fix(filemanager): docs and OpenAPI definitions

lib/workload/stateless/stacks/filemanager/deploy/constructs/functions/function.ts

@@ -116,7 +116,7 @@ export class Function extends Construct {
  },
  },
  memorySize: 128,
- timeout: Duration.seconds(300),
+ timeout: Duration.seconds(28),
  environment: {
  // No password here, using RDS IAM to generate credentials.
  PGHOST: props.host,

lib/workload/stateless/stacks/filemanager/docs/API_GUIDE.md

@@ -25,7 +25,7 @@ The API is designed to have a standard set of REST routes which can be used to q
 For example, to query a single record, use the `s3_object_id` in the path, which returns the JSON record:
 
 ```sh
-curl -H "Authorization: Bearer $TOKEN" "https://file.dev.umccr.org/api/v1/s3_objects/01912c56-c458-797f-9d3f-b803e093b7cf" | jq
+curl -H "Authorization: Bearer $TOKEN" "https://file.dev.umccr.org/api/v1/s3_objects/0190465f-68fa-76e4-9c36-12bdf1a1571d" | jq
 ```
 
 Multiple records can be reached using the same route, which returns an array of JSON records:
@@ -90,14 +90,14 @@ and `_` to match one character. These queries get converted to postgres `like` q
 on a key prefix:
 
 ```sh
-curl --get -H "Authorization: Bearer $TOKEN" --data-urlencode "key=temp_data%" \
-"https://file.dev.umccr.org/api/v1/s3_objects/01912c56-c458-797f-9d3f-b803e093b7cf" | jq
+curl --get -H "Authorization: Bearer $TOKEN" --data-urlencode "key=temp\_data%" \
+"https://file.dev.umccr.org/api/v1/s3_objects" | jq
 ```
 
 Case-insensitive wildcard matching, which gets converted to a postgres `ilike` statement, is supported by using `case_sensitive`:
 
 ```sh
-curl --get -H "Authorization: Bearer $TOKEN" --data-urlencode "key=temp_data%" \
+curl --get -H "Authorization: Bearer $TOKEN" --data-urlencode "key=temp\_data%" \
 "https://file.dev.umccr.org/api/v1/s3_objects?case_sensitive=false" | jq
 ```
 
@@ -118,18 +118,17 @@ Attributes are update using [JSON patch][json-patch].
 For example, update attributes on a single record:
 
 ```sh
-curl --patch -H "Authorization: Bearer $TOKEN" -H "Content-Type: application/json" \
- --data "{ "attributes": [ { "op": "add", "path": "/portal_run_id", "value": "202405212aecb782" } ] }" \
-"https://file.dev.umccr.org/api/v1/s3_objects/01912c56-c458-797f-9d3f-b803e093b7cf" | jq
+curl -X PATCH -H "Authorization: Bearer $TOKEN" -H "Content-Type: application/json" \
+--data '{ "attributes": [ { "op": "add", "path": "/portal_run_id", "value": "202405212aecb782" } ] }' \
+"https://file.dev.umccr.org/api/v1/s3_objects/0190465f-68fa-76e4-9c36-12bdf1a1571d" | jq
 ```
 
 Or, update attributes for multiple records with the same key prefix:
 
 ```sh
-curl --patch -H "Authorization: Bearer $TOKEN" -H "Content-Type: application/json" \
- --data "{ "attributes": [ { "op": "add", "path": "/attribute_id", "value": "attribute_id" } ] }" \
- --data-urlencode "key=temp_data%" \
-"https://file.dev.umccr.org/api/v1/s3_objects" | jq
+curl -X PATCH -H "Authorization: Bearer $TOKEN" -H "Content-Type: application/json" \
+--data '{ "attributes": [ { "op": "add", "path": "/portal_run_id", "value": "202405212aecb782" } ] }' \
+"https://file.dev.umccr.org/api/v1/s3_objects?key=%25202405212aecb782%25" | jq
 ```
 
 ## Count objects

lib/workload/stateless/stacks/filemanager/docs/ATTRIBUTE_LINKING.md

@@ -1,3 +1,7 @@
+> [!IMPORTANT] 
+> This document is a discussion on potential designs for filemanager attribute linking. The current implementation
+> isn't exactly like this, although it will probably contain components of the design here.
+
 # FileManager Attribute Linking
 
 The filemanager needs to be able to store data from other microservices on `s3_object` records in order to perform some

lib/workload/stateless/stacks/filemanager/filemanager/src/queries/list.rs

@@ -943,10 +943,7 @@ pub(crate) mod tests {
  false,
  )
  .await;
- assert_eq!(
- result,
- &s3_entries[0..2]
- );
+ assert_eq!(result, &s3_entries[0..2]);
  }
 
  #[sqlx::test(migrator = "MIGRATOR")]

lib/workload/stateless/stacks/filemanager/filemanager/src/queries/update.rs

@@ -4,15 +4,14 @@
 use json_patch::patch;
 use sea_orm::prelude::{Expr, Json};
 use sea_orm::sea_query::{
- Alias, Asterisk, CommonTableExpression, PostgresQueryBuilder, Query, SelectStatement,
- SimpleExpr, WithClause, WithQuery,
+ Alias, Asterisk, CommonTableExpression, Query, SelectStatement, SimpleExpr, WithClause,
+ WithQuery,
 };
 use sea_orm::{
  ColumnTrait, ConnectionTrait, EntityTrait, FromQueryResult, Iterable, ModelTrait, QueryFilter,
  QueryTrait, StatementBuilder, Value,
 };
 use serde_json::json;
-use tracing::trace;
 use uuid::Uuid;
 
 use crate::database::entities::{object, s3_object};
@@ -293,7 +292,6 @@ where
 
  fn trace_query(&self, message: &str) {
  self.select_to_update.trace_query(message);
- trace!("{message}: {}", self.update.to_string(PostgresQueryBuilder));
  }
 }
 

lib/workload/stateless/stacks/filemanager/filemanager/src/routes/filter/mod.rs

@@ -16,19 +16,19 @@ use utoipa::{IntoParams, ToSchema};
 #[serde(default)]
 #[into_params(parameter_in = Query)]
 pub struct S3ObjectsFilter {
- #[param(required = false)]
- /// Query by event type.
+ #[param(required = false, value_type = Wildcard)]
+ /// Query by event type. Supports wildcards.
  pub(crate) event_type: Option<WildcardEither<EventType>>,
  #[param(required = false)]
- /// Query by bucket.
+ /// Query by bucket. Supports wildcards.
  pub(crate) bucket: Option<Wildcard>,
  #[param(required = false)]
- /// Query by key.
+ /// Query by key. Supports wildcards.
  pub(crate) key: Option<Wildcard>,
  #[param(required = false)]
- /// Query by version_id.
+ /// Query by version_id. Supports wildcards.
  pub(crate) version_id: Option<Wildcard>,
- #[param(required = false)]
+ #[param(required = false, value_type = Wildcard)]
  /// Query by date. Supports wildcards.
  pub(crate) date: Option<WildcardEither<DateTimeWithTimeZone>>,
  #[param(required = false)]
@@ -37,14 +37,14 @@ pub struct S3ObjectsFilter {
  #[param(required = false)]
  /// Query by the sha256 checksum.
  pub(crate) sha256: Option<String>,
- #[param(required = false)]
- /// Query by the last modified date.
+ #[param(required = false, value_type = Wildcard)]
+ /// Query by the last modified date. Supports wildcards.
  pub(crate) last_modified_date: Option<WildcardEither<DateTimeWithTimeZone>>,
  #[param(required = false)]
  /// Query by the e_tag.
  pub(crate) e_tag: Option<String>,
- #[param(required = false)]
- /// Query by the storage class.
+ #[param(required = false, value_type = Wildcard)]
+ /// Query by the storage class. Supports wildcards.
  pub(crate) storage_class: Option<WildcardEither<StorageClass>>,
  #[param(required = false)]
  /// Query by the object delete marker.
@@ -54,7 +54,7 @@ pub struct S3ObjectsFilter {
  /// fields, e.g. `attributes[attribute_id]=...`. This only deserializes
  /// into string fields, and does not support other JSON types. E.g.
  /// `attributes[attribute_id]=1` converts to `{ "attribute_id" = "1" }`
- /// rather than `{ "attribute_id" = 1 }`.
+ /// rather than `{ "attribute_id" = 1 }`. Supports wildcards.
  pub(crate) attributes: Option<Json>,
 }
 
@@ -70,6 +70,6 @@ pub struct ObjectsFilter {
  /// fields, e.g. `attributes[attribute_id]=...`. This only deserializes
  /// into string fields, and does not support other JSON types. E.g.
  /// `attributes[attribute_id]=1` converts to `{ "attribute_id" = "1" }`
- /// rather than `{ "attribute_id" = 1 }`.
+ /// rather than `{ "attribute_id" = 1 }`. Supports wildcards.
  pub(crate) attributes: Option<Json>,
 }

lib/workload/stateless/stacks/filemanager/filemanager/src/routes/filter/wildcard.rs

@@ -6,7 +6,7 @@ use utoipa::ToSchema;
 
 /// An enum which deserializes into a concrete type or a wildcard. This is used for better
 /// type support when non-string filter parameters such as `StorageClass` or `EventType`.
-#[derive(Serialize, Deserialize, Debug, ToSchema, Eq, PartialEq)]
+#[derive(Serialize, Deserialize, Debug, Eq, PartialEq)]
 #[serde(untagged)]
 pub enum WildcardEither<T> {
  Or(T),
@@ -37,7 +37,7 @@ impl<T> WildcardEither<T> {
 }
 
 /// A wildcard type represents a filter to match arbitrary characters. Use '%' for multiple characters
-/// and '_' for a single character. Use '\' to escape these characters. Wildcards are converted to
+/// and '_' for a single character. Use '\\' to escape these characters. Wildcards are converted to
 /// postgres `like` or `ilike` queries.
 #[derive(Serialize, Deserialize, Debug, Default, ToSchema, Eq, PartialEq)]
 #[serde(default)]