Export BioCompute Object as JSON

export_json(x, file)

Arguments

x

BioCompute Object JSON string from convert_json

file

JSON file path

Value

Path to the output file

Examples

file_json <- tempfile(fileext = ".json") generate_example("HCV1a") %>% convert_json() %>% export_json(file_json) cat(paste(readLines(file_json), collapse = "\n"))
#> { #> "bco_spec_version": "https://w3id.org/biocompute/1.3.0/", #> "bco_id": "https://biocompute.sbgenomics.com/bco/e4998015-217b-43d3-9f9d-b854f1cd574b", #> "checksum": "31ad400fdc50d044255391288b9f48d33beb82a58bf16ec2185c58596277a243", #> "provenance_domain": { #> "name": "HCV1a ledipasvir resistance SNP detection", #> "version": "1.0.0", #> "review": [ #> { #> "status": "approved", #> "reviewer_comment": "Approved by [company name] staff. Waiting for approval from FDA Reviewer", #> "date": 1510507848, #> "reviewer": [ #> { #> "reviewer_name": "Jane Doe", #> "reviewer_affiliation": "Seven Bridges Genomics", #> "reviewer_email": "example@sevenbridges.com", #> "reviewer_contribution": "curatedBy", #> "reviewer_orcid": "https://orcid.org/0000-0000-0000-0000" #> } #> ] #> }, #> { #> "status": "approved", #> "reviewer_comment": "The revised BCO looks fine", #> "date": 1513110648, #> "reviewer": [ #> { #> "reviewer_name": "John Doe", #> "reviewer_affiliation": "U.S. Food and Drug Administration", #> "reviewer_email": "example@fda.gov", #> "reviewer_contribution": "curatedBy", #> "reviewer_orcid": "NA" #> } #> ] #> } #> ], #> "derived_from": "https://github.com/biocompute-objects/BCO_Specification/blob/1.2.1-beta/HCV1a.json", #> "obsolete_after": "2018-11-12T12:30:48-0500", #> "embargo": ["2017-10-12T13:30:48-0400", "2017-11-12T12:30:48-0500"], #> "created": "2017-01-20T09:40:17-0500", #> "modified": "2019-05-10T09:40:17-0500", #> "contributors": [ #> { #> "name": "Jane Doe", #> "affiliation": "Seven Bridges Genomics", #> "email": "example@sevenbridges.com", #> "contribution": ["createdBy", "curatedBy"], #> "orcid": "https://orcid.org/0000-0000-0000-0000" #> }, #> { #> "name": "John Doe", #> "affiliation": "U.S. Food and Drug Administration", #> "email": "example@fda.gov", #> "contribution": "authoredBy", #> "orcid": "NA" #> } #> ], #> "license": "https://creativecommons.org/licenses/by/4.0/" #> }, #> "usability_domain": ["Identify baseline single nucleotide polymorphisms (SNPs)[SO:0000694], (insertions)[SO:0000667], and (deletions)[SO:0000045] that correlate with reduced (ledipasvir)[pubchem.compound:67505836] antiviral drug efficacy in (Hepatitis C virus subtype 1)[taxonomy:31646]", "Identify treatment emergent amino acid (substitutions)[SO:1000002] that correlate with antiviral drug treatment failure", "Determine whether the treatment emergent amino acid (substitutions)[SO:1000002] identified correlate with treatment failure involving other drugs against the same virus"], #> "extension_domain": { #> "fhir_extension": { #> "fhir_endpoint": "https://fhirtest.uhn.ca/baseDstu3", #> "fhir_version": "3", #> "fhir_resources": [ #> [ #> { #> "fhir_id": "21376", #> "fhir_resource": "Sequence" #> } #> ], #> [ #> { #> "fhir_id": "6288583", #> "fhir_resource": "DiagnosticReport" #> } #> ], #> [ #> { #> "fhir_id": "25544", #> "fhir_resource": "ProcedureRequest" #> } #> ], #> [ #> { #> "fhir_id": "92440", #> "fhir_resource": "Observation" #> } #> ], #> [ #> { #> "fhir_id": "4588936", #> "fhir_resource": "FamilyMemberHistory" #> } #> ] #> ] #> }, #> "scm_extension": { #> "scm_repository": "https://github.com/example/repo1", #> "scm_type": "git", #> "scm_commit": "c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21", #> "scm_path": "workflow/hive-viral-mutation-detection.cwl", #> "scm_preview": "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl" #> } #> }, #> "description_domain": { #> "keywords": ["HCV1a", "Ledipasvir", "antiviral resistance", "SNP", "amino acid substitutions"], #> "xref": [ #> { #> "namespace": "pubchem.compound", #> "name": "PubChem-compound", #> "ids": "67505836", #> "access_time": "2017-01-20T09:40:17-0500" #> }, #> { #> "namespace": "pubmed", #> "name": "PubMed", #> "ids": "26508693", #> "access_time": "2017-01-21T09:40:17-0500" #> }, #> { #> "namespace": "so", #> "name": "Sequence Ontology", #> "ids": ["SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"], #> "access_time": "2017-01-22T09:40:17-0500" #> }, #> { #> "namespace": "taxonomy", #> "name": "Taxonomy", #> "ids": "31646", #> "access_time": "2017-01-23T09:40:17-0500" #> } #> ], #> "platform": "Seven Bridges Platform", #> "pipeline_steps": [ #> { #> "step_number": "1", #> "name": "HIVE-hexagon", #> "description": "Alignment of reads to a set of references", #> "version": "1.3", #> "prerequisite": [ #> { #> "name": "Hepatitis C virus genotype 1", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/22129792", #> "access_time": "2017-01-24 09:40:17" #> } #> }, #> { #> "name": "Hepatitis C virus type 1b complete genome", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/5420376", #> "access_time": "2017-01-24 09:40:17" #> } #> }, #> { #> "name": "Hepatitis C virus (isolate JFH-1) genomic RNA", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/13122261", #> "access_time": "2017-01-24 09:40:17" #> } #> }, #> { #> "name": "Hepatitis C virus clone J8CF, complete genome", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/386646758", #> "access_time": "2017-01-24 09:40:17" #> } #> }, #> { #> "name": "Hepatitis C virus S52 polyprotein gene", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/295311559", #> "access_time": "2017-01-24 09:40:17" #> } #> } #> ], #> "input_list": [ #> { #> "uri": "https://example.com/dna.cgi?cmd=objFile&ids=514683", #> "access_time": "2017-01-24 09:40:17" #> }, #> { #> "uri": "https://example.com/dna.cgi?cmd=objFile&ids=514682", #> "access_time": "2017-01-24 09:40:17" #> } #> ], #> "output_list": [ #> { #> "uri": "https://example.com/data/514769/allCount-aligned.csv", #> "access_time": "2017-01-24 09:40:17" #> }, #> { #> "uri": "https://example.com/data/514801/SNPProfile*.csv", #> "access_time": "2017-01-24 09:40:17" #> } #> ] #> } #> ] #> }, #> "execution_domain": { #> "script": "https://example.com/workflows/antiviral_resistance_detection_hive.py", #> "script_driver": "shell", #> "software_prerequisites": [ #> { #> "name": "HIVE-hexagon", #> "version": "babajanian.1", #> "uri": [ #> { #> "uri": "https://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-", #> "access_time": "2017-01-24 09:40:17", #> "sha1_chksum": "d60f506cddac09e9e816531e7905ca1ca6641e3c" #> } #> ] #> }, #> { #> "name": "HIVE-heptagon", #> "version": "albinoni.2", #> "uri": [ #> { #> "uri": "https://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-", #> "access_time": "2017-01-24 09:40:17", #> "sha1_chksum": "NA" #> } #> ] #> } #> ], #> "external_data_endpoints": [ #> [ #> { #> "name": "generic name", #> "url": "protocol://domain:port/application/path" #> } #> ], #> [ #> { #> "name": "access to ftp server", #> "url": "ftp://data.example.com:21/" #> } #> ], #> [ #> { #> "name": "access to e-utils web service", #> "url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" #> } #> ] #> ], #> "environment_variables": { #> "HOSTTYPE": "x86_64-linux", #> "EDITOR": "vim" #> } #> }, #> "parametric_domain": [ #> { #> "param": "seed", #> "value": "14", #> "step": "1" #> }, #> { #> "param": "minimum_match_len", #> "value": "66", #> "step": "1" #> }, #> { #> "param": "divergence_threshold_percent", #> "value": "0.30", #> "step": "1" #> }, #> { #> "param": "minimum_coverage", #> "value": "15", #> "step": "2" #> }, #> { #> "param": "freq_cutoff", #> "value": "0.10", #> "step": "2" #> } #> ], #> "io_domain": { #> "input_subdomain": [ #> { #> "uri": [ #> { #> "filename": "Hepatitis C virus genotype 1", #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/22129792", #> "access_time": "2017-01-24T09:40:17-0500" #> } #> ] #> }, #> { #> "uri": [ #> { #> "filename": "Hepatitis C virus type 1b complete genome", #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/5420376", #> "access_time": "2017-01-24T09:40:17-0500" #> } #> ] #> } #> ], #> "output_subdomain": [ #> { #> "mediatype": "text/csv", #> "uri": [ #> { #> "uri": "https://example.com/data/514769/dnaAccessionBased.csv", #> "access_time": "2017-01-24T09:40:17-0500" #> } #> ] #> }, #> { #> "mediatype": "text/csv", #> "uri": [ #> { #> "uri": "https://example.com/data/514801/SNPProfile*.csv", #> "access_time": "2017-01-24T09:40:17-0500" #> } #> ] #> } #> ] #> }, #> "error_domain": { #> "empirical_error": { #> "false_negative_alignment_hits": "<0.0010", #> "false_discovery": "<0.05" #> }, #> "algorithmic_error": { #> "false_positive_mutation_calls": "<0.00005", #> "false_discovery": "0.005" #> } #> } #> }