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Fix ability to see/add users in UI when there are not yet any organisms #2666

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Merged
merged 3 commits into from
Apr 29, 2025
Merged

Fix ability to see/add users in UI when there are not yet any organisms #2666

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72c19c5
Fix: see/add users in the UI when no organism
garrettjstevens Mar 17, 2025
897c7c6
Fix stuck at first loading with no organisms
garrettjstevens Apr 18, 2025
e0c1f6c
Don't use retired ubuntu image on CI
garrettjstevens Apr 18, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/python-apollo.yml
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Expand Up @@ -6,7 +6,7 @@ jobs:
test-python-apollo:
name: test-python-apollo

runs-on: ubuntu-20.04
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.9]
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8 changes: 5 additions & 3 deletions grails-app/controllers/org/bbop/apollo/UserController.groovy
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Expand Up @@ -295,9 +295,11 @@ class UserController {

UserOrganismPreference uop = preferenceService.getCurrentOrganismPreferenceInDB(dataObject.getString(FeatureStringEnum.CLIENT_TOKEN.value))

uop.nativeTrackList = dataObject.get("tracklist")
uop.save(flush: true)
log.info "Added userOrganismPreference ${uop.nativeTrackList}"
if (uop){
uop.nativeTrackList = dataObject.get("tracklist")
uop.save(flush: true)
log.info "Added userOrganismPreference ${uop.nativeTrackList}"
}
render new JSONObject() as JSON
}
catch (Exception e) {
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2 changes: 1 addition & 1 deletion grails-app/services/org/bbop/apollo/PermissionService.groovy
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Expand Up @@ -624,7 +624,7 @@ class PermissionService {
organism = organism ?: preferenceService.getCurrentOrganismPreferenceInDB(clientToken)?.organism
}
// don't set the preferences if it is coming off a script
if (clientToken != FeatureStringEnum.IGNORE.value) {
if (clientToken != FeatureStringEnum.IGNORE.value && organism) {
preferenceService.setCurrentOrganism(getCurrentUser(), organism, clientToken)
}
if(organism){
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9 changes: 7 additions & 2 deletions grails-app/services/org/bbop/apollo/PreferenceService.groovy
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Expand Up @@ -617,7 +617,11 @@ class PreferenceService {
UserOrganismPreferenceDTO preference = getSessionPreference(clientToken)
preference = preference ?: getSavingPreferences(user, sequenceName, clientToken)
log.debug "found in-memory preference: ${preference ? preference as JSON : null}"
return preference ?: getDTOFromPreference(getCurrentOrganismPreferenceInDB(user, sequenceName, clientToken))
UserOrganismPreference pref = getCurrentOrganismPreferenceInDB(user, sequenceName, clientToken)
if (pref) {
return getDTOFromPreference(pref)
}
return preference
}

def getSavingPreferences(User user, String sequenceName, String clientToken) {
Expand Down Expand Up @@ -700,7 +704,8 @@ class PreferenceService {
organism = Organism.first()
}
if (!organism) {
throw new PermissionException("User does not have permission for any organisms.")
log.warn("Not able to get organism preference")
return null
}

// sequence = sequence ?: Sequence.findByOrganism(organism, [sort: "end", order: "desc", max: 1])
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