SYS_PTRACE
# security_opt:
# - seccomp:unconfined
# volumes:
# - ${APP_DIR}:/kb/deployment/app
# Map local source into expected location within container
# - "${PWD}/react-app:/kb/deployment/app"
# # Map local configuration directory into expected location within container
# - "${PWD}/dev/gitlab-config:/kb/deployment/config"
# - ${PWD}/deployment/scripts:/kb/deployment/scripts
# # Map locally installed plugins into the expected location within container
# - ${PWD}/build/dist/deploy/plugins:/kb/deployment/app/public/deploy/plugins
# - ${SCRIPTS_DIR}:/kb/deployment/scripts

# just use dev for the image tag so we can easily clean
# up afterwards.
# image: kbase/kbase-ui:dev
networks:
- kbase-dev
environment:
# - PORT=80
- DEPLOY_ENV=${DEPLOY_ENV:-ci}
# - BASE_PATH=
# Required for a devcontainer -- keeps the container running.
# Don't worry, our main interaction with the container is through the
# VSC terminal, which for a devcontainer opens a shell within the
# container.
command: /bin/sh -c "while sleep 1000; do :; done"
kbase-ui-deploy:
image: nginx:1.25.1-alpine
container_name: kbase-ui-deploy
volumes:
- ../build:/usr/share/nginx/html
# - /Users/erikpearson/Work/KBase/2023/CE-255/kbase-ui-plugin-react-profile-view/dist/plugin:/usr/share/nginx/html/plugins/react-profile-view
# - /Users/erikpearson/Work/KBase/2023/UFI-60/kbase-ui-plugin-auth2-client/dist/plugin:/usr/share/nginx/html/plugins/auth2-client
# - /Users/erikpearson/Work/KBase/2023/helpdesk/UFI-48/kbase-ui-plugin-dataview/dist/plugin:/usr/share/nginx/html/plugins/dataview
# - /Users/erikpearson/Work/KBase/2023/helpdesk/UFI-48/kbase-ui-plugin-dataview/dist/plugin:/usr/share/nginx/html/plugins/dataview
# - /Users/erikpearson/Work/KBase/2022/fix-app-icons/kbase-ui-plugin-organizations/react-app:/usr/share/nginx/html/plugins/organizations
# - /Users/erikpearson/Work/KBase/2022/UIP-7/kbase-ui-plugin-auth2-client/dist/plugin:/usr/share/nginx/html/plugins/auth2-client
# - /Users/erikpearson/Work/KBase/2022/UIP-7/kbase-ui-plugin-auth2-client/dist/plugin:/usr/share/nginx/html/plugins/auth2-client
networks:
- kbase-dev
ports:
- "8081:80"
environment:
# um, does nothing?
# for now, set the proxy port to 80 to match the default
# nginx config.
# TODO: use the templating built into the nginx image.
# or switch to a custom image using dockerize.
- NGINX_HOST=kbase-ui-deploy.ci.kbase.us
- NGINX_PORT=5000
kbase-ui-proxy:
build:
context: ../tools/proxy
# there is only one proxy image, for local development, so just call it :dev
image: kbase/kbase-ui-proxy:dev
depends_on:
- kbase-ui
- kbase-ui-deploy
networks:
- kbase-dev
container_name: kbase-ui-proxy
ports:
- '80:80'
- '443:443'
dns:
# TODO: sort this out!
- 8.8.8.8
- 9.9.9.9
- 1.1.1.1
- 208.67.222.222
environment:
- BASE_PATH=/


# note that this is really a docker env file and is relative to the docker-compose file
# TODO: I think we may need to use an entrypoint which selects the deploy environment
# config (env) file based on the DEPLOY_ENV.

env_file:
- ../tools/proxy/conf/ci.env
- custom.env
kbase-ui:
build:
context: .
dockerfile: Dockerfile-devcontainer
image: kbase/kbase-ui:dev
container_name: kbase-ui
dns: 8.8.8.8
volumes:
# Update this to wherever you want VS Code to mount the folder of your project
- ..:/workspace:cached
networks:
- kbase-dev
env_file:
- runtime.env
# Required for a devcontainer -- keeps the container running.
# Don't worry, our main interaction with the container is through the
# VSC terminal, which for a devcontainer opens a shell within the
# container.
command: /bin/sh -c "while sleep 1000; do :; done"
kbase-ui-deploy:
image: nginx:1.25.4-alpine3.18
container_name: kbase-ui-deploy
volumes:
- ../build:/usr/share/nginx/html
# Example of volume mounts for local plugins
# - /Users/erikpearson/Work/KBase/2023/europa-integration/kbase-ui-plugin-auth2-client/dist/plugin:/usr/share/nginx/html/plugins/auth2-client
# - /Users/erikpearson/Work/KBase/2023/europa-integration/kbase-ui-plugin-catalog/dist/plugin:/usr/share/nginx/html/plugins/catalog
# - /Users/erikpearson/Work/KBase/2023/europa-integration/kbase-ui-plugin-dataview/dist/plugin:/usr/share/nginx/html/plugins/dataview
# - /Users/erikpearson/Work/KBase/2023/europa-integration/kbase-ui-plugin-typeview/dist/plugin:/usr/share/nginx/html/plugins/typeview
# - /Users/erikpearson/Work/KBase/2023/europa-integration/kbase-ui-plugin-data-search/dist/plugin:/usr/share/nginx/html/plugins/data-search
# - /Users/erikpearson/Work/KBase/2023/europa-integration/kbase-ui-plugin-jgi-search/dist/plugin:/usr/share/nginx/html/plugins/jgi-search
# - /Users/erikpearson/Work/KBase/2023/europa-integration/kbase-ui-plugin-organizations/dist/plugin:/usr/share/nginx/html/plugins/organizations
# - /Users/erikpearson/Work/KBase/2023/europa-integration/kbase-ui-plugin-samples/dist/plugin:/usr/share/nginx/html/plugins/samples
networks:
- kbase-dev
ports:
- '8081:80'
kbase-ui-proxy:
build:
context: ../tools/proxy
# there is only one proxy image, for local development, so just call it :dev
image: kbase/kbase-ui-proxy:dev
depends_on:
- kbase-ui
- kbase-ui-deploy
networks:
- kbase-dev
container_name: kbase-ui-proxy
ports:
- '80:80'
- '443:443'
dns:
# TODO: sort this out!
- 8.8.8.8
- 9.9.9.9
- 1.1.1.1
- 208.67.222.222
env_file:
- proxy.env
5 changes: 0 additions & 5 deletions .eslintignore

This file was deleted.

48 changes: 0 additions & 48 deletions .eslintrc.yml

This file was deleted.

20 changes: 10 additions & 10 deletions .github/workflows/manual.yml
Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
---
name: Manual
on:
workflow_dispatch:
workflow_dispatch:
jobs:
test:
uses: ./.github/workflows/reusable_test-crats.yml
build-push:
needs: test
uses: ./.github/workflows/reusable_build-push.yml
with:
name: '${{ github.event.repository.name }}'
tags: '${{ github.ref_name }}'
secrets: inherit
test:
uses: ./.github/workflows/reusable_test.yml
build-push:
needs: test
uses: ./.github/workflows/reusable_build-push.yml
with:
name: '${{ github.event.repository.name }}'
tags: 'manual-${{ github.ref_name }}'
secrets: inherit
32 changes: 16 additions & 16 deletions .github/workflows/pull-request-to-main-activity.yml
Original file line number Diff line number Diff line change
@@ -1,20 +1,20 @@
---
name: PR to main3 opened
on:
pull_request:
branches:
- main3
types:
- opened
- reopened
- synchronize
pull_request:
branches:
- main3
types:
- opened
- reopened
- synchronize
jobs:
test:
uses: ./.github/workflows/reusable_test.yml
build-push:
needs: test
uses: ./.github/workflows/reusable_build-push.yml
with:
name: '${{ github.event.repository.name }}'
tags: pr${{ github.event.number }}
secrets: inherit
test:
uses: ./.github/workflows/reusable_test.yml
build-push:
needs: test
uses: ./.github/workflows/reusable_build-push.yml
with:
name: '${{ github.event.repository.name }}'
tags: pr-${{ github.event.number }}
secrets: inherit
10 changes: 5 additions & 5 deletions .github/workflows/reusable_build-push.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out GitHub Repo
uses: actions/checkout@v3
uses: actions/checkout@v4

- name: Get current date
id: date
Expand All @@ -28,10 +28,10 @@ jobs:
run: ./Taskfile build-kbase-ui

- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3

- name: Login to GHCR
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
registry: ghcr.io
# note that the calling workflow must set `secrets: inherit`
Expand All @@ -40,7 +40,7 @@ jobs:

- name: Create github action tags from image tags
id: tags
uses: actions/github-script@v6
uses: actions/github-script@v7
with:
result-encoding: string
script: |
Expand All @@ -52,7 +52,7 @@ jobs:
}).join(',');

- name: Build and push
uses: docker/build-push-action@v3
uses: docker/build-push-action@v5
with:
context: .
file: ./Dockerfile
Expand Down
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