Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added Swagger UI and Dependencies Bumped #83

Merged
merged 10 commits into from
Jan 19, 2024
Merged

Added Swagger UI and Dependencies Bumped #83

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
a374e52
dep update
williamputraintan Jan 8, 2024
8bd5534
init
williamputraintan Jan 10, 2024
6436d1c
ts-to-zod provider
williamputraintan Jan 11, 2024
a613faa
paginated query
williamputraintan Jan 12, 2024
d5fe475
update
williamputraintan Jan 18, 2024
d07c68f
Add Query Swagger endpoint
williamputraintan Jan 19, 2024
ece855a
build(deps): bump @fastify/reply-from from 9.4.0 to 9.6.0 in /lib/wor…
dependabot[bot] Jan 19, 2024
8556b1e
build(deps-dev): bump @babel/traverse from 7.23.0 to 7.23.4 in /lib/w…
dependabot[bot] Jan 19, 2024
59fa51a
dep up
williamputraintan Jan 19, 2024
7037aee
Merge branch 'mm-openapi' of https://github.com/umccr/orcabus into mm…
williamputraintan Jan 19, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions lib/workload/stateless/metadata_manager/src/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,7 @@ dist

dbschema/edgeql-js
dbschema/queries.*
dbschema/queriesZodSchema.ts
dbschema/interfaces.ts

asset/
14 changes: 10 additions & 4 deletions lib/workload/stateless/metadata_manager/src/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,11 @@ stop:
# Build the app for deployment

edgetypes:
@npx generate queries --target ts --file --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret
@npx generate edgeql-js --target ts --output-dir dbschema/edgeql-js --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret
@npx generate interfaces --file dbschema/interfaces.ts --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret
@yarn run -B generate queries --target ts --file --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret
@yarn run -B generate edgeql-js --target ts --output-dir dbschema/edgeql-js --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret
@yarn run -B generate interfaces --file dbschema/interfaces.ts --dsn edgedb://orcabus_admin:admin@$(EDGEDB_HOST):5656 --tls-security insecure # pragma: allowlist secret
@yarn run ts-to-zod dbschema/queries.ts dbschema/queriesZodSchema.ts


build: edgetypes
@rm -rf asset
Expand All @@ -32,7 +34,6 @@ build: edgetypes
@zip -r asset/dependency.zip nodejs
@rm -rf nodejs


# Testing
test:
@yarn test
Expand All @@ -44,6 +45,11 @@ start-scenario-1: edgetypes
@yarn run insert-scenario-1
@yarn start

# Start in watch mode
watch: edgetypes
@yarn run insert-scenario-1
@yarn watch

# Inserting scenarios
insert-scenario-2:
@yarn run insert-scenario-2
Expand Down
4 changes: 3 additions & 1 deletion lib/workload/stateless/metadata_manager/src/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -114,8 +114,10 @@ http://localhost:8080/subject
http://localhost:8080/library
http://localhost:8080/specimen

# Swagger Endpoint
http://localhost:8080/documentation

<!-- GraphQL -->
# GraphQL Endpoint
http://localhost:8080/graphql/explore (UI)
http://localhost:8080/graphql (Only for graphql POST method)
```
Expand Down
2 changes: 1 addition & 1 deletion ...kload/stateless/metadata_manager/src/dbschema/queries/audit/updateSystemAuditEvent.edgeql
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,5 @@ filter .id = <uuid>$auditDbId
set
{
actionOutcome := <ActionOutcome>$actionOutcome,
details := <json>$details,
details := <optional json>$details,
}
49 changes: 47 additions & 2 deletions ...eless/metadata_manager/src/dbschema/queries/metadata/library/selectAllLibraryQuery.edgeql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,48 @@
select metadata::Library{
*

with

# Pagination parameter
offset_ := <optional int16>$offset ?? 0,
limit_ := <optional int16>$limit ?? 10,

libraries := (
select metadata::Library {
*
}
filter (
.orcaBusId ?= <optional str>$orcaBusId ?? .orcaBusId
AND
.internalId ?= <optional str>$internalId ?? .internalId
AND
.externalId ?= <optional str>$externalId ?? .externalId
AND
.phenotype ?= <optional str>$phenotype ?? .phenotype
AND
.assay ?= <optional str>$assay ?? .assay
AND
.coverage ?= <optional str>$coverage ?? .coverage
AND
.quality ?= <optional str>$quality ?? .quality
AND
.type ?= <optional str>$type ?? .type
AND
.workflow = <optional metadata::WorkflowTypes>$workflow ?? .workflow
)
)
select {

results := (
select libraries {
*
}
offset offset_
limit limit_
),
pagination := {
total := count(libraries),
`offset` := offset_,
`limit` := limit_
}

}

38 changes: 36 additions & 2 deletions ...ess/metadata_manager/src/dbschema/queries/metadata/specimen/selectAllSpecimenQuery.edgeql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,37 @@
select metadata::Specimen{
*
with

# Pagination parameter
offset_ := <optional int16>$offset ?? 0,
limit_ := <optional int16>$limit ?? 10,

libraries := (
select metadata::Specimen {
*
}
filter (
.orcaBusId ?= <optional str>$orcaBusId ?? .orcaBusId
AND
.internalId ?= <optional str>$internalId ?? .internalId
AND
.externalId ?= <optional str>$externalId ?? .externalId
AND
.source ?= <optional str>$source ?? .source
)
)
select {

results := (
select libraries {
*
}
offset offset_
limit limit_
),
pagination := {
total := count(libraries),
`offset` := offset_,
`limit` := limit_
}

}

35 changes: 33 additions & 2 deletions ...eless/metadata_manager/src/dbschema/queries/metadata/subject/selectAllSubjectQuery.edgeql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,34 @@
select metadata::Subject{
*
with

# Pagination parameter
offset_ := <optional int16>$offset ?? 0,
limit_ := <optional int16>$limit ?? 10,

libraries := (
select metadata::Subject {
*
}
filter (
.orcaBusId ?= <optional str>$orcaBusId ?? .orcaBusId
AND
.internalId ?= <optional str>$internalId ?? .internalId
AND
.externalId ?= <optional str>$externalId ?? .externalId
)
)
select {

results := (
select libraries {
*
}
offset offset_
limit limit_
),
pagination := {
total := count(libraries),
`offset` := offset_,
`limit` := limit_
}
}

Loading