SEAB-6700: Generate automatic DOIs for all new tags #6074
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## hotfix/1.16.6 #6074 +/- ##
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+ Coverage 45.16% 74.49% +29.32%
- Complexity 3414 5510 +2096
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Files 381 381
Lines 19800 19804 +4
Branches 2044 2046 +2
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+ Hits 8943 14753 +5810
+ Misses 10017 4069 -5948
- Partials 840 982 +142
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| @@ -2358,6 +2358,8 @@ public boolean updateAutoDoiGeneration(@Parameter(hidden = true) @Auth User user | |||
| @RequestBody(description = "The request to update DOI generation", required = true, content = @Content(schema = @Schema(implementation = AutoDoiRequest.class))) AutoDoiRequest autoDoiRequest) { | |||
| final Workflow workflow = workflowDAO.findById(workflowId); | |||
| checkNotNullEntry(workflow); | |||
| boolean canChange = canWrite(user, workflow) || isAdmin(user) || isCurator(user); | |||
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Here, we provide access to workflow owners, and maintain admin/curator access, in case we need to patch up a problem by hand.
Per our preferred practices, we are supposed to use the @RolesAllowed annotation to implement admin/curator access. However, what we're trying to do here is allow access a combination of owner users and admins/curators, which our current annotation setup doesn't support. Thus, the code here, instead.
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I lean towards just removing the admin/curator access since we will have a UI toggle for users to control. Another reason is that this endpoint won't be logged as a privileged endpoint and we may eventually forget about its admin/curator access in the future.
| UPDATE apptool SET autogeneratedois = TRUE WHERE NOT archived; | ||
| UPDATE notebook SET autogeneratedois = TRUE WHERE NOT archived; | ||
| UPDATE service SET autogeneratedois = TRUE WHERE NOT archived; | ||
| UPDATE workflow SET autogeneratedois = TRUE WHERE NOT archived; |
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Because we don't have any easy way to determine the provenance of if any existing false values (they could be the initial column value, or they could have been set to false in .dockstore.yml), this code potentially reverts any previous opt-outs. But, an inspection of a recent database dump indicates that the only opt-outs so far are due to our own testing, so we're ok here, I think.
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Description
This PR enables automatic DOI generation for all new tags on all entries except for "old-style" tools. To that end, it:
autoGenerateDoisflag via theautogeneratedoisendpoint, in addition to allowing curators and admins. This will allow us to implement a toggle in the UI for non-.dockstore.ymlentries.enableAutoDoisfield in.dockstore.ymlto be set to eithertrueorfalse.changeSetthat setsautoGenerateDoisto true.autoGenerateDoisproperty totruefor new Workflows, and adjust the data default values similarly.Review Instructions
.dockstore.yml-based Workflow, confirm that the value ofenableAutoDoisistrue..dockstore.ymlworkflow. Confirm that a DOI was automatically generated.enableAutoDoisfield tofalsein the.dockstore.yml. Tag , push, and confirm that a DOI was not automatically generated.enableAutoDoisfield totruein the.dockstore.yml. Tag, push, and confirm that a DOI was automatically generated.Perform a similar test on a manually-registered workflow, in which you change the value of
autoGenerateDoisusing the endpoint, instead of.dockstore.yml.Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-6700
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mvn clean install@RolesAllowedannotation