Parquet to BigQuery import for GCP-backed AnVIL snapshots (#6355) #6392

nadove-ucsc · 2024-07-10T06:03:29Z

Connected issues: #6355

Checklist

Author

PR is a draft
Target branch is develop
Name of PR branch matches issues/<GitHub handle of author>/<issue#>-<slug>
On ZenHub, PR is connected to all issues it (partially) resolves
PR description links to connected issues
PR title matches¹ that of a connected issue _{or comment in PR explains why they're different}
PR title references all connected issues
For each connected issue, there is at least one commit whose title references that issue

¹ when the issue title describes a problem, the corresponding PR
title is Fix: followed by the issue title

Author (partiality)

Added p tag to titles of partial commits
This PR is labeled partial _{or completely resolves all connected issues}
This PR partially resolves each of the connected issues _{or does not have the partial label}

Author (chains)

This PR is blocked by previous PR in the chain _{or is not chained to another PR}
The blocking PR is labeled base _{or this PR is not chained to another PR}
This PR is labeled chained _{or is not chained to another PR}

Author (reindex, API changes)

Added r tag to commit title _{or the changes introduced by this PR will not require reindexing of any deployment}
This PR is labeled reindex:dev _{or the changes introduced by it will not require reindexing of dev}
This PR is labeled reindex:anvildev _{or the changes introduced by it will not require reindexing of anvildev}
This PR is labeled reindex:anvilprod _{or the changes introduced by it will not require reindexing of anvilprod}
This PR is labeled reindex:prod _{or the changes introduced by it will not require reindexing of prod}
This PR is labeled reindex:partial and its description documents the specific reindexing procedure for dev, anvildev, anvilprod and prod _{or requires a full reindex or carries none of the labels reindex:dev, reindex:anvildev, reindex:anvilprod and reindex:prod}
This PR and its connected issues are labeled API _{or this PR does not modify a REST API}
Added a (A) tag to commit title for backwards (in)compatible changes _{or this PR does not modify a REST API}
Updated REST API version number in app.py _{or this PR does not modify a REST API}

Author (upgrading deployments)

Ran make image_manifests.json and committed the resulting changes _{or this PR does not modify azul_docker_images, or any other variables referenced in the definition of that variable}
Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading deployments}
Added u tag to commit title _{or this PR does not require upgrading deployments}
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This PR is labeled deploy:gitlab _{or does not require deploying the gitlab component}
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Author (hotfixes)

Added F tag to main commit title _{or this PR does not include permanent fix for a temporary hotfix}
Reverted the temporary hotfixes for any connected issues _{or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues connected to this PR}

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Rebased PR branch on develop, squashed old fixups
Ran make requirements_update _{or this PR does not modify requirements*.txt, common.mk, Makefile and Dockerfile}
Added R tag to commit title _{or this PR does not modify requirements*.txt}
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make integration_test passes in personal deployment _{or this PR does not modify functionality that could affect the IT outcome}

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Propagated the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels to the next promotion PRs _{or this PR carries none of these labels}
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PR is assigned to no one

Shorthand for review comments

L line is too long
W line wrapping is wrong
Q bad quotes
F other formatting problem

coveralls · 2024-07-10T06:25:54Z

coverage: 85.139% (-0.3%) from 85.398%
when pulling 78545b6 on issues/nadove-ucsc/6355-parquet-bigquery-import-gcp-anvil-snapshots
into 34a12fb on develop.

codecov · 2024-07-10T06:26:11Z

Codecov Report

Attention: Patch coverage is 10.66667% with 67 lines in your changes missing coverage. Please review.

Project coverage is 85.12%. Comparing base (34a12fb) to head (78545b6).

Files with missing lines	Patch %	Lines
src/azul/terra.py	9.83%	55 Missing ⚠️
src/azul/plugins/repository/tdr_anvil/__init__.py	14.28%	12 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6392      +/-   ##
===========================================
- Coverage    85.38%   85.12%   -0.26%     
===========================================
  Files          155      155              
  Lines        20754    20823      +69     
===========================================
+ Hits         17720    17725       +5     
- Misses        3034     3098      +64

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

dsotirho-ucsc · 2024-07-12T00:08:59Z

scripts/verify_tdr_sources.py

                'Actual Google project of TDR source differs from configured one',
-                source.project, source_spec.project)
+                source.project, source_spec.project, config.google_project())


Suggested change

source.project, source_spec.project, config.google_project())

source_spec.project, source.project, config.google_project())

to match the order of these variables in the condition part of the require()

I decided on a different approach here to make the diff clearer and hopefully make the intent more apparent.

Makefile

nadove-ucsc · 2024-07-12T01:25:20Z

I also moved some changes from the first commit to the 2nd, hence the other fixup.

dsotirho-ucsc

Approved.

hannes-ucsc · 2024-07-19T05:02:50Z

Makefile

+	python $(project_root)/scripts/reindex.py --import --sources "tdr:${GOOGLE_PROJECT}:snapshot/*"
+	python $(project_root)/scripts/verify_tdr_sources.py


I think these two commands should be extracted to a separate make target called import, and a corresponding GitLab job. We also need to think about sandbox and personal deployments that typically share the sources with a main deployment. I think #6426 will help with this which is why I've added it as a blocker of #6355.

hannes-ucsc · 2024-07-19T05:06:30Z

scripts/download_tdr_parquet.py

@@ -0,0 +1,103 @@
+"""
+Export parquet files from TDR and download them to local storage.


Suggested change

Export parquet files from TDR and download them to local storage.

Export Parquet files from TDR and download them to local storage.

Here and in elsewhere in documentation.

hannes-ucsc

Somethings amiss here. It appears that this adds code that isn't actually exercised because none of the sources are configured to use Parquet. We should switch one source in ~~dev, sandbox,~~ anvildev and anvilbox to use Parquet. Lets also discuss in PL what to do about personal deployments.

Subject: [PATCH] make fo
---
Index: src/azul/terra.py
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/src/azul/terra.py b/src/azul/terra.py
--- a/src/azul/terra.py	(revision 14df96cd41cd529093df1520abd73d725b44aa28)
+++ b/src/azul/terra.py	(date 1724981432852)
@@ -541,6 +541,7 @@
                         endpoint: furl,
                         response: urllib3.HTTPResponse
                         ) -> MutableJSON:
+        # REVIEW: Short comment here explaining when we'd expect a 202
         if response.status in (200, 202):
             return json.loads(response.data)
         # FIXME: Azul sometimes conflates 401 and 403
@@ -661,8 +662,8 @@
 
     def create_dataset(self, dataset_name: str):
         """
-        Create a BigQuery dataset in the project and region configured for the
-        current deployment.
+        Create a BigQuery dataset in the GCP project associated with the current
+        credentials and the GCP region configure for the current deployment.
 
         :param dataset_name: Unqualified name of the dataset to create.
                              `google.cloud.exceptions.Conflict` will be raised
@@ -670,10 +671,23 @@
         """
         bigquery = self._bigquery(self.credentials.project_id)
         ref = DatasetReference(bigquery.project, dataset_name)
+        # We get a false warning from PyCharm here, probably because of
+        #
+        # https://youtrack.jetbrains.com/issue/PY-23400/regression-PEP484-type-annotations-in-docstrings-nearly-completely-broken
+        #
+        # Google uses the docstring syntax to annotate types in its BQ client.
+        #
+        # noinspection PyTypeChecker
         dataset = Dataset(ref)
+        # REVIEW: This changes the meaning of AZUL_TDR_SOURCE_LOCATION somewhat.
+        #         While I don't think we need to introduce a new variable, we
+        #         should document the new semantics so that someone modifying
+        #         it is aware of the implications.
         dataset.location = config.tdr_source_location
         log.info('Creating BigQuery dataset %r in region %r',
                  dataset.dataset_id, dataset.location)
+        # REVIEW: This method returns something. Let's assert key aspects of the
+        #         return value.
         bigquery.create_dataset(dataset)
 
     def create_table(self,
@@ -692,8 +706,11 @@
 
         :param table_name: Unqualified name of the new table
 
+        REVIEW: Technically gs://… is a URI. If "URL" is TDR lingo I'm happy to
+                adopt it, otherwise we should use "URI".
+
         :param import_urls: URLs of Parquet file(s) to populate the table. These
-                            must be `gs://` URLS and the GCS bucket's region
+                            must be `gs://` URLs and the GCS bucket's region
                             must be compatible with the target dataset's. See
                             https://cloud.google.com/bigquery/docs/loading-data-cloud-storage-parquet#limitations
 
@@ -705,7 +722,7 @@
                                   https://cloud.google.com/bigquery/docs/clustered-tables
         """
         for url in import_urls:
-            require(url.scheme == 'gs', url)
+            require(url.scheme == 'gs', 'Expected gs:// URI', url)
         table_id = f'{dataset_name}.{table_name}'
         bigquery = self._bigquery(self.credentials.project_id)
         write_disposition = (
@@ -716,25 +733,26 @@
             clustering_fields=clustering_fields,
             source_format=SourceFormat.PARQUET,
             # Avoids convoluted data types for array fields
+            # REVIEW: Please elaborate
             parquet_options=ParquetOptions.from_api_repr(dict(enable_list_inference=True))
         )
-        log.info('Creating BigQuery table %r',
-                 f'{bigquery.project}.{dataset_name}.{table_name}')
+        table_ref = f'{bigquery.project}.{table_id}'
+        log.info('Creating BigQuery table %r', table_ref)
         load_job = bigquery.load_table_from_uri(source_uris=list(map(str, import_urls)),
                                                 destination=table_id,
                                                 job_config=job_config)
         load_job.result()
-        log.info('Table created successfully')
+        log.info('Table %r created successfully', table_ref)
 
     def export_parquet_urls(self,
                             snapshot_id: str
                             ) -> Optional[dict[str, list[mutable_furl]]]:
         """
         Obtain URLs of Parquet files for the data tables of the specified
-        snapshot. This is an time-consuming operation that usually takes on the
-        order of 1 minute to complete.
+        snapshot. This is a time-consuming operation that usually takes on the
+        order of one minute to complete.
 
-        :param snapshot_id: The UUID of the snapshot.
+        :param snapshot_id: The UUID of the snapshot
 
         :return: A mapping of table names to lists of Parquet file download
                  URLs, or `None` if if no Parquet downloads are available for
@@ -744,6 +762,8 @@
         url = self._repository_endpoint('snapshots', snapshot_id, 'export')
         # Required for Azure-backed snapshots
         url.args.add('validatePrimaryKeyUniqueness', False)
+        # REVIEW: We should apply a timeout here. I suggest five times the
+        #         longest observed duration
         while True:
             response = self._request('GET', url)
             response_body = self._check_response(url, response)
@@ -752,6 +772,8 @@
             if jobs_status == 'running':
                 url = self._repository_endpoint('jobs', job_id)
                 log.info('Waiting for job %r ...', job_id)
+                # REVIEW: What's this choice of two seconds based on? It seems
+                # rather short considering everything about TDR's robustness.
                 time.sleep(2)
             elif jobs_status == 'succeeded':
                 break
Index: .gitlab-ci.yml
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
--- a/.gitlab-ci.yml	(revision 14df96cd41cd529093df1520abd73d725b44aa28)
+++ b/.gitlab-ci.yml	(date 1724981655861)
@@ -100,6 +100,8 @@
 import:
   extends: .base_on_push
   stage: deploy
+  # REVIEW: Assume all sources need to be imported, estimate the expected
+  #         running time and double that. Remove the comment.
   timeout: 5m  # probably needs to be extended
   needs:
     - build_image

nadove-ucsc · 2024-09-18T19:31:04Z

@hannes-ucsc: "Regarding personal deployments, the import should only be performed on shared deployments. By the time developers upgrade their personal deployments to mirror the respective sandbox, the GitLab build for that sandbox will have already imported the snapshot. If someone really needs to import a snapshot for a personal deployment, they can temporarily enable the import for personal deployments."

hannes-ucsc

Conflicts.

hannes-ucsc · 2024-09-23T22:54:58Z

.gitlab-ci.yml

+import:
+  extends: .base_on_push
+  stage: deploy
+  # The 1000G snapshot on `anvildev` takes about 3.5 minutes to import. There


I'm not sure assuming that every snapshot is as big as 1000G leads to practical timeout.

A timeout is a heuristic defense against hung workloads, i.e., workloads that stop making significant progress. We don't want to constantly update the timeout, we don't want it to prematurely kill workloads that are progressing at the average rate, and we don't want the workload to be in the hung state for > 80% of it's running time. A 5min timeout goes against the first rule, a 30h timeout goes against the last.

hannes-ucsc · 2024-09-23T23:03:44Z

deployments/anvilbox/environment.py

@@ -73,7 +73,7 @@ def mkdict(previous_catalog: dict[str, str],


 anvil_sources = mkdict({}, 3, mkdelta([
-    mksrc('bigquery', 'datarepo-dev-e53e74aa', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),
+    mksrc('parquet', 'platform-anvil-dev', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),


The source spec should state where the source is, not where it will be when it is imported. The logic should be to import every parquet source. So I think this should read

Suggested change

mksrc('parquet', 'platform-anvil-dev', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),

mksrc('bigquery', 'platform-anvil-dev', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),

hannes-ucsc · 2024-09-23T23:04:15Z

deployments/anvildev/environment.py

@@ -64,7 +64,7 @@ def mkdict(previous_catalog: dict[str, str],


 anvil_sources = mkdict({}, 3, mkdelta([
-    mksrc('bigquery', 'datarepo-dev-e53e74aa', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),
+    mksrc('parquet', 'platform-anvil-dev', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),


Suggested change

mksrc('parquet', 'platform-anvil-dev', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),

mksrc('parquet', 'datarepo-dev-e53e74aa', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),

hannes-ucsc · 2024-09-23T23:15:51Z

Makefile

 endef

 $(eval $(call deploy,))
 $(eval $(call deploy,auto_))

+.PHONY: import
+import: check_python
+	python $(project_root)/scripts/reindex.py --import --sources "tdr:parquet:gcp:${GOOGLE_PROJECT}:*"


Suggested change

python $(project_root)/scripts/reindex.py --import --sources "tdr:parquet:gcp:${GOOGLE_PROJECT}:*"

python $(project_root)/scripts/reindex.py --import --sources "tdr:parquet:gcp:*"

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Elimindate typing.Optional in terra.py

b0f6ff9

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[u r] Parquet to BigQuery import for GCP-backed AnVIL snapshots (#6355)

5f4db61

[R] Add BigQuery table import to Makefile and rename post_deploy script

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Parquet to BigQuery import for GCP-backed AnVIL snapshots (#6355) #6392

Parquet to BigQuery import for GCP-backed AnVIL snapshots (#6355) #6392

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	source.project, source_spec.project, config.google_project())
	source_spec.project, source.project, config.google_project())

		python $(project_root)/scripts/reindex.py --import --sources "tdr:${GOOGLE_PROJECT}:snapshot/*"
		python $(project_root)/scripts/verify_tdr_sources.py

		@@ -0,0 +1,103 @@
		"""
		Export parquet files from TDR and download them to local storage.

	mksrc('parquet', 'platform-anvil-dev', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),
	mksrc('bigquery', 'platform-anvil-dev', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),

	mksrc('parquet', 'platform-anvil-dev', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),
	mksrc('parquet', 'datarepo-dev-e53e74aa', 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', 6804),

Parquet to BigQuery import for GCP-backed AnVIL snapshots (#6355) #6392

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Parquet to BigQuery import for GCP-backed AnVIL snapshots (#6355) #6392

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nadove-ucsc commented Jul 10, 2024 • edited Loading

Checklist

Author

Author (partiality)

Author (chains)

Author (reindex, API changes)

Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

Peer reviewer (after approval)

System administrator (after approval)

Operator (before pushing merge the commit)

System administrator

Operator (before pushing merge the commit)

Operator (chain shortening)

Operator (after pushing the merge commit)

Operator (reindex)

Operator

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