UIP-47: update clients #3556

ialarmedalien · 2024-06-05T16:30:09Z

Description of PR purpose/changes

Commit 1:

uses full paths for py modules instead of relative (commit 1)

Commit 2:

updates the clients where appropriate using kb-sdk install <client_name>
moves all the clients that the narrative uses to an installed_clients directory and removes all the duplicated base client.py files.
removes old directories

Commit 3:

updates some python deps that dependabot chose not to reveal until yesterday

Jira Ticket / Issue

Related Jira ticket: https://kbase-jira.atlassian.net/browse/UIP-47

Added the Jira Ticket to the title of the PR (e.g. DATAUP-69 Adds a PR template)

Testing Instructions

Details for how to test the PR:

Tests pass locally and in GitHub Actions
Changes available by spinning up a local narrative and navigating to X to see Y

Dev Checklist:

Updating Version and Release Notes (if applicable)

N/A

Version has been bumped for each release
Release notes have been updated for each release (and during the merge of feature branches)

…ingleton directories with the different clients in them.

ialarmedalien · 2024-06-05T16:41:59Z

src/biokbase/installed_clients/CatalogClient.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-


the changes in this file are due to running kb-sdk install catalog - the client has been updated since whenever this file was last touched.

ialarmedalien · 2024-06-05T16:43:42Z

src/biokbase/installed_clients/authclient.py

@@ -0,0 +1,94 @@
+"""


from a freshly generated kbase SDK module

ialarmedalien · 2024-06-05T16:44:28Z

src/biokbase/installed_clients/baseclient.py

-except ImportError:
-    from urlparse import urlparse as _urlparse  # py2
-
+import json


this is actually from a freshly-generated KBase sdk app with some typing stuff added.

ialarmedalien · 2024-06-05T16:46:32Z

src/biokbase/narrative/clients.py

+from biokbase.installed_clients.CatalogClient import Catalog
+from biokbase.installed_clients.execution_engine2Client import execution_engine2
+from biokbase.installed_clients.NarrativeMethodStoreClient import NarrativeMethodStore
+from biokbase.installed_clients.ServiceClient import Client as ServiceClient
+from biokbase.installed_clients.WorkspaceClient import Workspace


all clients now in the installed_clients folder

codecov · 2024-06-05T16:46:52Z

Codecov Report

Attention: Patch coverage is 97.50000% with 1 line in your changes missing coverage. Please review.

Project coverage is 29.70%. Comparing base (f56890d) to head (aa67a64).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #3556      +/-   ##
===========================================
+ Coverage    29.69%   29.70%   +0.01%     
===========================================
  Files          496      496              
  Lines        50444    50444              
===========================================
+ Hits         14977    14984       +7     
+ Misses       35467    35460       -7

Files	Coverage Δ
src/biokbase/auth.py	`100.00% <100.00%> (ø)`
src/biokbase/narrative/clients.py	`100.00% <100.00%> (ø)`
src/biokbase/narrative/common/exceptions.py	`68.75% <100.00%> (+1.00%)`	⬆️
src/biokbase/narrative/common/kblogging.py	`82.67% <100.00%> (-0.27%)`	⬇️
src/biokbase/narrative/common/narrative_logger.py	`100.00% <100.00%> (ø)`
src/biokbase/narrative/common/narrative_ref.py	`95.12% <100.00%> (-0.12%)`	⬇️
src/biokbase/narrative/common/url_config.py	`80.76% <100.00%> (ø)`
...rc/biokbase/narrative/contents/kbasecheckpoints.py	`84.61% <100.00%> (ø)`
src/biokbase/narrative/contents/kbasewsmanager.py	`26.63% <100.00%> (ø)`
src/biokbase/narrative/contents/narrativeio.py	`30.45% <100.00%> (-0.52%)`	⬇️
... and 7 more

... and 4 files with indirect coverage changes

Continue to review full report in Codecov by Sentry.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 8c1a4a7...aa67a64. Read the comment docs.

ialarmedalien · 2024-06-05T16:46:53Z

src/biokbase/narrative/clients.py

    """Retrieve the client for a KBase service."""
    return __init_client(client_name, token=token)


-def __init_client(client_name, token=None):
+@cache


cache the clients

ialarmedalien · 2024-06-05T16:48:55Z

src/scripts/py2_code_hunter/py2_code_hunter.py

@@ -9,8 +9,8 @@
 from lib2to3.refactor import RefactoringTool, get_fixers_from_package


Is this script and its test even worth keeping any more?

I hope not!

It was really used to notify users who had py2 code in their narratives way back before some major Python / IPython version switchover to make those fail. I think it hit single-digits of non-KBase-staff.

ialarmedalien · 2024-06-05T16:49:18Z

src/scripts/fix_ws_metadata/fix_workspace_info.py

@@ -12,8 +12,8 @@
 import sys


is this script still a going concern?

No, I don't think so. We should put it somewhere for reference, but it doesn't need to be maintained.

ialarmedalien · 2024-06-05T16:51:39Z

src/biokbase/installed_clients/baseclient.py

-        + "&fields=token"
-    )
-    ret = _requests.post(auth_svc, data=body, allow_redirects=True)
+    body = "user_id=" + quote(user_id) + "&password=" + quote(password) + "&fields=token"


requests.utils.quote is just a wrapper around url lib.parse.quote, so use the latter as the former has been deprecated.

ialarmedalien · 2024-06-05T16:55:20Z

src/biokbase/narrative/common/exceptions.py


-from biokbase.workspace.baseclient import ServerError
+from biokbase.installed_clients.baseclient import ServerError


new location for the base client file for importing ServerErrors from

ialarmedalien · 2024-06-05T16:56:44Z

src/biokbase/narrative/common/narrative_ref.py

-from biokbase.workspace.baseclient import ServerError
-
-from .exceptions import WorkspaceError
+from biokbase.narrative.common.exceptions import ServerError, WorkspaceError


get server errors from the kbase exceptions file so that if (for whatever reason) the ServerErrors got moved, the import statement in exceptions.py could be updated and nothing else would need to be touched.

Yup, that's the right way.

adding some python updates that didn't make it into the previous PR updating that accursed release notes file

sonarcloud · 2024-06-05T21:41:55Z

Quality Gate failed

Failed conditions
2 Security Hotspots

See analysis details on SonarCloud

briehl

Nice work on the consolidation and updates.

briehl · 2024-06-06T19:57:35Z

src/biokbase/narrative/common/narrative_ref.py

-from biokbase.workspace.baseclient import ServerError
-
-from .exceptions import WorkspaceError
+from biokbase.narrative.common.exceptions import ServerError, WorkspaceError


Yup, that's the right way.

briehl · 2024-06-06T20:01:52Z

src/scripts/fix_ws_metadata/fix_workspace_info.py

@@ -12,8 +12,8 @@
 import sys


No, I don't think so. We should put it somewhere for reference, but it doesn't need to be maintained.

briehl · 2024-06-06T20:02:05Z

src/scripts/py2_code_hunter/py2_code_hunter.py

@@ -9,8 +9,8 @@
 from lib2to3.refactor import RefactoringTool, get_fixers_from_package


I hope not!

briehl · 2024-06-06T20:03:12Z

src/scripts/py2_code_hunter/py2_code_hunter.py

@@ -9,8 +9,8 @@
 from lib2to3.refactor import RefactoringTool, get_fixers_from_package


It was really used to notify users who had py2 code in their narratives way back before some major Python / IPython version switchover to make those fail. I think it hit single-digits of non-KBase-staff.

ialarmedalien added 2 commits June 5, 2024 09:24

Use full paths to modules

174e0cb

move clients to 'installed_clients' dir and update code. Delete old s…

900d25a

…ingleton directories with the different clients in them.

ialarmedalien requested a review from briehl June 5, 2024 16:30

ialarmedalien self-assigned this Jun 5, 2024

ialarmedalien commented Jun 5, 2024

View reviewed changes

src/biokbase/installed_clients/authclient.py

@@ -0,0 +1,94 @@

"""

Copy link

Collaborator Author

ialarmedalien Jun 5, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

from a freshly generated kbase SDK module

ialarmedalien commented Jun 5, 2024

View reviewed changes

Cache clients

aa67a64

adding some python updates that didn't make it into the previous PR updating that accursed release notes file

ialarmedalien force-pushed the update_clients branch from a5916dc to aa67a64 Compare June 5, 2024 21:40

briehl approved these changes Jun 6, 2024

View reviewed changes

ialarmedalien merged commit b401562 into develop Jun 7, 2024
7 of 10 checks passed

ialarmedalien deleted the update_clients branch June 7, 2024 12:43

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

UIP-47: update clients #3556

UIP-47: update clients #3556

ialarmedalien commented Jun 5, 2024 •

edited

Loading

ialarmedalien Jun 5, 2024

ialarmedalien Jun 5, 2024

ialarmedalien Jun 5, 2024

ialarmedalien Jun 5, 2024

codecov bot commented Jun 5, 2024 •

edited

Loading

ialarmedalien Jun 5, 2024

ialarmedalien Jun 5, 2024

briehl Jun 6, 2024

briehl Jun 6, 2024

ialarmedalien Jun 5, 2024

briehl Jun 6, 2024

ialarmedalien Jun 5, 2024

ialarmedalien Jun 5, 2024

ialarmedalien Jun 5, 2024

briehl Jun 6, 2024

sonarcloud bot commented Jun 5, 2024

briehl left a comment

briehl Jun 6, 2024

briehl Jun 6, 2024

briehl Jun 6, 2024

briehl Jun 6, 2024

		@@ -9,8 +9,8 @@
		from lib2to3.refactor import RefactoringTool, get_fixers_from_package


		from biokbase.workspace.baseclient import ServerError
		from biokbase.installed_clients.baseclient import ServerError

UIP-47: update clients #3556

UIP-47: update clients #3556

Conversation

ialarmedalien commented Jun 5, 2024 • edited Loading

Description of PR purpose/changes

Jira Ticket / Issue

Testing Instructions

Dev Checklist:

Updating Version and Release Notes (if applicable)

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

codecov bot commented Jun 5, 2024 • edited Loading

Codecov Report

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

sonarcloud bot commented Jun 5, 2024

Quality Gate failed

briehl left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

ialarmedalien commented Jun 5, 2024 •

edited

Loading

codecov bot commented Jun 5, 2024 •

edited

Loading