progress in fixing tests

loculus-project · Jan 23, 2025 · 19959ca · 19959ca
1 parent fea3e3a
commit 19959ca
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Showing 3 changed files with 77 additions and 7 deletions.
diff --git a/backend/src/main/kotlin/org/loculus/backend/service/debug/DeleteSequenceDataService.kt b/backend/src/main/kotlin/org/loculus/backend/service/debug/DeleteSequenceDataService.kt
@@ -2,6 +2,7 @@ package org.loculus.backend.service.debug
 
 import org.jetbrains.exposed.sql.deleteAll
 import org.jetbrains.exposed.sql.insert
+import org.loculus.backend.config.BackendConfig
 import org.loculus.backend.service.datauseterms.DataUseTermsTable
 import org.loculus.backend.service.submission.CurrentProcessingPipelineTable
 import org.loculus.backend.service.submission.MetadataUploadAuxTable
@@ -13,7 +14,7 @@ import org.springframework.stereotype.Component
 import org.springframework.transaction.annotation.Transactional
 
 @Component
-class DeleteSequenceDataService(private val dateProvider: DateProvider) {
+class DeleteSequenceDataService(private val dateProvider: DateProvider, private val config: BackendConfig) {
     @Transactional
     fun deleteAllSequenceData() {
         SequenceEntriesTable.deleteAll()
@@ -22,9 +23,6 @@ class DeleteSequenceDataService(private val dateProvider: DateProvider) {
         SequenceUploadAuxTable.deleteAll()
         DataUseTermsTable.deleteAll()
         CurrentProcessingPipelineTable.deleteAll()
-        CurrentProcessingPipelineTable.insert {
-            it[versionColumn] = 1
-            it[startedUsingAtColumn] = dateProvider.getCurrentDateTime()
-        }
+        CurrentProcessingPipelineTable.setV1ForOrganismsIfNotExist(config.organisms.keys, dateProvider.getCurrentDateTime())
     }
 }
diff --git a/backend/src/main/resources/db/migration/V1.10__pipeline_version_per_organism.sql b/backend/src/main/resources/db/migration/V1.10__pipeline_version_per_organism.sql
@@ -29,3 +29,71 @@ DROP CONSTRAINT current_processing_pipeline_pkey;
 ALTER TABLE current_processing_pipeline
 ADD CONSTRAINT current_processing_pipeline_pkey PRIMARY KEY (organism, version);
 
+
+
+
+drop view if exists external_metadata_view cascade;
+
+create view external_metadata_view as
+select
+    cpd.accession,
+    cpd.version,
+    all_external_metadata.updated_metadata_at,
+    -- Combines metadata from preprocessed data with any external metadata updates
+    -- If there's no external metadata, just use the preprocessed data's metadata
+    -- If there is external metadata, merge it with preprocessed data (external takes precedence)
+    case
+        when all_external_metadata.external_metadata is null then
+            jsonb_build_object('metadata', (cpd.processed_data->'metadata'))
+        else
+            jsonb_build_object(
+                'metadata',
+                (cpd.processed_data->'metadata') || all_external_metadata.external_metadata
+            )
+    end as joint_metadata
+from
+    (
+        -- Get only the preprocessed data for the current pipeline version
+        select * from sequence_entries_preprocessed_data
+        where pipeline_version = (select version from current_processing_pipeline
+                                  where organism = (
+                                      select organism from sequence_entries se
+                                      where se.accession = sequence_entries_preprocessed_data.accession
+                                      and se.version = sequence_entries_preprocessed_data.version
+                                  ))
+    ) cpd
+    left join all_external_metadata on
+        all_external_metadata.accession = cpd.accession
+        and all_external_metadata.version = cpd.version;
+
+create view sequence_entries_view as
+select
+    se.*,
+    sepd.started_processing_at,
+    sepd.finished_processing_at,
+    sepd.processed_data as processed_data,
+    sepd.processed_data || em.joint_metadata as joint_metadata,
+    sepd.errors,
+    sepd.warnings,
+    case
+        when se.released_at is not null then 'APPROVED_FOR_RELEASE'
+        when se.is_revocation then 'AWAITING_APPROVAL'
+        when sepd.processing_status = 'IN_PROCESSING' then 'IN_PROCESSING'
+        when sepd.processing_status = 'HAS_ERRORS' then 'HAS_ERRORS'
+        when sepd.processing_status = 'FINISHED' then 'AWAITING_APPROVAL'
+        else 'RECEIVED'
+    end as status
+from
+    sequence_entries se
+    left join sequence_entries_preprocessed_data sepd on
+        se.accession = sepd.accession
+        and se.version = sepd.version
+        and sepd.pipeline_version = (select version from current_processing_pipeline
+                                     where organism = (
+                                         select organism from sequence_entries se
+                                         where se.accession = sepd.accession
+                                         and se.version = sepd.version
+                                     ))
+    left join external_metadata_view em on
+        se.accession = em.accession
+        and se.version = em.version;
diff --git a/backend/src/test/kotlin/org/loculus/backend/controller/EndpointTestExtension.kt b/backend/src/test/kotlin/org/loculus/backend/controller/EndpointTestExtension.kt
@@ -188,8 +188,12 @@ private fun clearDatabaseStatement(): String = """
             $USER_GROUPS_TABLE_NAME,
             $METADATA_UPLOAD_AUX_TABLE_NAME,
             $SEQUENCE_UPLOAD_AUX_TABLE_NAME,
-            $DATA_USE_TERMS_TABLE_NAME 
+            $DATA_USE_TERMS_TABLE_NAME,
+            $CURRENT_PROCESSING_PIPELINE_TABLE_NAME
             cascade;
         alter sequence $ACCESSION_SEQUENCE_NAME restart with 1;
-        update $CURRENT_PROCESSING_PIPELINE_TABLE_NAME set version = 1, started_using_at = now();
+        insert into $CURRENT_PROCESSING_PIPELINE_TABLE_NAME values
+            (1, now(), '$DEFAULT_ORGANISM'),
+            (1, now(), '$OTHER_ORGANISM'),
+            (1, now(), '$ORGANISM_WITHOUT_CONSENSUS_SEQUENCES');
     """