From 852cc971a07e730487b6e730f00a88db9e1817dd Mon Sep 17 00:00:00 2001 From: nkumar2 Date: Fri, 10 May 2024 15:58:19 +0100 Subject: [PATCH] review comments incorporated --- .../jobs/MonotonicAccessionRecoveryAgentCategoryRSTest.java | 6 +++--- ...onotonic-accession-recovery-agent-category-rs.properties | 2 +- ...onic_accession_recovery_agent_category_rs_test_data.sql} | 0 .../MonotonicAccessionRecoveryAgentCategorySSTest.java | 6 +++--- ...onotonic-accession-recovery-agent-category-ss.properties | 2 +- ...onic_accession_recovery_agent_category_ss_test_data.sql} | 0 6 files changed, 8 insertions(+), 8 deletions(-) rename eva-accession-clustering/src/test/resources/test-data/{monotonic_accession_recovery_agent_test_data.sql => monotonic_accession_recovery_agent_category_rs_test_data.sql} (100%) rename eva-accession-pipeline/src/test/resources/test-data/{monotonic_accession_recovery_agent_test_data.sql => monotonic_accession_recovery_agent_category_ss_test_data.sql} (100%) diff --git a/eva-accession-clustering/src/test/java/uk/ac/ebi/eva/accession/clustering/configuration/batch/jobs/MonotonicAccessionRecoveryAgentCategoryRSTest.java b/eva-accession-clustering/src/test/java/uk/ac/ebi/eva/accession/clustering/configuration/batch/jobs/MonotonicAccessionRecoveryAgentCategoryRSTest.java index 1906be0f2..d24baf00e 100644 --- a/eva-accession-clustering/src/test/java/uk/ac/ebi/eva/accession/clustering/configuration/batch/jobs/MonotonicAccessionRecoveryAgentCategoryRSTest.java +++ b/eva-accession-clustering/src/test/java/uk/ac/ebi/eva/accession/clustering/configuration/batch/jobs/MonotonicAccessionRecoveryAgentCategoryRSTest.java @@ -84,7 +84,7 @@ private void initializeMongoDbWithUncommittedAccessions() { clusteredVariantEntityList.add(entity); } - // Entries for 2nd block + // Entries for 2nd block - Missing 5 RS (3000000035l - 3000000039l) for (long i = 3000000030l; i <= 3000000034l; i++) { ClusteredVariant model = new ClusteredVariant("assembly", 1111, "contig", 100, VariantType.SNV, false, LocalDateTime.now()); @@ -119,7 +119,7 @@ private void initializeMongoDbWithUncommittedAccessions() { private void verifyInitialDBState() { // Initial state of Contiguous Id Block DB is 5 blocks are present but their "last_committed" is not updated - // (Initialized using "resources/test-data/monotonic_accession_recovery_agent_test_data.sql") + // (Initialized using "resources/test-data/monotonic_accession_recovery_agent_category_rs_test_data.sql") // block id first value last value last committed reserved last_updated_timestamp | remarks // 1 3000000000 3000000029 2999999999 true 1970-01-01 00:00:00 | should be recovered @@ -129,7 +129,7 @@ private void verifyInitialDBState() { // 5 3000000120 3000000149 3000000119 true 2099-01-01 00:00:00 | should not be recovered // Mongo DB - // 85 accessions have been used in mongoDB but are not reflected in the block allocation table + // 95 accessions have been used in mongoDB but are not reflected in the block allocation table // 30 accessions belong to 1st block (3000000000 to 3000000029), // 25 to the 2nd block (3000000030 to 300000034 and 3000000040 to 3000000059) // 30 to the 3rd block (3000000060 to 3000000089) diff --git a/eva-accession-clustering/src/test/resources/monotonic-accession-recovery-agent-category-rs.properties b/eva-accession-clustering/src/test/resources/monotonic-accession-recovery-agent-category-rs.properties index 66c32a40a..c07f9478f 100644 --- a/eva-accession-clustering/src/test/resources/monotonic-accession-recovery-agent-category-rs.properties +++ b/eva-accession-clustering/src/test/resources/monotonic-accession-recovery-agent-category-rs.properties @@ -5,7 +5,7 @@ spring.datasource.url=jdbc:hsqldb:mem:db;sql.syntax_pgs=true;DB_CLOSE_DELAY=-1 spring.datasource.username=SA spring.datasource.password= spring.datasource.schema=test-data/contiguous_id_blocks_schema.sql -spring.datasource.data=test-data/monotonic_accession_recovery_agent_test_data.sql +spring.datasource.data=test-data/monotonic_accession_recovery_agent_category_rs_test_data.sql spring.jpa.hibernate.ddl-auto=update parameters.vcf=src/test/resources/input-files/vcf/aggregated_accessioned.vcf.gz diff --git a/eva-accession-clustering/src/test/resources/test-data/monotonic_accession_recovery_agent_test_data.sql b/eva-accession-clustering/src/test/resources/test-data/monotonic_accession_recovery_agent_category_rs_test_data.sql similarity index 100% rename from eva-accession-clustering/src/test/resources/test-data/monotonic_accession_recovery_agent_test_data.sql rename to eva-accession-clustering/src/test/resources/test-data/monotonic_accession_recovery_agent_category_rs_test_data.sql diff --git a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/runner/MonotonicAccessionRecoveryAgentCategorySSTest.java b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/runner/MonotonicAccessionRecoveryAgentCategorySSTest.java index 130d65bf1..4c49a556e 100644 --- a/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/runner/MonotonicAccessionRecoveryAgentCategorySSTest.java +++ b/eva-accession-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/runner/MonotonicAccessionRecoveryAgentCategorySSTest.java @@ -80,7 +80,7 @@ private void initializeMongoDbWithUncommittedAccessions() { submittedVariantEntityList.add(entity); } - // Entries for 2nd block + // Entries for 2nd block - Missing 5 RS (3000000035l - 3000000039l) for (long i = 5000000030l; i <= 5000000034l; i++) { SubmittedVariant model = new SubmittedVariant("assembly", 1111, "project", "contig", 100, "A", "T", @@ -123,7 +123,7 @@ private void initializeMongoDbWithUncommittedAccessions() { private void verifyInitialDBState() { // Initial state of Contiguous Id Block DB is 5 blocks are present but their "last_committed" is not updated - // (Initialized using "resources/test-data/monotonic_accession_recovery_agent_test_data.sql") + // (Initialized using "resources/test-data/monotonic_accession_recovery_agent_category_ss_test_data.sql") // block id first value last value last committed reserved last_updated_timestamp | remarks // 1 5000000000 5000000029 4999999999 true 1970-01-01 00:00:00 | should be recovered @@ -133,7 +133,7 @@ private void verifyInitialDBState() { // 5 5000000120 5000000149 5000000119 true 2099-01-01 00:00:00 | should not be recovered // Mongo DB - // 85 accessions have been used in mongoDB but are not reflected in the block allocation table + // 95 accessions have been used in mongoDB but are not reflected in the block allocation table // 30 accessions belong to 1st block (5000000000 to 5000000029), // 25 to the 2nd block (5000000030 to 500000034 and 5000000040 to 5000000059) // 30 to the 3rd block (5000000060 to 5000000089) diff --git a/eva-accession-pipeline/src/test/resources/properties/monotonic-accession-recovery-agent-category-ss.properties b/eva-accession-pipeline/src/test/resources/properties/monotonic-accession-recovery-agent-category-ss.properties index ee85739f7..c250919ae 100644 --- a/eva-accession-pipeline/src/test/resources/properties/monotonic-accession-recovery-agent-category-ss.properties +++ b/eva-accession-pipeline/src/test/resources/properties/monotonic-accession-recovery-agent-category-ss.properties @@ -5,7 +5,7 @@ spring.datasource.url=jdbc:hsqldb:mem:db;sql.syntax_pgs=true;DB_CLOSE_DELAY=-1 spring.datasource.username=SA spring.datasource.password= spring.datasource.schema=test-data/contiguous_id_blocks_schema.sql -spring.datasource.data=test-data/monotonic_accession_recovery_agent_test_data.sql +spring.datasource.data=test-data/monotonic_accession_recovery_agent_category_ss_test_data.sql spring.jpa.hibernate.ddl-auto=update accessioning.submitted.categoryId=test-pipeline-ss diff --git a/eva-accession-pipeline/src/test/resources/test-data/monotonic_accession_recovery_agent_test_data.sql b/eva-accession-pipeline/src/test/resources/test-data/monotonic_accession_recovery_agent_category_ss_test_data.sql similarity index 100% rename from eva-accession-pipeline/src/test/resources/test-data/monotonic_accession_recovery_agent_test_data.sql rename to eva-accession-pipeline/src/test/resources/test-data/monotonic_accession_recovery_agent_category_ss_test_data.sql