v0.3-alpha

What's Changed

• Revert for next release by @satish-a0 in #12
• 395 setup docs 5 by @brian-cornally in #13
• [DI-77] Remove update study name for schema endpoint by @alicia-koh in #16
• [app-456] [Notebook] Notebook rename not working for Researcher account by @khairul-syazwan in #14
• 314 delete my user in both logto and usermgmt by @suwarnoong in #17
• 477 remove cdm download feature flag by @suwarnoong in #18
• Add pmc as codeowner by @satish-a0 in #20
• Update repo names by @satish-a0 in #26
• 430_dc-getaddrinfo-ENOTFOUND by @brian-cornally in #29
• 250 to support new line in env, escape newline for cert only by @suwarnoong in #31
• 184 upgrade bookmarks svc by @KangJingA in #15
• 465 fix terminology validity by @jerome-ng in #19
• [DP-484] Add cdm and pa config for duckdb by @brandantck in #33
• ADHOC_x-setup for alp-dbcli-v1.0.0.tgz by @brian-cornally in #28
• Remove limit on the number of search results by @csafreen in #30
• Fix pa config by @csafreen in #24
• Fix: Cdw svc to run fine if only HANA db configured by @csafreen in #34
• 430 add domain to dc container hostname again by @brian-cornally in #41
• [DI-466] Add error handling if database credentials env is missing by @alicia-koh in #38
• [DP-484] create duckdb cdm config 2 by @brandantck in #42
• 469 update logto refresh token seed, add offline_access scope by @suwarnoong in #47
• Concept recommended fix by @csafreen in #32
• [internal-259] healthchecks by @SantanM in #40
• [DI-78] Remove get vocab schema from cdm schema endpoint by @alicia-koh in #23
• Update genomics DM by @LSriragavan in #35
• [internal-40] fhir server by @SantanM in #25
• ADHOC add s3 profile to dc base cmd by @brian-cornally in #44
• ADHOC revert-dc-local-dataflow-gen-net by @brian-cornally in #51
• 397 oss docs update7 by @brian-cornally in #43
• 426 scripts update by @brian-cornally in #49
• 215 filter dataset visibility=hidden from non-researcher by @suwarnoong in #50
• 303 gha secrets to 1password by @brian-cornally in #55
• 134 register dashboard routes endpoint, fix typings by @suwarnoong in #53
• [Internal-124] analysis flow portal backend by @hengxian-jiang in #36
• add fhir-server to docker-compose-local.yml by @SantanM in #57
• Add route for translations by @jerome-ng in #54
• 255 enable tls in alp services by @KangJingA in #37
• Get user config by configId by @csafreen in #21
• Seed demo notebooks in starboard related to Kaplan Meier by @csafreen in #56
• cdw-svc: Get analytics db conn only when needed by @csafreen in #48
• [app-131] [Portal] Implement update vocab schema in db setup by @khairul-syazwan in #22
• Use database code instead of database name by @csafreen in #60
• [DP-432] Resolve duckdb and pg dialect difference by @brandantck in #58
• cdw-svc: Remove postgres connection and use env for duckdb by @csafreen in #52
• 542-update-concept-page-to-new-design by @KangJingA in #59
• BugFix: PA User Config by @csafreen in #65
• fix plugins json error by @KangJingA in #71
• Update error messages by @jerome-ng in #73
• use upper case for hana meili index by @jerome-ng in #66
• 540 concept sets user specific by @jerome-ng in #63
• [app-211] [PA] remove non-interactive mode by @khairul-syazwan in #70
• log errors in hooks by @SantanM in #67
• 536 update plugin env by @suwarnoong in #78
• 554 add health check in terminology svc by @KangJingA in #75
• Read tenant id from env instead of request body by @suwarnoong in #79
• [DP-452] Meilisearch index flow use client credential token by @brandantck in #72
• ADHOC - gen-tls - restart alp-caddy if name is not exactly container name ^alp-caddy by @brian-cornally in #81
• [DP-522[ Fix PA date filter by @brandantck in https://github.com//pull/77
• 538 use routing json instead of env variable for single services by @KangJingA in #62
• ADHOC gen-tls 2 by @brian-cornally in #83
• [DP-479] Analytics svc only connect to duckdb by @brandantck in #69
• ADHOC fix portal & dataflow-gen* services start by @brian-cornally in #87
• 89 1password ratelimit data by @brian-cornally in #90
• [DI-481] Transform remaining dataflows to plugins by @alicia-koh in #46
• [DI-543] Update metadataflow to include information about entity distribution in dataset by @alicia-koh in #74
• [DP-596] remove internal analytics svc call for cohort building by @brandantck in #88
• [ADHOC] Fix missing IDP__ISSUER_URL by @brandantck in #91
• 496 show as warning when DATABASE_CREDENTIALS is empty by @suwarnoong in #92
• 426 internal scripts3 by @brian-cornally in #94
• cdw-svc: Include mini duckdb files in image by @csafreen in #68
• Terminology-svc: Enable hybrid search by @csafreen in #86
• 426 internal scripts4 by @brian-cornally in #96
• [DI-546] Add plugin to run i2b2 datamodel creation by @alicia-koh in #80
• [DI-493] Move meilisearch index dataflow to plugin by @alicia-koh in #61
• 244 filter for concept sets in cohorts by @jerome-ng in #101
• 593 search dataset in portal by @suwarnoong in #102
• [DP-587] Add prefect flow for create duckdb database file by @brandantck in #99
• [DP-273] Add postgres support for datamart creation by @brandantck in #39
• Fix CD Dev/Test system by @satish-a0 in #107
• 556 use caddy for UI files by @KangJingA in #95
• Fix docker compose services startup by @satish-a0 in #110
• [DI-138] Prefect hooks for dataflow-gen UI flows by @alicia-koh in #84
• [DP-290] Unify dev_mode and sqlReturnOn by @brandantck in #108
• [DP-578] Fix DQD vocab input param by @brandantck in #112
• Assign priority to networks by @satish-a0 in #113
• 609 researcher dataset authorization in gateway by @KangJingA in #111
• [app-549] Add check datamodel updates button to dataset overview by @khairul-syazwan in #109
• Fix body parsing in proxy requests by @KangJingA in #118
• [DP-566] Add duckdb and meilisearch setup steps by @brandantck in #116
• [Internal-322] Delete flow deployment files from s3 when deleting prefect flow by @hengxian-jiang in #114
• [DP-613] Replace patient_id with person_id by @brandantck in #119
• PG: Reuse env variables by @csafreen in #105
• [DI-570] Rename reporting bi tests by @alicia-koh in #120
• [ADHOC] Fix python enum string comparison by @brandantck in #123
• Meilisearch: Calculate Embeddings by @csafreen in #97
• fix wrong date being sent in terminology fhir by @jerome-ng in #124
• [DP-260] Redact token in prefect input parameters by @brandantck in #126
• 598 add prefect graph: add missing apis required for graphs by @jerome-ng in #121
• alp-fhir ui and ui-server by @SantanM in #64
• 533 handle extra values by @jerome-ng in #106
• 599 auto redirect when 1 logto social connector is used by @suwarnoong in #130
• [internal-340] Add dicom server by @SantanM in #98
• [DP-508] Fix fetch version info flow for empty databasechangelog table by @brandantck in #129
• 640 show cohort quality by @KangJingA in #122
• fix alignment in docker-compose.yml by @SantanM in #137
• [DI-527-Test] Update docker-compose-local.yml by @alicia-koh in #134
• [Internal-642] Add schedule option to prefect flow run by @hengxian-jiang in #131
• Rename flow deployment S3 path by @hengxian-jiang in #127
• Add cleanup stage by @satish-a0 in #140
• [DP-564] Fix cdw-svc @ref to point to duckdb database file by @brandantck in #142
• CdwSvc: : Fix cdm config validation errors by @csafreen in #117
• [ADHOC] Fix DQD flow not loading version of DQD installed via dqd-plugin by @brandantck in #135
• [Internal-591] Connect portal backend and R code by @hengxian-jiang in #104
• [app-558] Adapt portal to use dataflow plugins by @khairul-syazwan in #115
• [Adhoc] Update entity count distribution dataType by @alicia-koh in #141
• [app-582] Use obs period start and date for cohort start and end date to populate in Add to cohort by @khairul-syazwan in #139
• [Internal-645] Seed default plugins by @hengxian-jiang in #133
• 251 add filters for flow runs by @suwarnoong in #145
• Optimize docker build & Push by @satish-a0 in #147
• 343 update connector name, description and (blank) logo by @suwarnoong in #148
• Dataflow: Update flow to create schema and load synpuf by @csafreen in #143
• CDW-Svc: Test case: Fix config and analytics connection error by @csafreen in #76
• [DI-159] Use dialect value from envConverter in dataflow-gen by @alicia-koh in #85
• 621 add concept hierachy in concept details by @KangJingA in #138
• [app-666] To not delete flow in Prefect when updating the deployment fails by @khairul-syazwan in #149
• 657 update d2e icon in login page by @suwarnoong in #150
• Internal 266 logto api seeding by @SantanM in #100
• [internal-170] strategus nodes by @SantanM in #125
• 🐛 Improve logic for create flow metadata by @khairul-syazwan in #152
• [DP-630] Remove db-svc files from alp-cr datanode-override by @brandantck in #132
• add npm install to logto init by @SantanM in #154
• Hide analysis tab at researcher portal by @hengxian-jiang in #156
• Hide patient summary config in Setup by @suwarnoong in #158
• [DP 669] Parameterize cohort dqd input by @brandantck in #155
• fix cohorts plugin path by @KangJingA in #157
• Use idp username for bookmarks by @KangJingA in #151
• [DP-691] Update duckdb to version 1.0.0 by @brandantck in #160
• 690 add dataset-search feature flag by @suwarnoong in #164
• [Internal-689] Create documentation for seeded plugins, add command to modify pat for internal user by @hengxian-jiang in #163
• hard code default plugin uuid by @hengxian-jiang in #159
• Update d-c for a working state on dev by @satish-a0 in #165
• Simplify logto api dns by @satish-a0 in #161
• 🐛 Check for data model updates returning 500 on test system by @khairul-syazwan in #167
• [DI-592-1] Rewrite db-mgmt-svc functionality in python by @alicia-koh in #136
• [internal-724] logto post init, update to correct ids as before by @SantanM in #168
• cdm and pa config for i2b2 by @csafreen in #153
• [DP-643] Fix concept set filter by @brandantck in #162
• [DP-185] Remove secrets, URLs and IPs by @brandantck in #169
• adjust order of plugin documentation, seed data-load plugin by @hengxian-jiang in #173
• fix typo in d-c-up.yml gh action by @SantanM in #174
• Fix test CD by @satish-a0 in #166
• Fix env gen by @satish-a0 in #175
• DF: Rename flow to create_cdm_schema by @csafreen in #171
• [DP-746] Remove duplicate gender concept id by @brandantck in #177
• [app-732] Data characterization fails by @khairul-syazwan in #180
• [internal-114] prefect results in s3 by @SantanM in #103
• Gateway: Parse body for terminology service by @csafreen in #181
• Fix cdm & pa duckdb config by @satish-a0 in #178
• [DI-592-Fix] Fix bugs by @alicia-koh in #170
• [Update docs] Fetch dataset metadata by @alicia-koh in #172
• [DP-753] Fix domain values service by @brandantck in #182
• Update concept.dto.ts by @KangJingA in #176
• [app-700] Concept sets to use logto username by @khairul-syazwan in #183
• [DP-761] Add limit for number of filtercards in PA by @brandantck in #187
• [DI-775] Add created date and updated date to version info flow by @alicia-koh in #191
• [DI-771] Remove db svc mgmt by @alicia-koh in #189
• 727 assign/revoke logto role based on azure group by @suwarnoong in #194
• [app-777] Terminology migration failing on the test system deployment by @khairul-syazwan in #192
• [app-718] Make text on landing page editable by @khairul-syazwan in #190
• [app-778] Display data model on dataset card attribute by @khairul-syazwan in #195
• [Adhoc]Add log messages for dataset operations by @alicia-koh in #188
• fix pull images in gh az deploy by @SantanM in #185
• [internal-758] fix init.sh and remove duplicates by @SantanM in #184
• 754 refresh token 3 mins before expiry by @suwarnoong in #198
• Update documentation for url and subdirectory job upload by @hengxian-jiang in #193
• 730 create logto user on first time entra login by @suwarnoong in #199
• Streamline Domain values fetch by @satish-a0 in #196
• 243 add kaplan meier chart by @jerome-ng in #200
• Fix PA - Add to cohort by @satish-a0 in #203
• [app-795] Create data mart failing by @khairul-syazwan in #204
• [Internal-675] fix strategus bug by @SantanM in #205
• Fix drop schema data characterization hook by @alicia-koh in #201
• remove 41120 port map by @SantanM in #202
• [DI-780] I2b2 metadata flow by @alicia-koh in #197
• Run data load plugin and update vocab documentation by @csafreen in #186
• 604 option to create fhir server staging in dataset creation by @KangJingA in #144
• Use logto API generated secrets by @satish-a0 in #208
• [app-800] Change dashboard url params to use name by @khairul-syazwan in #207
• [internal-785] remove async and use cdm schema name with 25 characters or less by @SantanM in #206
• Use volume for r libs by @jerome-ng in #210
• Update documentation on loading synpuf1k data by @csafreen in #209
• [Adhoc] datamart fixes by @alicia-koh in #211
• Fix minerva wait startup by @satish-a0 in #212
• [Adhoc] datamart fixes 2 by @alicia-koh in #213
• OSS fixes by @satish-a0 in #214

New Contributors

• @alicia-koh made their first contribution in #16
• @khairul-syazwan made their first contribution in #14
• @suwarnoong made their first contribution in #17
• @KangJingA made their first contribution in #15
• @jerome-ng made their first contribution in #19
• @SantanM made their first contribution in #40
• @hengxian-jiang made their first contribution in #36

Full Changelog: v0.2-alpha...v0.3-alpha