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Implement mirror_file, mirror_part & finalize_file (#6862) #7043

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@nadove-ucsc nadove-ucsc commented Apr 15, 2025

Connected issues: #6862

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Shorthand for review comments

  • L line is too long
  • W line wrapping is wrong
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@github-actions github-actions bot added the orange [process] Done by the Azul team label Apr 15, 2025
@nadove-ucsc nadove-ucsc added the chained [process] PR needs to based of develop before merging label Apr 15, 2025
@nadove-ucsc nadove-ucsc changed the base branch from develop to issues/nadove-ucsc/6861-implement-mirror-partition April 15, 2025 03:36
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codecov bot commented Apr 15, 2025

Codecov Report

Attention: Patch coverage is 57.47126% with 74 lines in your changes missing coverage. Please review.

Project coverage is 85.27%. Comparing base (cb13133) to head (cd69dc8).
Report is 6 commits behind head on develop.

Files with missing lines Patch % Lines
src/azul/indexer/mirror_service.py 53.12% 45 Missing ⚠️
src/azul/azulclient.py 50.98% 25 Missing ⚠️
src/azul/indexer/mirror_controller.py 55.55% 4 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #7043      +/-   ##
===========================================
- Coverage    85.47%   85.27%   -0.20%     
===========================================
  Files          150      151       +1     
  Lines        21678    21846     +168     
===========================================
+ Hits         18529    18629     +100     
- Misses        3149     3217      +68     

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

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@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/6861-implement-mirror-partition branch 4 times, most recently from aa9f3d5 to 0171653 Compare April 23, 2025 19:58
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/6862-implement-mirror-file branch from 7bec7cb to 9f01c2a Compare April 23, 2025 21:55
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/6861-implement-mirror-partition branch 8 times, most recently from bf67c7d to 5847dcd Compare May 1, 2025 00:05
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/6862-implement-mirror-file branch from ff6f582 to 788dda8 Compare May 1, 2025 02:12
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/6861-implement-mirror-partition branch from 6191b82 to f09c3cb Compare May 1, 2025 07:43
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/nadove-ucsc/6861-implement-mirror-partition branch from 91f35b8 to 78469d7 Compare May 1, 2025 17:51
@dsotirho-ucsc dsotirho-ucsc changed the base branch from issues/nadove-ucsc/6861-implement-mirror-partition to develop May 1, 2025 20:32
@dsotirho-ucsc dsotirho-ucsc removed the chained [process] PR needs to based of develop before merging label May 1, 2025
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/6862-implement-mirror-file branch 2 times, most recently from 9dc1566 to 2c91700 Compare May 1, 2025 23:23
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coveralls commented May 1, 2025

Coverage Status

coverage: 85.452% (-0.2%) from 85.65%
when pulling cd69dc8 on issues/nadove-ucsc/6862-implement-mirror-file
into cb13133 on develop.

@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/6862-implement-mirror-file branch from 2c91700 to a2f9717 Compare May 2, 2025 07:22
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Notes on test coverage: since most files are > 10 MB, it's common for no files at all to be mirrored during the IT, so we effectively have no IT coverage for the mirror_file functionality. I confirmed everything's working by running the mirror.py script and checking for errors in CloudWatch.

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nadove-ucsc commented May 2, 2025

Note on scale/cost/efficiency: on my personal deployment, running mirror.py across all catalogs (dcp3, lungmap, lm2) with he 10 MB limit in place resulted in mirroring 180 files with a cumulative size of 536 MB. Multiplying by 16 to simulate the effect of removing the common prefix yields 8.58 GB.

@hannes-ucsc hannes-ucsc force-pushed the issues/nadove-ucsc/6862-implement-mirror-file branch from 33d63d0 to 50f39fb Compare May 6, 2025 00:01
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/6862-implement-mirror-file branch 2 times, most recently from e4b935c to 37c4900 Compare May 6, 2025 02:34
@nadove-ucsc nadove-ucsc requested a review from hannes-ucsc May 6, 2025 03:02
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Subject: [PATCH] REVIEW 1
---
Index: src/azul/indexer/mirror_service.py
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/src/azul/indexer/mirror_service.py b/src/azul/indexer/mirror_service.py
--- a/src/azul/indexer/mirror_service.py	(revision 0e764360a78161c7bb8d54e7e8cde365f2052d34)
+++ b/src/azul/indexer/mirror_service.py	(date 1746498183684)
@@ -52,8 +52,8 @@
     """
     A part of a mirrored file
     """
-    #: The part number, starting at 0 for the first part. Note that the S3 API
-    #: numbers parts starting at 1.
+    #: The part number, starting at 0 for the first part, unlike S3 API part
+    #: numbers, which start at 1.
     #:
     index: int
 
@@ -64,7 +64,7 @@
     #:
     size: int
 
-    #: Various quotas related to parts and part sizes
+    #: Various S3 quotas related to parts and part sizes
     #: https://docs.aws.amazon.com/AmazonS3/latest/userguide/qfacts.html
     #:
     min_size: ClassVar[int] = 5 * 1024 ** 2
@@ -102,14 +102,13 @@
         last part.
         """
         assert file.size is not None, R('File size unknown', file)
-        stop = self.offset + self.size
-        if stop == file.size:
+        next_offset = self.offset + self.size
+        if next_offset == file.size:
             return None
-        elif 0 < stop < file.size:
-            return attr.evolve(self,
-                               index=self.index + 1,
-                               offset=stop,
-                               size=min(self.size, file.size - stop))
+        elif 0 < next_offset < file.size:
+            next_index = self.index + 1
+            next_size = min(self.size, file.size - next_offset)
+            return attr.evolve(self, index=next_index, offset=next_offset, size=next_size)
         else:
             assert False, R('Part range exceeds file size', self, file)
 
Index: src/azul/azulclient.py
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/src/azul/azulclient.py b/src/azul/azulclient.py
--- a/src/azul/azulclient.py	(revision 0e764360a78161c7bb8d54e7e8cde365f2052d34)
+++ b/src/azul/azulclient.py	(date 1746509333358)
@@ -759,7 +759,7 @@
                       etags: Sequence[str]
                       ):
         file = self.load_file(catalog, file_json)
-        assert etags
+        assert len(etags) > 0
         self.mirror_service.finish_mirroring_file(file, upload_id, etags)
         log.info('Successfully mirrored file %r via multi-part upload', file.uuid)
 

Comment on lines +56 to +60
self.client.mirror_file_part(message['catalog'],
message['file'],
message['part'],
message['upload_id'],
message['etags'])
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This is getting unwieldy. It is essentially the deserialization counterpart to mirror_part_message in AzulClient. So the two things that should be really close to each other, since they are so tightly coupled, are actually far apart. So that's brittle. Then again, we should stop writing this type of code and use the serialization framework in azul.attrs instead. The bodies of the SQS messages really want to be represented by a class.

The use of positional arguments is also brittle. There are even two neighboring arguments of the same type so there is real danger of accidentally swapping them. On top of that, I am really surprised that this even gets past the type checker. Each value in the message dict is of type AnyJSON but mypy silently narrows them to the more specific types of the arguments declared in the mirror_file_part signature. Something must be wrong with mypy or how mypy analyzes the code in azulclient.

This is all somewhat worrying and we need to improve this as quickly as possible. I will take a stab at it as soon as we have a functional version.

@hannes-ucsc hannes-ucsc removed their assignment May 6, 2025
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/6862-implement-mirror-file branch from 0071471 to fe9a0b3 Compare May 6, 2025 06:40
@nadove-ucsc nadove-ucsc requested a review from hannes-ucsc May 6, 2025 08:03
@hannes-ucsc hannes-ucsc self-assigned this May 6, 2025
@hannes-ucsc hannes-ucsc added 1 review [process] Lead requested changes once and removed 0 reviews [process] Lead didn't request any changes labels May 6, 2025
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Security design review

  • Security design review completed; this PR does not
    • … affect authentication; for example:
      • OAuth 2.0 with the application (API or Swagger UI)
      • Authentication of developers with Google Cloud APIs
      • Authentication of developers with AWS APIs
      • Authentication with a GitLab instance in the system
      • Password and 2FA authentication with GitHub
      • API access token authentication with GitHub
      • Authentication with Terra
    • … affect the permissions of internal users like access to
      • Cloud resources on AWS and GCP
      • GitLab repositories, projects and groups, administration
      • an EC2 instance via SSH
      • GitHub issues, pull requests, commits, commit statuses, wikis, repositories, organizations
    • … affect the permissions of external users like access to
      • TDR snapshots
    • … affect permissions of service or bot accounts
      • Cloud resources on AWS and GCP
    • … affect audit logging in the system, like
      • adding, removing or changing a log message that represents an auditable event
      • changing the routing of log messages through the system
    • … affect monitoring of the system
    • … introduce a new software dependency like
      • Python packages on PYPI
      • Command-line utilities
      • Docker images
      • Terraform providers
    • … add an interface that exposes sensitive or confidential data at the security boundary
    • … affect the encryption of data at rest
    • … require persistence of sensitive or confidential data that might require encryption at rest
    • … require unencrypted transmission of data within the security boundary
    • … affect the network security layer; for example by
      • modifying, adding or removing firewall rules
      • modifying, adding or removing security groups
      • changing or adding a port a service, proxy or load balancer listens on
  • Documentation on any unchecked boxes is provided in comments below

@hannes-ucsc hannes-ucsc force-pushed the issues/nadove-ucsc/6862-implement-mirror-file branch from 6cdc15d to cd69dc8 Compare May 6, 2025 16:13
@hannes-ucsc hannes-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label May 6, 2025
@achave11-ucsc achave11-ucsc merged commit f5c01a4 into develop May 6, 2025
11 checks passed
@achave11-ucsc achave11-ucsc removed the base [process] Another PR needs to be rebased before merging this one label May 6, 2025
@achave11-ucsc achave11-ucsc deleted the issues/nadove-ucsc/6862-implement-mirror-file branch May 6, 2025 19:16
@achave11-ucsc achave11-ucsc removed their assignment May 6, 2025
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