@orcabus/platform-cdk-constructs 1.2.5 → 1.2.7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.jsii +183 -6
- package/api-gateway/api-gateway.js +1 -1
- package/deployment-stack-pipeline/artifact-bucket.js +1 -1
- package/deployment-stack-pipeline/pipeline.js +1 -1
- package/dynamodb/index.js +2 -2
- package/ecs/index.js +1 -1
- package/eventbridge-rules/sfn-slack-notification.js +1 -1
- package/lambda/index.js +1 -1
- package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/__init__.py +8 -0
- package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq/query_helpers.py +20 -8
- package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/filemanager/file_helpers.py +6 -2
- package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/metadata/__init__.py +2 -1
- package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/workflow/workflow_run_helpers.py +1 -1
- package/monitored-queue/index.js +1 -1
- package/named-lambda-role/index.js +1 -1
- package/package.json +16 -16
- package/provider-function/index.js +1 -1
- package/shared-config/networking.js +2 -2
- package/shared-config/slack.js +1 -1
package/.jsii
CHANGED
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},
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"dependencies": {
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"@aws-cdk/aws-lambda-python-alpha": "^2.
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"aws-cdk-lib": "^2.
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"constructs": "^10.
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"@aws-cdk/aws-lambda-python-alpha": "^2.244.0-alpha.0",
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"aws-cdk-lib": "^2.244.0",
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"constructs": "^10.6.0"
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"dependencyClosure": {
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"@aws-cdk/asset-awscli-v1": {
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"aws-cdk-lib.aws_bedrockmantle": {
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"targets": {
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"dotnet": {
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"namespace": "Amazon.CDK.AWS.BedrockMantle"
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"java": {
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"package": "software.amazon.awscdk.services.bedrockmantle"
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"aws-cdk-lib.aws_billingconductor": {
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"aws-cdk-lib.aws_computeoptimizer": {
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"aws-cdk-lib.aws_directconnect": {
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class OrcaBusApiGateway extends constructs_1.Construct {
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static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "1.2.7" };
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exports.CROSS_DEPLOYMENT_ARTIFACT_KMS_ALIAS = "orcabus-cross-deployment-codepipeline-artifact";
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exports.CROSS_DEPLOYMENT_ARTIFACT_KMS_ARN_SSM_PARAMETER_NAME = "/orcabus/deployment-stack-pipeline/artifact-bucket/kms-key-arn";
|
|
15
15
|
class CrossDeploymentArtifactBucket extends constructs_1.Construct {
|
|
16
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "1.2.
|
|
16
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "1.2.7" };
|
|
17
17
|
/**
|
|
18
18
|
* The S3 bucket used to store artifacts for cross-deployment pipelines.
|
|
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19
|
*/
|
|
@@ -45,7 +45,7 @@ exports.DEFAULT_INSTALL_COMMANDS = [
|
|
|
45
45
|
* before using this construct.
|
|
46
46
|
*/
|
|
47
47
|
class DeploymentStackPipeline extends constructs_1.Construct {
|
|
48
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "1.2.
|
|
48
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "1.2.7" };
|
|
49
49
|
/**
|
|
50
50
|
* The code pipeline construct that is created.
|
|
51
51
|
*/
|
package/dynamodb/index.js
CHANGED
|
@@ -40,7 +40,7 @@ const dynamodb = __importStar(require("aws-cdk-lib/aws-dynamodb"));
|
|
|
40
40
|
const aws_cdk_lib_1 = require("aws-cdk-lib");
|
|
41
41
|
const config_1 = require("./config");
|
|
42
42
|
class DynamoDbPartitionedConstruct extends constructs_1.Construct {
|
|
43
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "1.2.
|
|
43
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "1.2.7" };
|
|
44
44
|
table;
|
|
45
45
|
constructor(scope, id, props) {
|
|
46
46
|
super(scope, id);
|
|
@@ -75,7 +75,7 @@ class DynamoDbPartitionedConstruct extends constructs_1.Construct {
|
|
|
75
75
|
}
|
|
76
76
|
exports.DynamoDbPartitionedConstruct = DynamoDbPartitionedConstruct;
|
|
77
77
|
class DynamoDbNonPartitionedConstruct extends constructs_1.Construct {
|
|
78
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "1.2.
|
|
78
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "1.2.7" };
|
|
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|
table;
|
|
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|
constructor(scope, id, props) {
|
|
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|
super(scope, id);
|
package/ecs/index.js
CHANGED
|
@@ -55,7 +55,7 @@ exports.LAMBDA_ARCHITECTURE_MAP = {
|
|
|
55
55
|
['ARM64']: lambda.Architecture.ARM_64
|
|
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56
|
};
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|
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57
|
class EcsFargateTaskConstruct extends constructs_1.Construct {
|
|
58
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "1.2.
|
|
58
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "1.2.7" };
|
|
59
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|
cluster;
|
|
60
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|
taskDefinition;
|
|
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61
|
taskExecutionRole;
|
|
@@ -17,7 +17,7 @@ var SfnEventStatus;
|
|
|
17
17
|
SfnEventStatus["ABORTED"] = "ABORTED";
|
|
18
18
|
})(SfnEventStatus || (exports.SfnEventStatus = SfnEventStatus = {}));
|
|
19
19
|
class SfnSlackNotification extends constructs_1.Construct {
|
|
20
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.eventbridgeRule.SfnSlackNotification", version: "1.2.
|
|
20
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.eventbridgeRule.SfnSlackNotification", version: "1.2.7" };
|
|
21
21
|
rule;
|
|
22
22
|
constructor(scope, id, props) {
|
|
23
23
|
super(scope, id);
|
package/lambda/index.js
CHANGED
|
@@ -57,7 +57,7 @@ function getPythonUvDockerImage() {
|
|
|
57
57
|
return aws_cdk_lib_1.DockerImage.fromBuild(path_1.default.join(__dirname, 'build_python'));
|
|
58
58
|
}
|
|
59
59
|
class PythonUvFunction extends aws_lambda_python_alpha_1.PythonFunction {
|
|
60
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "1.2.
|
|
60
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "1.2.7" };
|
|
61
61
|
// Class constructs, to be used for caching the layers
|
|
62
62
|
// This means that if there are multiple lambdas throughout the stack
|
|
63
63
|
// They will all use the same layer
|
|
@@ -27,6 +27,7 @@ from typing import List, Unpack
|
|
|
27
27
|
from fastapi.encoders import jsonable_encoder
|
|
28
28
|
|
|
29
29
|
# Local imports
|
|
30
|
+
from .. import DEFAULT_BATCH_SIZE
|
|
30
31
|
from . import get_fastq_request_response_results, get_fastq_request
|
|
31
32
|
from .globals import FASTQ_ENDPOINT, FASTQ_SET_ENDPOINT, RGID_ENDPOINT
|
|
32
33
|
from .models import (
|
|
@@ -166,7 +167,7 @@ def get_fastqs_in_library_list(
|
|
|
166
167
|
return get_fastqs_batched(
|
|
167
168
|
item_key="library",
|
|
168
169
|
item_list=library_id_list,
|
|
169
|
-
batch_size=
|
|
170
|
+
batch_size=DEFAULT_BATCH_SIZE
|
|
170
171
|
)
|
|
171
172
|
|
|
172
173
|
|
|
@@ -177,12 +178,23 @@ def get_fastqs_in_libraries_and_instrument_run_id(library_id_list, instrument_ru
|
|
|
177
178
|
:param instrument_run_id:
|
|
178
179
|
:return:
|
|
179
180
|
"""
|
|
180
|
-
return
|
|
181
|
-
|
|
182
|
-
|
|
183
|
-
|
|
184
|
-
|
|
185
|
-
|
|
181
|
+
# If we only have a 'few' libraries, we can return all in one
|
|
182
|
+
# Otherwise we need to batch
|
|
183
|
+
if len(library_id_list) < DEFAULT_BATCH_SIZE:
|
|
184
|
+
return get_fastqs(
|
|
185
|
+
instrumentRunId=instrument_run_id,
|
|
186
|
+
**{
|
|
187
|
+
"library[]": library_id_list,
|
|
188
|
+
}
|
|
189
|
+
)
|
|
190
|
+
# Uses batching
|
|
191
|
+
# Then filter over instrument run id
|
|
192
|
+
return list(filter(
|
|
193
|
+
lambda fastq_obj_iter_: fastq_obj_iter_['instrumentRunId'] == instrument_run_id,
|
|
194
|
+
get_fastqs_in_library_list(
|
|
195
|
+
library_id_list=library_id_list
|
|
196
|
+
)
|
|
197
|
+
))
|
|
186
198
|
|
|
187
199
|
|
|
188
200
|
def get_fastqs_in_sample(sample_id: str):
|
|
@@ -203,7 +215,7 @@ def get_fastqs_in_sample_list(sample_id_list: List[str]):
|
|
|
203
215
|
return get_fastqs_batched(
|
|
204
216
|
item_key="sample",
|
|
205
217
|
item_list=sample_id_list,
|
|
206
|
-
batch_size=
|
|
218
|
+
batch_size=DEFAULT_BATCH_SIZE
|
|
207
219
|
)
|
|
208
220
|
|
|
209
221
|
|
|
@@ -11,6 +11,7 @@ import boto3
|
|
|
11
11
|
from datetime import datetime, timedelta, timezone
|
|
12
12
|
from urllib.parse import urlparse, unquote, urlunparse
|
|
13
13
|
from itertools import batched
|
|
14
|
+
import re
|
|
14
15
|
|
|
15
16
|
# Local imports
|
|
16
17
|
from .errors import S3FileNotFoundError, S3DuplicateFileCopyError
|
|
@@ -129,10 +130,13 @@ def list_files_from_portal_run_id(
|
|
|
129
130
|
if not remove_log_files:
|
|
130
131
|
return all_files_list
|
|
131
132
|
|
|
133
|
+
# Filter out logs and cache files
|
|
134
|
+
logs_re_obj = re.compile(rf"logs/[\w|-]+/{portal_run_id}/")
|
|
135
|
+
cache_re_obj = re.compile(rf"cache/[\w|-]+/{portal_run_id}/")
|
|
132
136
|
return list(filter(
|
|
133
137
|
lambda file_iter_: not (
|
|
134
|
-
|
|
135
|
-
|
|
138
|
+
logs_re_obj.match(file_iter_['key']) or
|
|
139
|
+
cache_re_obj.match(file_iter_['key'])
|
|
136
140
|
),
|
|
137
141
|
all_files_list
|
|
138
142
|
))
|
|
@@ -12,6 +12,7 @@ from ..utils.requests_helpers import (
|
|
|
12
12
|
)
|
|
13
13
|
|
|
14
14
|
# Local imports
|
|
15
|
+
from .. import DEFAULT_BATCH_SIZE
|
|
15
16
|
from .globals import METADATA_SUBDOMAIN_NAME
|
|
16
17
|
|
|
17
18
|
|
|
@@ -74,7 +75,7 @@ def get_item_from_item_id_list_batched(
|
|
|
74
75
|
item_identifier: str,
|
|
75
76
|
endpoint: str,
|
|
76
77
|
accept_missing: bool = False,
|
|
77
|
-
batch_size: int =
|
|
78
|
+
batch_size: int = DEFAULT_BATCH_SIZE
|
|
78
79
|
) -> List[Dict[str, Any]]:
|
|
79
80
|
"""
|
|
80
81
|
Get items from a list of item ids
|
package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/workflow/workflow_run_helpers.py
CHANGED
|
@@ -126,7 +126,7 @@ def add_comment_to_workflow_run(
|
|
|
126
126
|
post_workflow_request(
|
|
127
127
|
f"{WORKFLOW_RUN_ENDPOINT}/{workflow_run_orcabus_id}/comment",
|
|
128
128
|
{
|
|
129
|
-
"
|
|
129
|
+
"text": comment,
|
|
130
130
|
"createdBy": author,
|
|
131
131
|
# workflowRun parameter required but not actually used
|
|
132
132
|
"workflowRun": workflow_run_orcabus_id
|
package/monitored-queue/index.js
CHANGED
|
@@ -13,7 +13,7 @@ const aws_cloudwatch_actions_1 = require("aws-cdk-lib/aws-cloudwatch-actions");
|
|
|
13
13
|
* SNS topic.
|
|
14
14
|
*/
|
|
15
15
|
class MonitoredQueue extends constructs_1.Construct {
|
|
16
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "1.2.
|
|
16
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "1.2.7" };
|
|
17
17
|
queue;
|
|
18
18
|
deadLetterQueue;
|
|
19
19
|
alarm;
|
|
@@ -7,7 +7,7 @@ const aws_iam_1 = require("aws-cdk-lib/aws-iam");
|
|
|
7
7
|
* A construct which represents a named role that a Lambda function can assume.
|
|
8
8
|
*/
|
|
9
9
|
class NamedLambdaRole extends aws_iam_1.Role {
|
|
10
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "1.2.
|
|
10
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "1.2.7" };
|
|
11
11
|
constructor(scope, id, props) {
|
|
12
12
|
super(scope, id, {
|
|
13
13
|
assumedBy: new aws_iam_1.ServicePrincipal("lambda.amazonaws.com"),
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@orcabus/platform-cdk-constructs",
|
|
3
|
-
"version": "1.2.
|
|
3
|
+
"version": "1.2.7",
|
|
4
4
|
"description": "CDK Package for OrcaBus infrastructure.",
|
|
5
5
|
"main": "index.ts",
|
|
6
6
|
"types": "index.d.ts",
|
|
@@ -23,25 +23,25 @@
|
|
|
23
23
|
"organization": true
|
|
24
24
|
},
|
|
25
25
|
"devDependencies": {
|
|
26
|
-
"@aws-cdk/aws-lambda-python-alpha": "2.
|
|
27
|
-
"@types/jest": "^
|
|
28
|
-
"@types/node": "^
|
|
29
|
-
"aws-cdk": "^2.
|
|
30
|
-
"aws-cdk-lib": "
|
|
26
|
+
"@aws-cdk/aws-lambda-python-alpha": "2.244.0-alpha.0",
|
|
27
|
+
"@types/jest": "^30.0.0",
|
|
28
|
+
"@types/node": "^25.5.0",
|
|
29
|
+
"aws-cdk": "^2.1113.0",
|
|
30
|
+
"aws-cdk-lib": "2.244.0",
|
|
31
31
|
"cdk-nag": "^2.37.55",
|
|
32
|
-
"constructs": "10.
|
|
33
|
-
"jest": "^
|
|
34
|
-
"jsii": "^5.9.
|
|
35
|
-
"jsii-pacmak": "^1.
|
|
36
|
-
"publib": "^0.2.
|
|
32
|
+
"constructs": "10.6.0",
|
|
33
|
+
"jest": "^30.3.0",
|
|
34
|
+
"jsii": "^5.9.34",
|
|
35
|
+
"jsii-pacmak": "^1.127.0",
|
|
36
|
+
"publib": "^0.2.1038",
|
|
37
37
|
"ts-jest": "^29.4.6",
|
|
38
|
-
"typedoc": "^0.28.
|
|
39
|
-
"typedoc-plugin-markdown": "^4.
|
|
38
|
+
"typedoc": "^0.28.18",
|
|
39
|
+
"typedoc-plugin-markdown": "^4.11.0"
|
|
40
40
|
},
|
|
41
41
|
"peerDependencies": {
|
|
42
|
-
"@aws-cdk/aws-lambda-python-alpha": "^2.
|
|
43
|
-
"aws-cdk-lib": "^2.
|
|
44
|
-
"constructs": "^10.
|
|
42
|
+
"@aws-cdk/aws-lambda-python-alpha": "^2.244.0-alpha.0",
|
|
43
|
+
"aws-cdk-lib": "^2.244.0",
|
|
44
|
+
"constructs": "^10.6.0"
|
|
45
45
|
},
|
|
46
46
|
"stability": "experimental",
|
|
47
47
|
"jsii": {
|
|
@@ -15,7 +15,7 @@ const aws_cdk_lib_1 = require("aws-cdk-lib");
|
|
|
15
15
|
* to the provider framework.
|
|
16
16
|
*/
|
|
17
17
|
class ProviderFunction extends constructs_1.Construct {
|
|
18
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "1.2.
|
|
18
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "1.2.7" };
|
|
19
19
|
_function;
|
|
20
20
|
_response;
|
|
21
21
|
constructor(scope, id, props) {
|
|
@@ -23,7 +23,7 @@ exports.VPC_LOOKUP_PROPS = {
|
|
|
23
23
|
* Helper for looking up the shared OrcaBus VPC.
|
|
24
24
|
*/
|
|
25
25
|
class OrcaBusVpc {
|
|
26
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "1.2.
|
|
26
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "1.2.7" };
|
|
27
27
|
/**
|
|
28
28
|
* The shared VPC that is used by OrcaBus.
|
|
29
29
|
* @param scope
|
|
@@ -42,7 +42,7 @@ exports.SHARED_SECURITY_GROUP_NAME = "OrcaBusSharedComputeSecurityGroup";
|
|
|
42
42
|
* Helper for looking up the shared compute security group by name.
|
|
43
43
|
*/
|
|
44
44
|
class OrcaBusSharedComputeSecurityGroup {
|
|
45
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "1.2.
|
|
45
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "1.2.7" };
|
|
46
46
|
/**
|
|
47
47
|
* The shared security group that is used by compute resources to access the database.
|
|
48
48
|
* @param scope
|
package/shared-config/slack.js
CHANGED
|
@@ -11,7 +11,7 @@ exports.SLACK_ALERTS_SNS_TOPIC = "AwsChatBotTopic-alerts";
|
|
|
11
11
|
* A helper class to construct the arn for the slack SNS topic.
|
|
12
12
|
*/
|
|
13
13
|
class SlackAlerts {
|
|
14
|
-
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "1.2.
|
|
14
|
+
static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "1.2.7" };
|
|
15
15
|
/**
|
|
16
16
|
* Format the ARN for the slack alerts SNS topic for the current stack.
|
|
17
17
|
* @param stack
|