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Fixed BSSH mock event generator script #682

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May 29, 2024
Merged

Fixed BSSH mock event generator script #682

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36 changes: 17 additions & 19 deletions docs/pipeline/automation/bssh_sqs_event_replay.py
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Original file line number Diff line number Diff line change
@@ -1,26 +1,24 @@
import ast
import json
#import os
from datetime import datetime, timezone
from urllib.parse import urlparse, ParseResult

#import pandas as pd
import requests

from urllib.parse import urlparse, ParseResult
from aws_requests_auth.boto_utils import BotoAWSRequestsAuth

# Usage:
# export AWS_PROFILE=prod
# python data/make_event.py

runs = [
["230602_A00130_0258_BH55TMDSX7","r.EgZe1CMokEKBAOInwt7WvQ"],
["230608_A01052_0153_AH53JWDSX7","r.ZbhluFYOykKAkMl6lztRwg"],
["230629_A01052_0154_BH7WF5DSX7","r.BDX5uxzx7EGVAVNiUHhcaw"],
["230707_A00130_0264_BH7WJTDSX7","r.Doo1NoNLkUedSP9Pud3ukQ"],
["230714_A01052_0158_AH7WGHDSX7","r.4zqT3NKkxUulz6mMCP3RkA"]
["230602_A00130_0258_BH55TMDSX7", "r.EgZe1CMokEKBAOInwt7WvQ"],
["230608_A01052_0153_AH53JWDSX7", "r.ZbhluFYOykKAkMl6lztRwg"],
["230629_A01052_0154_BH7WF5DSX7", "r.BDX5uxzx7EGVAVNiUHhcaw"],
["230707_A00130_0264_BH7WJTDSX7", "r.Doo1NoNLkUedSP9Pud3ukQ"],
["230714_A01052_0158_AH7WGHDSX7", "r.4zqT3NKkxUulz6mMCP3RkA"]
]


# ---


Expand All @@ -29,17 +27,17 @@ def get_event_tpl():
"Records": [
{
"messageId": "b2b8b423-3dd8-4aea-bbf2-f13108eaeb20",
"receiptHandle": "AQEB+PZKPwzpzgx7scoO5gFmC4hNDc+bPnmpG8hBmZ+loFXqEA7cH2i4TvtNcALsdB8wvUD1/M6DIHU+auIBnAidbQxYZqSQUEGlI8aye1hekSFiXVWI0IBj5tdy24TfCL3Yfm+T40NAJbft/wtV2hFM8eTL3gkIPoGzq1hyD396w5Av1uNkkbVRHZKEylVrDeRZkvjAsD/xl45lwtU+cF8fE95y/Q0Od1VYFQANEOtSK9YQm63irr+8Ce8TrAUQFhQ2RGUuXRBSSuVvYIPVLJ+LfZB0XaeNKmz53cf+M8M8/apGyU2go3m8tIgCJFRUqmB8l3vE+mAwHk7vvE+hTR5Gbukt+lgSqKhIfydsparQ7Q6JZANbUJSrHO+zOj8kyPHT6TW88dA7E8ulHw+lRUAhbqNGrQLBVWl/7Umg+d3/r2jhJ97leLSVcWz4nlHxsj0X",
"receiptHandle": "AQEB+PZKPwzpzgx7sc...LSVcWz4nlHxsj0X", # pragma: allowlist secret
"body": None,
"attributes": {
"ApproximateReceiveCount": "2",
"SentTimestamp": "1637706092924",
"SenderId": "AROARFCPI2IGXEV3HSTQ5:5cb0370d-7d39-4bb1-8108-ba27121643c4",
"SenderId": "AROARFCPI2IGX3HSTQ5:5cb0370d-7d39-4bb1-8108-ba27121643c4", # pragma: allowlist secret
"ApproximateFirstReceiveTimestamp": "1637706092925"
},
"messageAttributes": {
"subscription-urn": {
"stringValue": "urn:ilmn:igp:us-east-1:YXdzLXVzLXBsYXRmb3JtOjEwMDAwNTM3OjBiYTU5YWUxLWZkYWUtNDNiYS1hM2I1LTRkMzY3YTQzYWJkNQ:subscription:sub.1025",
"stringValue": "urn:ilmn:igp:us-east-1:YX.NQ:subscription:sub.1025", # pragma: allowlist secret
"stringListValues": [],
"binaryListValues": [],
"dataType": "String"
Expand Down Expand Up @@ -81,8 +79,8 @@ def get_event_tpl():
"dataType": "String"
}
},
"md5OfMessageAttributes": "18e31cf8c7e82c76901a7d29b0bd589d",
"md5OfBody": "fc38bcadba65d115d4eed663219b9e0c",
"md5OfMessageAttributes": "18e31cf8c7e82c7901a7d29b0bd589d", # pragma: allowlist secret
"md5OfBody": "fc38bcadba65d115d4ed663219b9e0c", # pragma: allowlist secret
"eventSource": "aws:sqs",
"eventSourceARN": "arn:aws:sqs:ap-southeast-2:472057503814:data-portal-prod-iap-ens-event-queue",
"awsRegion": "ap-southeast-2"
Expand All @@ -93,7 +91,7 @@ def get_event_tpl():
return event_tpl


def get_bssh_event(instrument_run_id, run_id, status="PendingAnalysis"):
def get_bssh_event(instrument_run_id_, run_id_, status="PendingAnalysis"):
obj: ParseResult = urlparse("https://api.data.prod.umccr.org/iam/sequencerun")

auth = BotoAWSRequestsAuth(
Expand All @@ -106,8 +104,8 @@ def get_bssh_event(instrument_run_id, run_id, status="PendingAnalysis"):
url=obj.geturl(),
auth=auth,
params={
'instrument_run_id': instrument_run_id,
'run_id': run_id,
'instrument_run_id': instrument_run_id_,
'run_id': run_id_,
'status': status,
}
)
Expand All @@ -119,8 +117,8 @@ def get_bssh_event(instrument_run_id, run_id, status="PendingAnalysis"):

for run in runs:
instrument_run_id = run[0]
run_id=run[1]
event = get_bssh_event(instrument_run_id=instrument_run_id, run_id=run_id)
run_id = run[1]
event = get_bssh_event(instrument_run_id_=instrument_run_id, run_id_=run_id)

results = event['results']
assert len(results) > 0
Expand Down