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Develop #126

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merged 51 commits into from
Sep 6, 2024
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c3e5d1b
wip
MatsJohansen87 Dec 19, 2023
ec50f0b
feat(negotiate): add base64 query to request
MatsJohansen87 Dec 21, 2023
7a12896
feat: WIP - project manager connection
torbrenner Jan 16, 2024
51b1ed7
fix: make requests work
torbrenner Feb 28, 2024
2a4fe75
feature: send CQL to project manager
torbrenner Mar 19, 2024
1b0f87d
fix: get site from siteCollectionMap
torbrenner Mar 19, 2024
eccb36a
fix: send collectionId to project manager
torbrenner Mar 19, 2024
3e1e5ab
fix: send return url only with params if user defined criteria
torbrenner Mar 19, 2024
8c48e00
docs: added test environment
torbrenner Mar 28, 2024
28a92ec
docs: added test environment
torbrenner Mar 28, 2024
a8a815b
feat(env): set ports
MatsJohansen87 Apr 3, 2024
1052bdc
Merge branch 'feat/project-manager-connection' of https://github.com/…
MatsJohansen87 Apr 9, 2024
959fdb1
feat(environment): add environment variables to the project
MatsJohansen87 Apr 11, 2024
80f1a60
feat(project manager): add jump to project manager
MatsJohansen87 Apr 22, 2024
8dfd37b
feat(WIP: project manager): add refresh token support
MatsJohansen87 Apr 24, 2024
d558973
Merge branch 'develop' into feat/project-manager-connection
MatsJohansen87 Apr 25, 2024
e32ecba
feat(authentication wip): get refresh token
MatsJohansen87 Apr 30, 2024
39a4258
feat(wip authentication): refactor authentication
MatsJohansen87 Jun 5, 2024
e1e88d7
feat(wip negotiate): get auth from project manager
MatsJohansen87 Jun 18, 2024
7bdcaa9
fix: regex of age, will filter everything between 10 - 120
patrickskowronekdkfz Jul 15, 2024
c933ec7
fix: allow age diagram 0-9
patrickskowronekdkfz Jul 16, 2024
450cc4a
Merge pull request #115 from samply/fix/diagnosis_age_regex
MatsJohansen87 Jul 16, 2024
558e445
Added Berlin for Data Evaluation
torbrenner Aug 1, 2024
f6e0857
Merge pull request #116 from samply/add-berlin
torbrenner Aug 1, 2024
9c3f010
feat: added dktk project based search
patrickskowronekdkfz Aug 12, 2024
f57dedb
feat(result_summary): add samples to summary
1000daysofcode Aug 12, 2024
cda1498
Merge pull request #118 from samply/feature/add-sample-result_summary
MatsJohansen87 Aug 12, 2024
76c4015
Merge pull request #117 from samply/project_based_search
patrickskowronekdkfz Aug 13, 2024
2022af2
fix: typo in url
patrickskowronekdkfz Aug 14, 2024
7691df6
Merge pull request #119 from samply/fix/typo_project_based_search
patrickskowronekdkfz Aug 14, 2024
3d77029
feat(wip negotiate): get correct tokens
MatsJohansen87 Aug 19, 2024
8fd8b3a
feat(auth): add proper token refreshing via forward proxy
MatsJohansen87 Aug 20, 2024
e8ce240
fix(SingleSelectComponent): remove redundant 'Add All'
1000daysofcode Aug 20, 2024
0ffce2b
refactor(AddAll): change text to German for CCP
1000daysofcode Aug 21, 2024
ea1df82
Merge pull request #120 from samply/fix/remove_redundant_add_all
MatsJohansen87 Aug 21, 2024
d2c0bd3
feat(options): move catalog response key map
MatsJohansen87 Aug 28, 2024
d8c7c6f
chore(logs): remove logs
MatsJohansen87 Aug 28, 2024
640fb99
feat(options): update prod and demo options to new schema
MatsJohansen87 Sep 2, 2024
2cc93c6
Merge pull request #121 from samply/feat/move-response-key-map-in-opt…
MatsJohansen87 Sep 2, 2024
f0a68d2
0.3.0
MatsJohansen87 Sep 2, 2024
60a67e0
Merge branch 'feat/project-manager-connection' into feature/merge-dev…
MatsJohansen87 Sep 2, 2024
5275d03
feat(negotiate): add schema for options and move from demo to dev
MatsJohansen87 Sep 2, 2024
353533e
feat(catalogues): add staging catalogue
MatsJohansen87 Sep 4, 2024
02a3502
feat(negotiate): add config to change negotiation service
MatsJohansen87 Sep 5, 2024
945fb4c
fix(auth): remove negotiator authentiation from frontend code
MatsJohansen87 Sep 5, 2024
a5c614b
feat(date picker): add date picker component
MatsJohansen87 Sep 6, 2024
bfceafa
refactor: adjust deployment configuration
torbrenner Sep 6, 2024
7fdcc1a
refactor: add project-manager.env to gitignore
torbrenner Sep 6, 2024
56de19f
Merge pull request #125 from samply/review-project-manager-connection…
MatsJohansen87 Sep 6, 2024
bd931f2
Merge pull request #123 from samply/feature/merge-develop-and-project…
MatsJohansen87 Sep 6, 2024
d9fd9c9
Merge pull request #124 from samply/feature/date-picker-component
MatsJohansen87 Sep 6, 2024
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2 changes: 2 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -29,3 +29,5 @@ TODO
docker-compose.override.yml
*.priv.pem
traefik.yaml

project-manager.env
22 changes: 22 additions & 0 deletions docker-compose.dev.yml
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,28 @@ services:
profiles:
- "beam"

project-manager:
image: samply/project-manager:develop
ports:
- 8097:8097
env_file:
- env/project-manager.env
volumes:
- "./templates:/templates"
- "./documents:/documents"
- "./public-documents:/public-documents"
profiles:
- "project-manager"

project-manager-db:
image: postgres:alpine
environment:
POSTGRES_DB: dev
POSTGRES_USER: dev
POSTGRES_PASSWORD: dev
profiles:
- "project-manager"

secrets:
proxy.pem:
file: /etc/lens/pki/${LOCAL_BEAM_ID}.priv.pem
Expand Down
4 changes: 4 additions & 0 deletions docker-compose.yml
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,8 @@ services:
- OAUTH2_PROXY_CLIENT_SECRET=${OAUTH_CLIENT_SECRET}
- OAUTH2_PROXY_COOKIE_SECRET=${AUTHENTICATION_SECRET}
- OAUTH2_PROXY_COOKIE_DOMAINS=.${GUI_HOST}
- OAUTH2_PROXY_COOKIE_REFRESH=4m
- OAUTH2_PROXY_COOKIE_EXPIRE=24h
- OAUTH2_PROXY_HTTP_ADDRESS=:4180
- OAUTH2_PROXY_REVERSE_PROXY=true
- OAUTH2_PROXY_WHITELIST_DOMAINS=.${GUI_HOST}
Expand Down Expand Up @@ -58,6 +60,7 @@ services:

spot:
image: samply/rustyspot:main
platform: linux/amd64
ports:
- "8055:8055"
environment:
Expand Down Expand Up @@ -93,6 +96,7 @@ services:

beam-proxy:
image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
platform: linux/amd64
environment:
BROKER_URL: https://${BROKER_HOST}
PROXY_ID: ${LOCAL_BEAM_ID}.${BROKER_HOST}
Expand Down
4 changes: 2 additions & 2 deletions package-lock.json

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2 changes: 1 addition & 1 deletion package.json
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"name": "@samply/lens",
"description": "A web component library for clinical data search and visualisation",
"version": "0.2.2",
"version": "0.3.0",
"type": "module",
"module": "dist/lens.js",
"main": "dist/lens.umd.js",
Expand Down
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