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Posted to github@beam.apache.org by GitBox <gi...@apache.org> on 2021/03/15 15:53:50 UTC
[GitHub] [beam] macksclark opened a new pull request #14233: Adding LRO counters to FhirIO
macksclark opened a new pull request #14233:
URL: https://github.com/apache/beam/pull/14233
Adding counters for the success/failure counters that are output in the operation metadata after an LRO completes. We increment the counters after the operation is complete since we already wait on them.
Tested that this change works properly for Import but I don't have tests for the other LROs.
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[GitHub] [beam] pabloem commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
pabloem commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-800602523
thanks ! seems like you need to fix the formatting.
Regarding the counter checks: I don't think they're necessary. Feel free to add them if you'd like.
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[GitHub] [beam] macksclark commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-802286536
These two tests are failing pretty reliably (they've failed every run for the past 3)
org.apache.beam.sdk.io.gcp.pubsub.PubsubReadIT.testReadPubsubMessageId
org.apache.beam.sdk.io.gcp.pubsub.PubsubReadIT.testReadPublicData
Is that expected?
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[GitHub] [beam] macksclark commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-802339040
Thanks Pablo!
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[GitHub] [beam] macksclark commented on a change in pull request #14233: Adding LRO counters to FhirIO
Posted by GitBox <gi...@apache.org>.
macksclark commented on a change in pull request #14233:
URL: https://github.com/apache/beam/pull/14233#discussion_r595526804
##########
File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##########
@@ -378,6 +381,29 @@ public static Deidentify deidentify(
return new Deidentify(sourceFhirStore, destinationFhirStore, deidConfig);
}
+ /**
+ * Increments success and failure counters for an LRO. To be used after the LRO has completed.
+ * This function leverages the fact that the LRO metadata is always of the format: "counter": {
+ * "success": "1", "failure": "1" }
+ *
+ * @param operation LRO operation object.
+ * @param successCounter the success counter for this operation.
+ * @param failureCounter the failure counter for this operation.
+ */
+ private static void incrementLroCounters(
+ Operation operation, Counter successCounter, Counter failureCounter) {
+ Map<String, Object> opMetadata = operation.getMetadata();
+ if (opMetadata.containsKey(LRO_COUNTER_KEY)) {
+ Map<String, String> counters = (Map<String, String>) opMetadata.get(LRO_COUNTER_KEY);
Review comment:
We are technically guaranteed that this will be a map since the GetOperation method is in GA with a 2 year deprecation period (if it's ever decided to deprecate or change it) - but I put it all in a try catch block anyways.
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[GitHub] [beam] macksclark commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-801421069
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[GitHub] [beam] macksclark commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-801981620
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[GitHub] [beam] macksclark commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-801177858
Can we hold off on merging this? I got some internal feedback that maybe we should change the counter names like:
import_success_count -> import_resource_success_count
Or something similar, because import_success_count could easily indicate the entire import succeeded, which is not what we are trying to track with these counters. Please let me know if you have an opinion on this naming convention. Thanks!
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[GitHub] [beam] pabloem commented on a change in pull request #14233: Adding LRO counters to FhirIO
Posted by GitBox <gi...@apache.org>.
pabloem commented on a change in pull request #14233:
URL: https://github.com/apache/beam/pull/14233#discussion_r594632249
##########
File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##########
@@ -378,6 +381,29 @@ public static Deidentify deidentify(
return new Deidentify(sourceFhirStore, destinationFhirStore, deidConfig);
}
+ /**
+ * Increments success and failure counters for an LRO. To be used after the LRO has completed.
+ * This function leverages the fact that the LRO metadata is always of the format: "counter": {
+ * "success": "1", "failure": "1" }
+ *
+ * @param operation LRO operation object.
+ * @param successCounter the success counter for this operation.
+ * @param failureCounter the failure counter for this operation.
+ */
+ private static void incrementLroCounters(
+ Operation operation, Counter successCounter, Counter failureCounter) {
+ Map<String, Object> opMetadata = operation.getMetadata();
+ if (opMetadata.containsKey(LRO_COUNTER_KEY)) {
+ Map<String, String> counters = (Map<String, String>) opMetadata.get(LRO_COUNTER_KEY);
Review comment:
are we guaranteed that this will always be a map? should we handle any potential cast exceptions?
##########
File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##########
@@ -378,6 +381,29 @@ public static Deidentify deidentify(
return new Deidentify(sourceFhirStore, destinationFhirStore, deidConfig);
}
+ /**
+ * Increments success and failure counters for an LRO. To be used after the LRO has completed.
+ * This function leverages the fact that the LRO metadata is always of the format: "counter": {
+ * "success": "1", "failure": "1" }
+ *
+ * @param operation LRO operation object.
+ * @param successCounter the success counter for this operation.
+ * @param failureCounter the failure counter for this operation.
+ */
+ private static void incrementLroCounters(
+ Operation operation, Counter successCounter, Counter failureCounter) {
+ Map<String, Object> opMetadata = operation.getMetadata();
+ if (opMetadata.containsKey(LRO_COUNTER_KEY)) {
+ Map<String, String> counters = (Map<String, String>) opMetadata.get(LRO_COUNTER_KEY);
+ if (counters.containsKey(LRO_SUCCESS_KEY)) {
+ successCounter.inc(Long.parseLong(counters.get(LRO_SUCCESS_KEY)));
Review comment:
maybe we can handle cast / parsing exceptions in a single try/catch block?
I understand that this is highly unlikely, but since we don't have a way to guarantee this at compilation time, we could be stuck with pipelines failing indefinitely if the API were to change in any way in the future and we were to forget to update this.
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[GitHub] [beam] macksclark commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-801216271
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[GitHub] [beam] macksclark commented on pull request #14233: Adding LRO counters to FhirIO
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-799531814
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[GitHub] [beam] macksclark commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-800606413
Thanks! I won't worry about the counter checks for now.
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[GitHub] [beam] macksclark commented on a change in pull request #14233: Adding LRO counters to FhirIO
Posted by GitBox <gi...@apache.org>.
macksclark commented on a change in pull request #14233:
URL: https://github.com/apache/beam/pull/14233#discussion_r595528069
##########
File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##########
@@ -378,6 +381,29 @@ public static Deidentify deidentify(
return new Deidentify(sourceFhirStore, destinationFhirStore, deidConfig);
}
+ /**
+ * Increments success and failure counters for an LRO. To be used after the LRO has completed.
+ * This function leverages the fact that the LRO metadata is always of the format: "counter": {
+ * "success": "1", "failure": "1" }
+ *
+ * @param operation LRO operation object.
+ * @param successCounter the success counter for this operation.
+ * @param failureCounter the failure counter for this operation.
+ */
+ private static void incrementLroCounters(
+ Operation operation, Counter successCounter, Counter failureCounter) {
+ Map<String, Object> opMetadata = operation.getMetadata();
+ if (opMetadata.containsKey(LRO_COUNTER_KEY)) {
+ Map<String, String> counters = (Map<String, String>) opMetadata.get(LRO_COUNTER_KEY);
+ if (counters.containsKey(LRO_SUCCESS_KEY)) {
+ successCounter.inc(Long.parseLong(counters.get(LRO_SUCCESS_KEY)));
Review comment:
I agree, although we still need to check if the keys exist because, for example if there are no failures in the LRO, the counters will look like:
{"counters":{"success":"1"}} - with no failure field at all.
Catching all exceptions as discussed because we don't want to block anything on this function.
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[GitHub] [beam] macksclark commented on pull request #14233: Adding LRO counters to FhirIO
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-799547640
R: @pabloem
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[GitHub] [beam] macksclark commented on pull request #14233: Adding LRO counters to FhirIO
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-799548320
Hi Pablo, can you please take a look at this PR? I'm not sure if the tests are failing because of my change or if they were already failing. Thanks!
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[GitHub] [beam] pabloem merged pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
pabloem merged pull request #14233:
URL: https://github.com/apache/beam/pull/14233
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[GitHub] [beam] pabloem commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
pabloem commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-800649831
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[GitHub] [beam] pabloem commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
pabloem commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-802334728
Thanks for retrying the tests. I think this is fine. We'll get someone to address these other tests which you clearly didn't affect in this change.
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[GitHub] [beam] macksclark commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-801215925
Updated. Pablo, if you approve of the new names it's good to merge. Thanks!
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[GitHub] [beam] macksclark commented on pull request #14233: Adding LRO counters to FhirIO
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-800593683
Regarding the tests you mentioned running - they are passing reliably for me (I have yet to see any flakes) - did you want me to add asserts on the counters I just added, or would that be redundantly verifying that the LROs worked properly?
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[GitHub] [beam] macksclark commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
macksclark commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-801116270
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[GitHub] [beam] pabloem commented on pull request #14233: [BEAM-11733] Adding LRO counters to FhirIO and re-enable FhirIO tests
Posted by GitBox <gi...@apache.org>.
pabloem commented on pull request #14233:
URL: https://github.com/apache/beam/pull/14233#issuecomment-800634173
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