From 776fbae002f79db8fa22e4663f3cf3e1264eb0af Mon Sep 17 00:00:00 2001 From: Onur Sumer Date: Tue, 20 Aug 2024 12:00:08 -0400 Subject: [PATCH] add unit tests for clinical data counts sql (#10933) --- .../StudyViewMapperClinicalDataCountTest.java | 243 ++++++++++++++++++ .../StudyViewMapperTest.java | 2 - src/test/resources/clickhouse_data.sql | 98 ++++++- 3 files changed, 340 insertions(+), 3 deletions(-) create mode 100644 src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java new file mode 100644 index 00000000000..17847278f9c --- /dev/null +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperClinicalDataCountTest.java @@ -0,0 +1,243 @@ +package org.cbioportal.persistence.mybatisclickhouse; + +import org.cbioportal.model.ClinicalDataCount; +import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig; +import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter; +import org.cbioportal.web.parameter.ClinicalDataFilter; +import org.cbioportal.web.parameter.DataFilterValue; +import org.cbioportal.web.parameter.StudyViewFilter; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase; +import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest; +import org.springframework.context.annotation.Import; +import org.springframework.test.annotation.DirtiesContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit4.SpringRunner; + +import java.math.BigDecimal; +import java.util.Collections; +import java.util.List; + +import static org.junit.Assert.assertEquals; + +@RunWith(SpringRunner.class) +@Import(MyBatisConfig.class) +@DataJpaTest +@DirtiesContext +@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE) +@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class) +public class StudyViewMapperClinicalDataCountTest extends AbstractTestcontainers { + private static final String STUDY_ACC_TCGA = "acc_tcga"; + private static final String STUDY_GENIE_PUB = "study_genie_pub"; + + @Autowired + private StudyViewMapper studyViewMapper; + + @Test + public void getMutationCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + var mutationsCounts = studyViewMapper.getClinicalDataCounts( + studyViewFilter, + CategorizedClinicalDataCountFilter.getBuilder().build(), + false, + List.of("mutation_count"), + Collections.emptyList() + ); + + assertEquals(6, mutationsCounts.size()); + assertEquals(1, findClinicaDataCount(mutationsCounts, "11")); + assertEquals(1, findClinicaDataCount(mutationsCounts, "6")); + assertEquals(2, findClinicaDataCount(mutationsCounts, "4")); + assertEquals(4, findClinicaDataCount(mutationsCounts, "2")); + assertEquals(2, findClinicaDataCount(mutationsCounts, "1")); + // 1 empty string + 1 'NAN' + 11 samples with no data + assertEquals(13, findClinicaDataCount(mutationsCounts, "NA")); + } + + @Test + public void getCenterCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + var categoricalClinicalDataCounts = studyViewMapper.getClinicalDataCounts( + studyViewFilter, + CategorizedClinicalDataCountFilter.getBuilder().build(), + false, + List.of("center"), + Collections.emptyList() + ); + + assertEquals(7, categoricalClinicalDataCounts.size()); + assertEquals(3, findClinicaDataCount(categoricalClinicalDataCounts, "msk")); + assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "dfci")); + assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "chop")); + assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "mda")); + assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ohsu")); + assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ucsf")); + // 1 empty string + 1 'NA' + 11 samples with no data + assertEquals(13, findClinicaDataCount(categoricalClinicalDataCounts, "NA")); + } + + @Test + public void getMutationAndCenterCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + var combinedClinicalDataCounts = studyViewMapper.getClinicalDataCounts( + studyViewFilter, + CategorizedClinicalDataCountFilter.getBuilder().build(), + false, + List.of("mutation_count", "center"), + Collections.emptyList() + ); + + assertEquals(13, combinedClinicalDataCounts.size()); + } + + @Test + public void getAgeCounts() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + var ageCounts = studyViewMapper.getClinicalDataCounts( + studyViewFilter, + CategorizedClinicalDataCountFilter.getBuilder().build(), + false, + List.of("age"), + Collections.emptyList() + ); + + assertAgeCounts(ageCounts); + + // 1 empty string + 1 'NAN' + 1 'N/A' + 1 patient without data + assertEquals(4, findClinicaDataCount(ageCounts, "NA")); + } + + @Test + public void getAgeCountsForMultipleStudies() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB, STUDY_ACC_TCGA)); + + var ageCounts = studyViewMapper.getClinicalDataCounts( + studyViewFilter, + CategorizedClinicalDataCountFilter.getBuilder().build(), + false, + List.of("age"), + Collections.emptyList() + ); + + // everything should be exactly the same as single study (STUDY_GENIE_PUB) filter + // except NA counts + assertAgeCounts(ageCounts); + + // TODO this fails because of a known issue + // (https://github.com/cBioPortal/rfc80-team/issues/39) + // 1 empty string + 1 'NAN' + 1 'N/A' + 1 GENIE_PUB patient without data + 4 ACC_TCGA data without data + // assertEquals(8, findClinicaDataCount(ageCounts, "NA")); + } + + private void assertAgeCounts(List ageCounts) { + assertEquals(14, ageCounts.size()); + + assertEquals(3, findClinicaDataCount(ageCounts, "<18")); + assertEquals(1, findClinicaDataCount(ageCounts, "18")); + assertEquals(1, findClinicaDataCount(ageCounts, "22")); + assertEquals(2, findClinicaDataCount(ageCounts, "42")); + assertEquals(1, findClinicaDataCount(ageCounts, "66")); + assertEquals(1, findClinicaDataCount(ageCounts, "66")); + assertEquals(1, findClinicaDataCount(ageCounts, "68")); + assertEquals(1, findClinicaDataCount(ageCounts, "77")); + assertEquals(1, findClinicaDataCount(ageCounts, "78")); + assertEquals(1, findClinicaDataCount(ageCounts, "79")); + assertEquals(2, findClinicaDataCount(ageCounts, "80")); + assertEquals(2, findClinicaDataCount(ageCounts, "82")); + assertEquals(1, findClinicaDataCount(ageCounts, "89")); + assertEquals(2, findClinicaDataCount(ageCounts, ">89")); + } + + @Test + public void getMutationCountsFilteredByAge() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + // filter patients with age between 20 and 70 + // (there are 5 patients within this range, which are 307..311) + ClinicalDataFilter filter = buildClinicalDataFilter("age", 20, 70); + studyViewFilter.setClinicalDataFilters(List.of(filter)); + + var mutationCountsFiltered = studyViewMapper.getClinicalDataCounts( + studyViewFilter, + CategorizedClinicalDataCountFilter + .getBuilder() + .setPatientNumericalClinicalDataFilters(List.of(filter)) + .build(), + true, + List.of("mutation_count"), + Collections.emptyList() + ); + + assertEquals(3, mutationCountsFiltered.size()); + assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "2")); + assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "1")); + assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "NA")); + } + + @Test + public void getMutationCountsFilteredByAgeWithSpecialValues() { + StudyViewFilter studyViewFilter = new StudyViewFilter(); + studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB)); + + // filter patients with age less than 20 + // (there are 4 patients within this range, which are 301,302,303, and 306) + ClinicalDataFilter filter = buildClinicalDataFilter("age", null, 20); + studyViewFilter.setClinicalDataFilters(List.of(filter)); + + var mutationCountsFiltered = studyViewMapper.getClinicalDataCounts( + studyViewFilter, + CategorizedClinicalDataCountFilter + .getBuilder() + .setPatientNumericalClinicalDataFilters(List.of(filter)) + .build(), + true, + List.of("mutation_count"), + Collections.emptyList() + ); + + // TODO commented out tests below are failing due to a known issue + // (https://github.com/cBioPortal/rfc80-team/issues/32) + // assertEquals(4, mutationCountsFiltered.size()); + // assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "11")); // patient 301 + // assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "6")); // patient 302 + // assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 303 + assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 306 + + // no patients/samples with NA + assertEquals(0, findClinicaDataCount(mutationCountsFiltered, "NA")); + } + + private ClinicalDataFilter buildClinicalDataFilter(String attributeId, Integer start, Integer end) { + DataFilterValue value = new DataFilterValue(); + if (start != null) { + value.setStart(BigDecimal.valueOf(start)); + } + if (end != null) { + value.setEnd(BigDecimal.valueOf(end)); + } + + ClinicalDataFilter filter = new ClinicalDataFilter(); + filter.setAttributeId(attributeId); + filter.setValues(List.of(value)); + + return filter; + } + + private int findClinicaDataCount(List counts, String attrValue) { + var count = counts.stream().filter(c -> c.getValue().equals(attrValue)).findAny().orElse(null); + + return count == null ? 0 : count.getCount(); + } +} diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java index d12e87042dc..fd42e6a80bc 100644 --- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java +++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java @@ -25,7 +25,6 @@ import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.junit4.SpringRunner; -import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; import java.util.List; @@ -236,5 +235,4 @@ public void getSampleTreatmentCounts() { assertEquals(0, sampleTreatmentCounts.size()); } - } \ No newline at end of file diff --git a/src/test/resources/clickhouse_data.sql b/src/test/resources/clickhouse_data.sql index 0b47aedeb0a..51d74dbf92c 100644 --- a/src/test/resources/clickhouse_data.sql +++ b/src/test/resources/clickhouse_data.sql @@ -6,6 +6,7 @@ insert into `reference_genome` values (2, 'human', 'hg38', 'grch38', null, 'http insert into cancer_study (cancer_study_id,cancer_study_identifier,type_of_cancer_id,name,description,public,pmid,citation,groups,status,import_date,reference_genome_id) values(1,'study_tcga_pub','brca','breast invasive carcinoma (tcga, nature 2012)','the cancer genome atlas (tcga) breast invasive carcinoma project. 825 cases.
nature 2012. raw data via the tcga data portal.',1,'23000897,26451490','tcga, nature 2012, ...','su2c-pi3k;public;gdac',0,'2011-12-18 13:17:17+00:00',1); insert into cancer_study (cancer_study_id,cancer_study_identifier,type_of_cancer_id,name,description,public,pmid,citation,groups,status,import_date,reference_genome_id) values(2,'acc_tcga','acc','adrenocortical carcinoma (tcga, provisional)','tcga adrenocortical carcinoma; raw data at the nci.',1,'23000897','tcga, nature 2012','su2c-pi3k;public;gdac',0,'2013-10-12 11:11:15+00:00',1); +insert into cancer_study (cancer_study_id,cancer_study_identifier,type_of_cancer_id,name,description,public,pmid,citation,groups,status,import_date,reference_genome_id) values(3,'study_genie_pub','mixed','GENIE Cohort public','GENIE public','1','','','GENIEPUB;GENIE',0,'2024-04-03 20:12:24.000000',1); insert into cancer_study_tags (cancer_study_id,tags) values(1,'{"analyst": {"name": "jack", "email": "jack@something.com"}, "load id": 35}'); insert into cancer_study_tags (cancer_study_id,tags) values(2,'{"load id": 36}'); @@ -102,6 +103,30 @@ insert into patient (internal_id,stable_id,cancer_study_id) values (15,'tcga-a1- insert into patient (internal_id,stable_id,cancer_study_id) values (16,'tcga-a1-b0sp',2); insert into patient (internal_id,stable_id,cancer_study_id) values (17,'tcga-a1-b0sq',2); insert into patient (internal_id,stable_id,cancer_study_id) values (18,'tcga-a1-a0sb',2); +insert into patient (internal_id,stable_id,cancer_study_id) values (301,'GENIE-TEST-301',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (302,'GENIE-TEST-302',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (303,'GENIE-TEST-303',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (304,'GENIE-TEST-304',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (305,'GENIE-TEST-305',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (306,'GENIE-TEST-306',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (307,'GENIE-TEST-307',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (308,'GENIE-TEST-308',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (309,'GENIE-TEST-309',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (310,'GENIE-TEST-310',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (311,'GENIE-TEST-311',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (312,'GENIE-TEST-312',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (313,'GENIE-TEST-313',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (314,'GENIE-TEST-314',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (315,'GENIE-TEST-315',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (316,'GENIE-TEST-316',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (317,'GENIE-TEST-317',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (318,'GENIE-TEST-318',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (319,'GENIE-TEST-319',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (320,'GENIE-TEST-320',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (321,'GENIE-TEST-321',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (322,'GENIE-TEST-322',3); +insert into patient (internal_id,stable_id,cancer_study_id) values (323,'GENIE-TEST-323',3); + insert into genetic_profile_samples (genetic_profile_id,ordered_sample_list) values(10,'1,2,3,4,5,6,7,8,9,10,11,'); insert into sample (internal_id,stable_id,sample_type,patient_id) values (1,'tcga-a1-a0sb-01','primary solid tumor',1); @@ -123,6 +148,29 @@ insert into sample (internal_id,stable_id,sample_type,patient_id) values (16,'tc insert into sample (internal_id,stable_id,sample_type,patient_id) values (17,'tcga-a1-b0sq-01','primary solid tumor',17); insert into sample (internal_id,stable_id,sample_type,patient_id) values (18,'tcga-a1-a0sb-02','primary solid tumor',1); insert into sample (internal_id,stable_id,sample_type,patient_id) values (19,'tcga-a1-a0sb-01','primary solid tumor',18); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (301,'GENIE-TEST-301-01','primary solid tumor',301); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (302,'GENIE-TEST-302-01','primary solid tumor',302); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (303,'GENIE-TEST-303-01','primary solid tumor',303); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (304,'GENIE-TEST-304-01','primary solid tumor',304); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (305,'GENIE-TEST-305-01','primary solid tumor',305); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (306,'GENIE-TEST-306-01','primary solid tumor',306); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (307,'GENIE-TEST-307-01','primary solid tumor',307); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (308,'GENIE-TEST-308-01','primary solid tumor',308); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (309,'GENIE-TEST-309-01','primary solid tumor',309); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (310,'GENIE-TEST-310-01','primary solid tumor',310); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (311,'GENIE-TEST-311-01','primary solid tumor',311); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (312,'GENIE-TEST-312-01','primary solid tumor',312); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (313,'GENIE-TEST-313-01','primary solid tumor',313); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (314,'GENIE-TEST-314-01','primary solid tumor',314); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (315,'GENIE-TEST-315-01','primary solid tumor',315); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (316,'GENIE-TEST-316-01','primary solid tumor',316); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (317,'GENIE-TEST-317-01','primary solid tumor',317); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (318,'GENIE-TEST-318-01','primary solid tumor',318); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (319,'GENIE-TEST-319-01','primary solid tumor',319); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (320,'GENIE-TEST-320-01','primary solid tumor',320); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (321,'GENIE-TEST-321-01','primary solid tumor',321); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (322,'GENIE-TEST-322-01','primary solid tumor',322); +insert into sample (internal_id,stable_id,sample_type,patient_id) values (323,'GENIE-TEST-323-01','primary solid tumor',323); insert into mutation_event (mutation_event_id,entrez_gene_id,chr,start_position,end_position,reference_allele,tumor_seq_allele,protein_change,mutation_type,ncbi_build,strand,variant_type,db_snp_rs,db_snp_val_status,refseq_mrna_id,codon_change,uniprot_accession,protein_pos_start,protein_pos_end,canonical_transcript,keyword) values (2038,672,'17',41244748,41244748,'g','a','q934*','nonsense_mutation','37','+','snp','rs80357223','unknown','nm_007294','c.(2800-2802)cag>tag','p38398',934,934,1,'brca1 truncating'); @@ -336,6 +384,40 @@ insert into clinical_patient (internal_id,attr_id,attr_value) values (15,'dfs_st insert into clinical_patient (internal_id,attr_id,attr_value) values (15,'os_months','12.3'); insert into clinical_patient (internal_id,attr_id,attr_value) values (15,'os_status','0:living'); insert into clinical_patient (internal_id,attr_id,attr_value) values (18,'retrospective_collection','no'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (301,'center','msk'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (302,'center','msk'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (303,'center','msk'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (304,'center','dfci'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (305,'center','dfci'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (306,'center','chop'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (307,'center','chop'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (308,'center','mda'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (309,'center','ohsu'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (310,'center','ucsf'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (311,'center','NA'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (312,'center',''); +insert into clinical_patient (internal_id,attr_id,attr_value) values (301,'age','<18'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (302,'age','<18'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (303,'age','<18'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (304,'age','>89'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (305,'age','>89'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (306,'age','18'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (307,'age','22'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (308,'age','42'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (309,'age','42'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (310,'age','66'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (311,'age','68'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (312,'age','77'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (313,'age','78'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (314,'age','79'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (315,'age','80'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (316,'age','80'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (317,'age','82'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (318,'age','82'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (319,'age','89'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (320,'age','N/A'); +insert into clinical_patient (internal_id,attr_id,attr_value) values (321,'age',''); +insert into clinical_patient (internal_id,attr_id,attr_value) values (322,'age','NAN'); insert into clinical_sample (internal_id,attr_id,attr_value) values (1,'other_sample_id','5c631ce8-f96a-4c35-a459-556fc4ab21e1'); insert into clinical_sample (internal_id,attr_id,attr_value) values (1,'days_to_collection','276'); @@ -348,7 +430,18 @@ insert into clinical_sample (internal_id,attr_id,attr_value) values (2,'sample_t insert into clinical_sample (internal_id,attr_id,attr_value) values (15,'other_sample_id','91e7f41c-17b3-4724-96ef-d3c207b964e1'); insert into clinical_sample (internal_id,attr_id,attr_value) values (15,'days_to_collection','111'); insert into clinical_sample (internal_id,attr_id,attr_value) values (19,'days_to_collection','111'); - +insert into clinical_sample (internal_id,attr_id,attr_value) values (301,'mutation_count','11'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (302,'mutation_count','6'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (303,'mutation_count','4'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (304,'mutation_count','4'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (305,'mutation_count','2'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (306,'mutation_count','2'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (307,'mutation_count','2'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (308,'mutation_count','2'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (309,'mutation_count','1'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (310,'mutation_count','1'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (311,'mutation_count','NAN'); +insert into clinical_sample (internal_id,attr_id,attr_value) values (312,'mutation_count',''); insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('retrospective_collection','tissue retrospective collection indicator','text indicator for the time frame of tissue procurement,indicating that the tissue was obtained and stored prior to the initiation of the project.','string',1,'1',1); insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('prospective_collection','tissue prospective collection indicator','text indicator for the time frame of tissue procurement,indicating that the tissue was procured in parallel to the project.','string',1,'1',1); @@ -378,6 +471,9 @@ insert into clinical_attribute_meta (attr_id,display_name,description,datatype,p insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('oct_embedded','oct embedded','oct embedded','string',0,'1',2); insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('pathology_report_file_name','pathology report file name','pathology report file name','string',0,'1',2); insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('sample_type','sample type','the type of sample (i.e.,normal,primary,met,recurrence).','string',0,'1',2); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('mutation_count','mutaiton count','mutation count','number',0,'30',3); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('age','age at metastatic diagnosis (years)','age at metastatic diagnosis (years)','number',1,'3',3); +insert into clinical_attribute_meta (attr_id,display_name,description,datatype,patient_attribute,priority,cancer_study_id) values ('center','center','center of sequencing','string',1,'1',3); -- add genes, genetic entities and structural variants for structural_variant insert into genetic_entity (id,entity_type) values(21,'gene');