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feat(backend): adapt validation for other endpoints
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 * technical endpoints not changed
 * get sequences of user and stream data to edit: needs decision on how it should look like
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@TobiasKampmann
TobiasKampmann committed Dec 22, 2023
1 parent 4a54882 commit bda0dbf
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Showing 28 changed files with 454 additions and 433 deletions.
38 changes: 26 additions & 12 deletions backend/src/main/kotlin/org/pathoplexus/backend/controller/GroupManagementController.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ import org.springframework.web.bind.annotation.DeleteMapping
import org.springframework.web.bind.annotation.GetMapping
import org.springframework.web.bind.annotation.PathVariable
import org.springframework.web.bind.annotation.PostMapping
import org.springframework.web.bind.annotation.RequestBody
import org.springframework.web.bind.annotation.ResponseStatus
import org.springframework.web.bind.annotation.RestController

Expand All @@ -23,19 +24,24 @@ class GroupManagementController(

@Operation(description = "Create a new Group. The user creating the group will be added to the group.")
@ResponseStatus(HttpStatus.NO_CONTENT)
@PostMapping("/groups/{newGroupName}", produces = [MediaType.APPLICATION_JSON_VALUE])
@PostMapping("/groups", produces = [MediaType.APPLICATION_JSON_VALUE])
fun createNewGroup(
@UsernameFromJwt username: String,
@Parameter(
description = "The name of the newly created group",
) @PathVariable newGroupName: String,
) = groupManagementDatabaseService.createNewGroup(newGroupName, username)
) @RequestBody group: GroupName,
) = groupManagementDatabaseService.createNewGroup(group.groupName, username)

@Operation(description = "Get details of a group that the user is a member of.")
@ResponseStatus(HttpStatus.OK)
@GetMapping("/groups/{detailsOfGroupName}", produces = [MediaType.APPLICATION_JSON_VALUE])
fun getUsersOfGroup(@UsernameFromJwt username: String, @PathVariable detailsOfGroupName: String): GroupDetails {
return groupManagementDatabaseService.getDetailsOfGroup(detailsOfGroupName, username)
@GetMapping("/groups/{groupName}", produces = [MediaType.APPLICATION_JSON_VALUE])
fun getUsersOfGroup(
@UsernameFromJwt username: String,
@Parameter(
description = "The name of the group to get details of.",
) @PathVariable groupName: String,
): GroupDetails {
return groupManagementDatabaseService.getDetailsOfGroup(groupName, username)
}

@Operation(description = "Get all groups the user is a member of.")
Expand All @@ -54,27 +60,35 @@ class GroupManagementController(

@Operation(description = "Add user to a group.")
@ResponseStatus(HttpStatus.NO_CONTENT)
@PostMapping("/groups/{groupName}/users/{usernameToAdd}", produces = [MediaType.APPLICATION_JSON_VALUE])
@PostMapping("/groups/{groupName}/users", produces = [MediaType.APPLICATION_JSON_VALUE])
fun addUserToGroup(
@UsernameFromJwt groupMember: String,
@Parameter(
description = "The group name the user should be added to.",
) @PathVariable groupName: String,
@Parameter(
description = "The user name that should be added to the group.",
) @PathVariable usernameToAdd: String,
) = groupManagementDatabaseService.addUserToGroup(groupMember, groupName, usernameToAdd)
) @RequestBody usernameToAdd: Username,
) = groupManagementDatabaseService.addUserToGroup(groupMember, groupName, usernameToAdd.username)

@Operation(description = "Remove user from a group.")
@ResponseStatus(HttpStatus.NO_CONTENT)
@DeleteMapping("/groups/{groupName}/users/{usernameToRemove}", produces = [MediaType.APPLICATION_JSON_VALUE])
@DeleteMapping("/groups/{groupName}/users", produces = [MediaType.APPLICATION_JSON_VALUE])
fun removeUserFromGroup(
@UsernameFromJwt groupMember: String,
@Parameter(
description = "The group name the user should be removed from.",
) @PathVariable groupName: String,
@Parameter(
description = "The user name that should be removed from the group.",
) @PathVariable usernameToRemove: String,
) = groupManagementDatabaseService.removeUserFromGroup(groupMember, groupName, usernameToRemove)
) @RequestBody usernameToRemove: Username,
) = groupManagementDatabaseService.removeUserFromGroup(groupMember, groupName, usernameToRemove.username)

data class GroupName(
val groupName: String,
)

data class Username(
val username: String,
)
}
84 changes: 43 additions & 41 deletions backend/src/main/kotlin/org/pathoplexus/backend/controller/SubmissionController.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -18,9 +18,9 @@ import org.pathoplexus.backend.api.SubmissionIdMapping
import org.pathoplexus.backend.api.SubmittedProcessedData
import org.pathoplexus.backend.api.UnprocessedData
import org.pathoplexus.backend.model.ReleasedDataModel
import org.pathoplexus.backend.model.SubmissionParams
import org.pathoplexus.backend.model.SubmitModel
import org.pathoplexus.backend.service.submission.DatabaseService
import org.pathoplexus.backend.service.submission.UploadType
import org.pathoplexus.backend.utils.Accession
import org.pathoplexus.backend.utils.IteratorStreamer
import org.springframework.http.HttpHeaders
Expand Down Expand Up @@ -64,15 +64,39 @@ class SubmissionController(
@Parameter(description = GROUP_DESCRIPTION) @RequestParam groupName: String,
@Parameter(description = METADATA_FILE_DESCRIPTION) @RequestParam metadataFile: MultipartFile,
@Parameter(description = SEQUENCE_FILE_DESCRIPTION) @RequestParam sequenceFile: MultipartFile,
): List<SubmissionIdMapping> = submitModel.processSubmissions(
UUID.randomUUID().toString(),
metadataFile,
sequenceFile,
username,
groupName,
organism,
UploadType.ORIGINAL,
)
): List<SubmissionIdMapping> {
val params = SubmissionParams.OriginalSubmissionParams(
organism,
username,
metadataFile,
sequenceFile,
groupName,
)
return submitModel.processSubmissions(UUID.randomUUID().toString(), params)
}

@Operation(description = REVISE_DESCRIPTION)
@ApiResponse(responseCode = "200", description = REVISE_RESPONSE_DESCRIPTION)
@PostMapping("/revise", consumes = ["multipart/form-data"])
fun revise(
@PathVariable @Valid
organism: Organism,
@UsernameFromJwt username: String,
@Parameter(
description = REVISED_METADATA_FILE_DESCRIPTION,
) @RequestParam metadataFile: MultipartFile,
@Parameter(
description = SEQUENCE_FILE_DESCRIPTION,
) @RequestParam sequenceFile: MultipartFile,
): List<SubmissionIdMapping> {
val params = SubmissionParams.RevisionSubmissionParams(
organism,
username,
metadataFile,
sequenceFile,
)
return submitModel.processSubmissions(UUID.randomUUID().toString(), params)
}

@Operation(description = EXTRACT_UNPROCESSED_DATA_DESCRIPTION)
@ApiResponse(
Expand Down Expand Up @@ -158,6 +182,9 @@ class SubmissionController(
@PathVariable @Valid
organism: Organism,
@UsernameFromJwt username: String,
@Parameter(
description = GROUP_DESCRIPTION,
) @RequestParam groupName: String,
@Max(
value = MAX_EXTRACTED_SEQUENCE_ENTRIES,
message = "You can extract at max $MAX_EXTRACTED_SEQUENCE_ENTRIES sequence entries at once.",
Expand All @@ -167,9 +194,7 @@ class SubmissionController(
val headers = HttpHeaders()
headers.contentType = MediaType.parseMediaType(MediaType.APPLICATION_NDJSON_VALUE)

val streamBody = StreamingResponseBody { outputStream ->
databaseService.streamDataToEdit(username, numberOfSequenceEntries, outputStream, organism)
}
val streamBody = databaseService.streamDataToEdit(username, groupName, numberOfSequenceEntries, organism)

return ResponseEntity(streamBody, headers, HttpStatus.OK)
}
Expand All @@ -182,8 +207,11 @@ class SubmissionController(
@PathVariable accession: Accession,
@PathVariable version: Long,
@UsernameFromJwt username: String,
): SequenceEntryVersionToEdit =
databaseService.getSequenceEntryVersionToEdit(username, AccessionVersion(accession, version), organism)
): SequenceEntryVersionToEdit = databaseService.getSequenceEntryVersionToEdit(
username,
AccessionVersion(accession, version),
organism,
)

@Operation(description = SUBMIT_EDITED_DATA_DESCRIPTION)
@ResponseStatus(HttpStatus.NO_CONTENT)
Expand Down Expand Up @@ -217,32 +245,6 @@ class SubmissionController(
databaseService.approveProcessedData(username, body.accessionVersions, organism)
}

@Operation(description = REVISE_DESCRIPTION)
@ApiResponse(responseCode = "200", description = REVISE_RESPONSE_DESCRIPTION)
@PostMapping("/revise", consumes = ["multipart/form-data"])
fun revise(
@PathVariable @Valid
organism: Organism,
@UsernameFromJwt username: String,
@Parameter(
description = GROUP_DESCRIPTION,
) @RequestParam groupName: String,
@Parameter(
description = REVISED_METADATA_FILE_DESCRIPTION,
) @RequestParam metadataFile: MultipartFile,
@Parameter(
description = SEQUENCE_FILE_DESCRIPTION,
) @RequestParam sequenceFile: MultipartFile,
): List<SubmissionIdMapping> = submitModel.processSubmissions(
UUID.randomUUID().toString(),
metadataFile,
sequenceFile,
username,
groupName,
organism,
UploadType.REVISION,
)

@Operation(description = REVOKE_DESCRIPTION)
@PostMapping("/revoke", produces = [MediaType.APPLICATION_JSON_VALUE])
fun revoke(
Expand Down
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