Support for HCA data_use_restriction (#6131) #6207

dsotirho-ucsc · 2024-04-26T18:25:37Z

Connected issues: #6131

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}
This PR is labeled upgrade _{or does not require upgrading deployments}
This PR is labeled deploy:shared _{or does not modify image_manifests.json, and does not require deploying the shared component for any other reason}
This PR is labeled deploy:gitlab _{or does not require deploying the gitlab component}
This PR is labeled deploy:runner _{or does not require deploying the runner image}

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}

Author (before every review)

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}
This PR is labeled reqs _{or does not modify requirements*.txt}
make integration_test passes in personal deployment _{or this PR does not modify functionality that could affect the IT outcome}

Peer reviewer (after approval)

PR is not a draft
Ticket is in Review requested column
PR is awaiting requested review from system administrator
PR is assigned to only the system administrator

System administrator (after approval)

Actually approved the PR
Labeled connected issues as demo or no demo
Commented on connected issues about demo expectations _{or all connected issues are labeled no demo}
Decided if PR can be labeled no sandbox
A comment to this PR details the completed security design review
PR title is appropriate as title of merge commit
N reviews label is accurate
Moved ticket to Approved column
PR is assigned to only the operator

Operator (before pushing merge the commit)

System administrator

Background migrations for dev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
Background migrations for anvildev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
PR is assigned to only the operator

Operator (before pushing merge the commit)

Operator (chain shortening)

Changed the target branch of the blocked PR to develop _{or this PR is not labeled base}
Removed the chained label from the blocked PR _{or this PR is not labeled base}
Removed the blocking relationship from the blocked PR _{or this PR is not labeled base}
Removed the base label from this PR _{or this PR is not labeled base}

Operator (after pushing the merge commit)

Operator (reindex)

Operator

Propagated the deploy:shared, deploy:gitlab, deploy:runner, reindex:partial, reindex:anvilprod and reindex:prod labels to the next promotion PRs _{or this PR carries none of these labels}
Propagated any specific instructions related to the deploy:shared, deploy:gitlab, deploy:runner, reindex:partial, reindex:anvilprod and reindex:prod labels, from the description of this PR to that of the next promotion PRs _{or this PR carries none of these labels}
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

codecov · 2024-04-29T22:00:48Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.39%. Comparing base (6e485c1) to head (3eefe27).
Report is 4 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6207      +/-   ##
===========================================
+ Coverage    85.38%   85.39%   +0.01%     
===========================================
  Files          155      155              
  Lines        20739    20758      +19     
===========================================
+ Hits         17707    17726      +19     
  Misses        3032     3032

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

coveralls · 2024-04-29T22:00:54Z

coverage: 85.41% (+0.01%) from 85.397%
when pulling 3eefe27 on issues/dsotirho-ucsc/6131-new-field-data-use-restriction
into 6e485c1 on develop.

dsotirho-ucsc · 2024-05-06T18:59:30Z

6207_IT_2024-05-06.txt

achave11-ucsc

It looks like when bionetworkName was introduced (which seems like a similar set of changes) it had also changed the openapi.json file with the addition of the minor version bump for the azul-service API, as well as the associated issue being labeled API. Should this PR also have a similar bump to the API version and label?

dsotirho-ucsc · 2024-05-07T18:02:06Z

6207_IT_2024-05-07.txt

achave11-ucsc

Approved ✅

dsotirho-ucsc · 2024-09-09T17:16:22Z

With six bundles indexed for one project, project entity values in the /index/files response for example depend on which bundle the file inner entity file came from. Since the data_use_restriction value was only added to one of these bundles, this meant the resulting hit[].projects[].dataUseRestriction value would either be [None] or ['NRES']. Furthermore, in the case of the /index/projects response, only one bundle's project values are represented, which was not the bundle I had modified.

Ticket #6552 has been created to address the issue.

hannes-ucsc · 2024-09-11T17:04:04Z

test/service/test_response.py

+        """
+        Verify the data_use_restriction field
+        """


Suggested change

"""

Verify the data_use_restriction field

"""

This is obvious given the name of the method.

hannes-ucsc · 2024-09-11T17:05:46Z

test/service/test_response.py

+            url = self.base_url.set(path=('index', entity_type), args=params)
+            response = requests.get(url)
+            response.raise_for_status()
+            response_json = response.json()


Suggested change

response_json = response.json()

response = response.json()

test/service/test_response.py

hannes-ucsc · 2024-09-11T17:08:36Z

test/service/test_response.py

+            response = requests.get(url)
+            response.raise_for_status()
+            response_json = response.json()
+            self.assertGreater(len(response_json['hits']), 0)


Suggested change

self.assertGreater(len(response_json['hits']), 0)

hits = response_json['hits']

self.assertGreater(len(hits), 0)

hannes-ucsc · 2024-09-11T17:08:53Z

test/service/test_response.py

+            response.raise_for_status()
+            response_json = response.json()
+            self.assertGreater(len(response_json['hits']), 0)
+            for hit in response_json['hits']:


Suggested change

for hit in response_json['hits']:

for hit in hits:

dsotirho-ucsc · 2024-09-11T18:46:12Z

6207_IT_2024-09-11.txt

hannes-ucsc

Second commit lacks subtitle.

hannes-ucsc · 2024-09-13T02:35:32Z

test/service/test_response.py

+            'sort': 'dataUseRestriction',
+            'filters': json.dumps({'dataUseRestriction': {'is': ['NRES']}})
+        }
+        for entity_type in ('bundles', 'files', 'projects', 'samples'):


We have plugin method for this.

hannes-ucsc · 2024-09-13T02:35:53Z

test/service/test_response.py

+            hits = response['hits']
+            self.assertGreater(len(hits), 0)
+            for hit in hits:
+                expected = 'NRES' if entity_type == 'projects' else ['NRES']


expected is constant over the loop

hannes-ucsc

I addressed the above comments.

hannes-ucsc · 2024-09-13T02:38:47Z

Security design review

Add the data_use_restriction field to an existing canned bundle

Add implementation and test

Refactor test

github-actions bot added the orange [process] Done by the Azul team label Apr 26, 2024

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6131-new-field-data-use-restriction branch 2 times, most recently from f6d1822 to 00f9bb7 Compare April 29, 2024 21:38

dsotirho-ucsc added reindex:dev [process] PR requires reindexing dev reindex:anvildev [process] PR requires reindexing anvildev reindex:anvilprod [process] PR requires reindexing anvilprod reindex:prod [process] PR requires reindexing prod labels Apr 29, 2024

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6131-new-field-data-use-restriction branch 4 times, most recently from 7ab826f to 7e18d9f Compare May 6, 2024 17:43

dsotirho-ucsc requested a review from achave11-ucsc May 6, 2024 20:35

dsotirho-ucsc assigned achave11-ucsc May 6, 2024

This comment was marked as outdated.

Sign in to view

achave11-ucsc reviewed May 7, 2024

View reviewed changes

achave11-ucsc removed their assignment May 7, 2024

dsotirho-ucsc dismissed achave11-ucsc’s stale review via 8515168 May 7, 2024 17:36

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6131-new-field-data-use-restriction branch from 7e18d9f to 8515168 Compare May 7, 2024 17:36

dsotirho-ucsc added the API API change affecting callers label May 7, 2024

dsotirho-ucsc requested a review from achave11-ucsc May 7, 2024 18:02

dsotirho-ucsc assigned achave11-ucsc May 7, 2024

achave11-ucsc previously approved these changes May 7, 2024

View reviewed changes

achave11-ucsc marked this pull request as ready for review May 7, 2024 18:08

achave11-ucsc requested a review from hannes-ucsc as a code owner May 7, 2024 18:08

achave11-ucsc assigned achave11-ucsc and unassigned achave11-ucsc May 7, 2024

dsotirho-ucsc requested a review from hannes-ucsc September 9, 2024 22:43

dsotirho-ucsc assigned hannes-ucsc Sep 10, 2024

hannes-ucsc requested changes Sep 11, 2024

View reviewed changes

hannes-ucsc removed their assignment Sep 11, 2024

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6131-new-field-data-use-restriction branch from 4813f88 to d37ce67 Compare September 11, 2024 18:18

dsotirho-ucsc requested a review from hannes-ucsc September 12, 2024 00:29

dsotirho-ucsc assigned hannes-ucsc Sep 12, 2024

hannes-ucsc requested changes Sep 13, 2024

View reviewed changes

hannes-ucsc force-pushed the issues/dsotirho-ucsc/6131-new-field-data-use-restriction branch from d37ce67 to baaa83a Compare September 13, 2024 02:36

hannes-ucsc approved these changes Sep 13, 2024

View reviewed changes

hannes-ucsc assigned achave11-ucsc and unassigned hannes-ucsc Sep 13, 2024

achave11-ucsc force-pushed the issues/dsotirho-ucsc/6131-new-field-data-use-restriction branch from baaa83a to c9baf85 Compare September 13, 2024 23:07

achave11-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Sep 13, 2024

hannes-ucsc force-pushed the issues/dsotirho-ucsc/6131-new-field-data-use-restriction branch 2 times, most recently from 819d4ab to fd24b51 Compare September 16, 2024 17:16

achave11-ucsc assigned dsotirho-ucsc and unassigned achave11-ucsc Sep 16, 2024

dsotirho-ucsc removed the sandbox [process] Resolution is being verified in sandbox deployment label Sep 16, 2024

dsotirho-ucsc and others added 3 commits September 16, 2024 12:41

[1/3] [r a] Support for HCA data_use_restriction (#6131)

f873304

Add the data_use_restriction field to an existing canned bundle

[2/3] [r a] Support for HCA data_use_restriction (#6131)

ec7898a

Add implementation and test

[3/3] [r a] Support for HCA data_use_restriction (#6131)

3eefe27

Refactor test

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6131-new-field-data-use-restriction branch from fd24b51 to 3eefe27 Compare September 16, 2024 19:41

dsotirho-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Sep 16, 2024

dsotirho-ucsc merged commit 054205d into develop Sep 16, 2024
11 checks passed

dsotirho-ucsc deleted the issues/dsotirho-ucsc/6131-new-field-data-use-restriction branch September 16, 2024 22:39

dsotirho-ucsc removed their assignment Sep 30, 2024

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Support for HCA data_use_restriction (#6131) #6207

Support for HCA data_use_restriction (#6131) #6207

dsotirho-ucsc commented Apr 26, 2024 •

edited

Loading

codecov bot commented Apr 29, 2024 •

edited

Loading

coveralls commented Apr 29, 2024 •

edited

Loading

dsotirho-ucsc commented May 6, 2024

This comment was marked as outdated.

achave11-ucsc left a comment

dsotirho-ucsc commented May 7, 2024

achave11-ucsc left a comment

dsotirho-ucsc commented Sep 9, 2024 •

edited

Loading

hannes-ucsc Sep 11, 2024

hannes-ucsc Sep 11, 2024

hannes-ucsc Sep 11, 2024

hannes-ucsc Sep 11, 2024

dsotirho-ucsc commented Sep 11, 2024

hannes-ucsc left a comment

hannes-ucsc Sep 13, 2024

hannes-ucsc Sep 13, 2024

hannes-ucsc left a comment

hannes-ucsc commented Sep 13, 2024

	self.assertGreater(len(response_json['hits']), 0)
	hits = response_json['hits']
	self.assertGreater(len(hits), 0)

Support for HCA data_use_restriction (#6131) #6207

Support for HCA data_use_restriction (#6131) #6207

Conversation

dsotirho-ucsc commented Apr 26, 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

Shorthand for review comments

codecov bot commented Apr 29, 2024 • edited Loading

Codecov Report

coveralls commented Apr 29, 2024 • edited Loading

dsotirho-ucsc commented May 6, 2024

This comment was marked as outdated.

achave11-ucsc left a comment

Choose a reason for hiding this comment

dsotirho-ucsc commented May 7, 2024

achave11-ucsc left a comment

Choose a reason for hiding this comment

dsotirho-ucsc commented Sep 9, 2024 • edited Loading

hannes-ucsc Sep 11, 2024

Choose a reason for hiding this comment

hannes-ucsc Sep 11, 2024

Choose a reason for hiding this comment

hannes-ucsc Sep 11, 2024

Choose a reason for hiding this comment

hannes-ucsc Sep 11, 2024

Choose a reason for hiding this comment

dsotirho-ucsc commented Sep 11, 2024

hannes-ucsc left a comment

Choose a reason for hiding this comment

hannes-ucsc Sep 13, 2024

Choose a reason for hiding this comment

hannes-ucsc Sep 13, 2024

Choose a reason for hiding this comment

hannes-ucsc left a comment

Choose a reason for hiding this comment

hannes-ucsc commented Sep 13, 2024

Security design review

dsotirho-ucsc commented Apr 26, 2024 •

edited

Loading

codecov bot commented Apr 29, 2024 •

edited

Loading

coveralls commented Apr 29, 2024 •

edited

Loading

dsotirho-ucsc commented Sep 9, 2024 •

edited

Loading