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medco-i2b2-cell/src/test/ch/epfl/lca1/medco/loader/MedCoDataLoaderTests.java
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MedCoDataLoaderTests.java
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package ch.epfl.lca1.medco.loader;
import ch.epfl.lca1.medco.ConfiguredTests;
import ch.epfl.lca1.medco.MedCoDataLoader;
import ch.epfl.lca1.medco.i2b2.ont.I2B2ONTCell;
import ch.epfl.lca1.medco.i2b2.pm.UserAuthentication;
import ch.epfl.lca1.medco.loader.clinical.OntologyLoader;
import ch.epfl.lca1.medco.util.exceptions.UnlynxException;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import org.junit.Test;
import java.io.IOException;
/**
* Created by misbach on 16.06.17.
*/
public class MedCoDataLoaderTests extends ConfiguredTests {
@Test
public void testClinicalOntLoader() throws I2B2Exception, UnlynxException {
String[] headers = new String[] {
"sample_id", "patient_id", "test_enc_1", "test enc 2", "some clear1", "clear2", "ency3"
};
DataType[] types = new DataType[] {
DataType.SAMPLE_ID,
DataType.PATIENT_ID,
DataType.ENC,
DataType.ENC,
DataType.CLEAR,
DataType.CLEAR,
DataType.ENC
};
UserAuthentication auth = new UserAuthentication("i2b2demotest", "Demo", "demo", false, 0, "demouser");
OntologyLoader loader = new OntologyLoader(headers, types, "chuv");
loader.parseEntry(new String[]{"22", "333F", "A", "B", "A", "33", "5630"});
loader.parseEntry(new String[]{"22", "33F", "B", "B", "B", "33", "511630"});
loader.parseEntry(new String[]{"223", "33F", "A", "C", "A", "353", "5630"});
loader.parseEntry(new String[]{"22F", "33f3F", "B", "B", "C", "333", "5630"});
loader.parseEntry(new String[]{"22F", "3f33F", "C", "L", "A", "33", "563220"});
loader.loadOntology(new I2B2ONTCell(auth));
}
@Test
public void testClinicalLoader() throws UnlynxException, IOException, I2B2Exception {
String clinicalPath_full = "/home/misbach/repositories/i2b2-core-server-medco/ch.epfl.lca1.medco/testfiles/datasets/full/skcm_broad/data_clinical_skcm_broad.txt",
clinicalPath_part1 = "/home/misbach/repositories/i2b2-core-server-medco/ch.epfl.lca1.medco/testfiles/datasets/full/skcm_broad/data_clinical_skcm_broad_part1.txt",
clinicalPath_part2 = "/home/misbach/repositories/i2b2-core-server-medco/ch.epfl.lca1.medco/testfiles/datasets/full/skcm_broad/data_clinical_skcm_broad_part2.txt",
clinicalPath_part3 = "/home/misbach/repositories/i2b2-core-server-medco/ch.epfl.lca1.medco/testfiles/datasets/full/skcm_broad/data_clinical_skcm_broad_part3.txt";
// --- mapping for the test dataset
//SAMPLE_ID PATIENT_ID AGE DISTANT_METASTASIS_PATHOLOGIC_SPREAD GENDER
// HISTOLOGICAL_SUBTYPE ICD_O_3_HISTOLOGY ICD_O_3_SITE PRETREATMENT_HISTORY
// PRIMARY_TUMOR_PATHOLOGIC_SPREAD PRIOR_DIAGNOSIS RESIDUAL_TUMOR
// TOBACCO_SMOKING_HISTORY_INDICATOR TUMOR_STAGE_2009 OS_STATUS OS_MONTHS
// DFS_STATUS DFS_MONTHS CANCER_TYPE CANCER_TYPE_DETAILED
/*
DataType[] typesClinical = new DataType[]{
DataType.SAMPLE_ID,
DataType.PATIENT_ID,
DataType.CLEAR,
DataType.ENC,
DataType.CLEAR,
DataType.ENC,
DataType.ENC,
DataType.ENC,
DataType.CLEAR,
DataType.CLEAR,
DataType.CLEAR,
DataType.ENC,
DataType.IGNORE,
DataType.ENC,
DataType.CLEAR,
DataType.CLEAR,
DataType.ENC,
DataType.ENC,
DataType.CLEAR,
DataType.IGNORE
};*/
// --- mapping for the skcm_broad dataset
// SAMPLE_ID PATIENT_ID GENDER(C) AGE(C) AGE_AT_PROCUREMENT(C) PRIMARY_DIAGNOSIS(C)
// [PRIMARY_TUMOR_LOCALIZATION_TYPE](S)
// PRIMARY_SITE(C) BRESLOW_DEPTH(C) CANCER_TYPE(C) [CANCER_TYPE_DETAILED](S)
DataType[] typesClinical = new DataType[]{
DataType.SAMPLE_ID,
DataType.PATIENT_ID,
DataType.CLEAR,
DataType.CLEAR,
DataType.CLEAR,
DataType.CLEAR,
DataType.ENC,
DataType.CLEAR,
DataType.CLEAR,
DataType.CLEAR,
DataType.ENC
};
{
loadSrv1Conf();
MedCoDataLoader loader = new MedCoDataLoader("chuv1", "skcm_broad_part1", "i2b2demotest", "Demo", "demo", "demouser");
loader.loadClinicalFileOntology(clinicalPath_full, '\t', '\u0000', 5, typesClinical);
loader.loadClinicalFileData(clinicalPath_part1, '\t', '\u0000', 0, typesClinical);
} {
loadSrv3Conf();
MedCoDataLoader loader = new MedCoDataLoader("chuv2", "skcm_broad_part2", "i2b2demotest", "Demo", "demo", "demouser");
loader.loadClinicalFileOntology(clinicalPath_full, '\t', '\u0000', 5, typesClinical);
loader.loadClinicalFileData(clinicalPath_part2, '\t', '\u0000', 0, typesClinical);
} {
loadSrv5Conf();
MedCoDataLoader loader = new MedCoDataLoader("chuv3", "skcm_broad_part3", "i2b2demotest", "Demo", "demo", "demouser");
loader.loadClinicalFileOntology(clinicalPath_full, '\t', '\u0000', 5, typesClinical);
loader.loadClinicalFileData(clinicalPath_part3, '\t', '\u0000', 0, typesClinical);
}
/*
<ns2:load_data_response>
<upload_id>1</upload_id>
<user_id>demo</user_id>
<data_file_location_uri>/opt/FRC_files/Demo/pdoUploadchuv.xml</data_file_location_uri>
<load_status>COMPLETED</load_status>
<start_date>2017-07-20T16:54:25.121Z</start_date>
<end_date>2017-07-20T16:54:26.761Z</end_date>
<message />
<observation_set inserted_record="847" ignored_record="0" total_record="847" />
<patient_set inserted_record="121" ignored_record="0" total_record="121" />
<event_set inserted_record="118" ignored_record="3" total_record="121" />
<observer_set inserted_record="1" ignored_record="0" total_record="1" />
<concept_set inserted_record="199" ignored_record="0" total_record="199" />
<pid_set inserted_record="242" ignored_record="-121" total_record="121" />
<eventid_set inserted_record="242" ignored_record="-121" total_record="121" />
</ns2:load_data_response>
*/
}
@Test
public void testGenomicLoader() throws UnlynxException, IOException, I2B2Exception {
String genomicPath_part1 = "/home/misbach/repositories/i2b2-core-server-medco/ch.epfl.lca1.medco/testfiles/datasets/full/skcm_broad/data_mutations_extended_skcm_broad_part1.txt",
genomicPath_part2 = "/home/misbach/repositories/i2b2-core-server-medco/ch.epfl.lca1.medco/testfiles/datasets/full/skcm_broad/data_mutations_extended_skcm_broad_part2.txt",
genomicPath_part3 = "/home/misbach/repositories/i2b2-core-server-medco/ch.epfl.lca1.medco/testfiles/datasets/full/skcm_broad/data_mutations_extended_skcm_broad_part3.txt";
DataType[] typesGenomic = new DataType[]{
// Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.CHROMOSOME,
DataType.START_POS,
DataType.ANNOTATION,
DataType.ANNOTATION,
// Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.REF_ALLELES,
DataType.ALT_ALLELES,
DataType.ANNOTATION,
DataType.ANNOTATION,
// dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1
DataType.ANNOTATION,
DataType.SAMPLE_ID,
DataType.ANNOTATION,
DataType.ANNOTATION,
// Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// Sequence_Source Validation_Method Score BAM_File Sequencer MA:FImpact MA:FIS MA:protein.change
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// MA:link.MSA MA:link.PDB MA:link.var Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE SYMBOL SYMBOL_SOURCE
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION
};
// dataset test
/*
DataType[] typesGenomic = new DataType[] {
// Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.CHROMOSOME,
DataType.START_POS,
DataType.ANNOTATION,
DataType.ANNOTATION,
// Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.REF_ALLELES,
DataType.ALT_ALLELES,
DataType.ANNOTATION,
DataType.ANNOTATION,
// dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2
DataType.ANNOTATION,
DataType.IGNORE,
DataType.IGNORE,
DataType.SAMPLE_DATA,
DataType.SAMPLE_DATA,
// Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2
DataType.SAMPLE_DATA,
DataType.SAMPLE_DATA,
DataType.SAMPLE_DATA,
DataType.SAMPLE_DATA,
// Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// Score BAM_File Sequencer MA:FImpact MA:FIS MA:protein.change MA:link.MSA MA:link.PDB MA:link.var
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.SAMPLE_DATA,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number
DataType.IGNORE,
DataType.IGNORE,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type
DataType.SAMPLE_DATA,
DataType.SAMPLE_DATA,
DataType.SAMPLE_DATA,
DataType.SAMPLE_DATA,
DataType.SAMPLE_DATA,
DataType.SAMPLE_DATA,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// DISTANCE SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
// ExAC_AF_SAS GENE_PHENO FILTER SAMPLE_ID
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.ANNOTATION,
DataType.SAMPLE_ID
};
*/
{
loadSrv1Conf();
MedCoDataLoader loader = new MedCoDataLoader("chuv1", "skcm_broad_part1","i2b2demotest", "Demo", "demo", "demouser");
loader.loadGenomicFile(genomicPath_part1, '\t', '\u0000',0, typesGenomic);
} {
loadSrv3Conf();
MedCoDataLoader loader = new MedCoDataLoader("chuv2", "skcm_broad_part2","i2b2demotest", "Demo", "demo", "demouser");
loader.loadGenomicFile(genomicPath_part2, '\t', '\u0000',0, typesGenomic);
} {
loadSrv5Conf();
MedCoDataLoader loader = new MedCoDataLoader("chuv3", "skcm_broad_part3","i2b2demotest", "Demo", "demo", "demouser");
loader.loadGenomicFile(genomicPath_part3, '\t', '\u0000',0, typesGenomic);
}
}
@Test
public void testTranslateIdsToNums() throws UnlynxException, IOException, I2B2Exception {
{
loadSrv1Conf();
MedCoDataLoader loader = new MedCoDataLoader("chuv1", "skcm_broad_part1","i2b2demotest", "Demo", "demo", "demouser");
loader.translateIdsToNums();
} {
loadSrv3Conf();
MedCoDataLoader loader = new MedCoDataLoader("chuv2", "skcm_broad_part2","i2b2demotest", "Demo", "demo", "demouser");
loader.translateIdsToNums();
} {
loadSrv5Conf();
MedCoDataLoader loader = new MedCoDataLoader("chuv3", "skcm_broad_part3","i2b2demotest", "Demo", "demo", "demouser");
loader.translateIdsToNums();
}
}
}
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