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greater test coverage of application.py; updated browser data to hand…
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…le it
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@talavis
talavis committed Apr 6, 2019
1 parent e1cef73 commit f1e90f5
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Showing 2 changed files with 17 additions and 2 deletions.
14 changes: 13 additions & 1 deletion backend/tests/test_application.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,9 +26,21 @@ def test_get_schema():
assert len(data) == 10
assert data['name'] == 'SweFreq'
assert data['@type'] == 'DataCatalog'
response = requests.get(f'{BASE_URL}/api/schema/dataset/SweGen/version/20180409')

dataset = 'SweGen'
ds_version = '20180409'
response = requests.get(f'{BASE_URL}/api/schema/dataset/{dataset}/version/{ds_version}')
data = json.loads(response.text)
assert len(data) == 11
assert data['dataset']['@type'] == 'Dataset'
assert data['dataset']['name'] == 'SweGen'

dataset = 'SweGen'
ds_version = 'BAD_VERSION'
response = requests.get(f'{BASE_URL}/api/schema/dataset/{dataset}/version/{ds_version}')
assert response.status_code == 404

dataset = 'SweGen'
ds_version = '20171025'
response = requests.get(f'{BASE_URL}/api/schema/dataset/{dataset}/version/{ds_version}')
assert response.status_code == 403
5 changes: 4 additions & 1 deletion test/data/browser_test_data.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ COPY data.studies (id, pi_name, pi_email, contact_name, contact_email, title, st

COPY data.datasets (id, study, short_name, full_name, browser_uri, beacon_uri, beacon_description, avg_seq_depth, seq_type, seq_tech, seq_center, dataset_size) FROM stdin;
1 1 SweGen SweGen url \N \N 0 type method place 0
2 1 SweGen2 SweGen2 url \N \N 0 type method place 0
\.

COPY data.reference_sets (id, reference_build, reference_name, ensembl_version, gencode_version, dbnsfp_version) FROM stdin;
Expand All @@ -26,9 +27,10 @@ COPY data.reference_sets (id, reference_build, reference_name, ensembl_version,

COPY data.dataset_versions (id, dataset, reference_set, dataset_version, dataset_description, terms, var_call_ref, available_from, ref_doi, data_contact_name, data_contact_link, num_variants, coverage_levels) FROM stdin;
2 1 1 20170823 desc terms hg19 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100}
3 1 1 20171025 desc terms hg19 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100}
3 1 1 20171025 desc terms hg19 2222-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100}
1 1 1 20161223 desc terms hg19 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100}
4 1 1 20180409 desc terms hg19 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100}
5 2 1 20180409 desc terms hg19 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100}
\.

COPY data.coverage (id, dataset_version, chrom, pos, mean, median, coverage) FROM stdin;
Expand Down Expand Up @@ -2646,6 +2648,7 @@ COPY data.variants (id, dataset_version, variant_type, rsid, chrom, pos, ref, al
1658 4 \N \N 22 16370948 A G 39928.6992 {22-16370948-A-G,22-16370948-A-T,22-16370948-AG-A} 0 0.111500002 PASS 22-16370948-A-G 223 2000 {"DP": "40090", "FS": "19.411", "MQ": "27.61", "QD": "3.05", "VQSLOD": "-0.7957", "MQRankSum": "-0.19", "BaseQRankSum": "0.606", "ReadPosRankSum": "0.098", "ClippingRankSum": "0.066"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000230471", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GG", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "1", "SYMBOL": "LA16c-2F2.8", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "lincRNA", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000428118", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "2132", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000231565", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GG", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "1", "SYMBOL": "NEK2P2", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "processed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000438441", "HGNC_ID": "37816", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "4744", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}]
1665 4 \N 75186185 22 16371114 A G 191977 {22-16371114-A-G} 0 0.30399999 VQSRTrancheSNP99.90to100.00 22-16371114-A-G 608 2000 {"DP": "84373", "FS": "2.211", "MQ": "31.17", "QD": "3.14", "VQSLOD": "-50.73", "MQRankSum": "-1.184", "BaseQRankSum": "-4.11", "ReadPosRankSum": "1.07", "ClippingRankSum": "0.012"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000231565", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "G", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "1", "SYMBOL": "NEK2P2", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "processed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000438441", "HGNC_ID": "37816", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "4910", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs4068944", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000230471", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "G", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "1", "SYMBOL": "LA16c-2F2.8", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "lincRNA", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000428118", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "1967", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs4068944", "MOTIF_SCORE_CHANGE": ""}]
1668 4 \N 783 22 29461622 G A 715011 {22-29461622-G-A} 772 0.62349999 PASS 22-29461622-G-A 1247 2000 {"DP": "36991", "FS": "0", "MQ": "60", "QD": "22.28", "VQSLOD": "22.38", "MQRankSum": "0.023", "BaseQRankSum": "2.44", "ReadPosRankSum": "0.313", "ClippingRankSum": "-0.031"} [{"LoF": "", "TSL": "", "CCDS": "CCDS13848.1", "ENSP": "ENSP00000216071", "EXON": "", "GMAF": "G:0.4289", "Gene": "ENSG00000100249", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "C22orf31", "TREMBL": "", "AFR_MAF": "A:0.5681", "AMR_MAF": "A:0.4654", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "A:0.5466", "EUR_MAF": "A:0.664", "Feature": "ENST00000216071", "HGNC_ID": "26931", "SAS_MAF": "A:0.5798", "SOMATIC": "", "UNIPARC": "UPI0000073FE0", "CLIN_SIG": "", "DISTANCE": "3790", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "CV031_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs783", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "G:0.4289", "Gene": "", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "", "SYMBOL": "", "TREMBL": "", "AFR_MAF": "A:0.5681", "AMR_MAF": "A:0.4654", "BIOTYPE": "promoter_flanking_region", "DOMAINS": "", "EAS_MAF": "A:0.5466", "EUR_MAF": "A:0.664", "Feature": "ENSR00001731804", "HGNC_ID": "", "SAS_MAF": "A:0.5798", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "regulatory_region_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "RegulatoryFeature", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs783", "MOTIF_SCORE_CHANGE": ""}]
1669 5 \N 373706802 22 16080482 CAT C 117760 {22-16080482-CAT-C,22-16080482-C-CAT,22-16080482-C-CATACATATATATTGTATATGTAT} 8 0.157947689 PASS 22-16080482-CAT-C 314 1988 {"DP": "37043", "FS": "0", "MQ": "58.61", "QD": "10.1", "VQSLOD": "4.57", "MQRankSum": "0.052", "BaseQRankSum": "0.181", "ReadPosRankSum": "0", "ClippingRankSum": "0.017", "InbreedingCoeff": "-0.24"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000235265", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "LA16c-4G1.5", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "unprocessed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000413156", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "3765", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs373706802", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000229286", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "LA16c-4G1.4", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "unprocessed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000448070", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "4311", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs373706802", "MOTIF_SCORE_CHANGE": ""}]
\.

COPY data.variant_genes (id, variant, gene) FROM stdin;
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