public File create(String resourceName) throws IOException, CatalogException {
File file;
URI uri = getResourceUri(resourceName);
file = fileMetadataReader.create(studyId, uri, "data/vcfs/", "", true, null, sessionId).first();
catalogFileUtils.upload(uri, file, null, sessionId, false, false, true, false, Long.MAX_VALUE);
return catalogManager.getFile(file.getId(), sessionId).first();
}
@Before
public void before() throws Exception {
catalogPropertiesFile = getResourceUri("catalog.properties").getPath();
Properties properties = new Properties();
properties.load(
CatalogManagerTest.class.getClassLoader().getResourceAsStream("catalog.properties"));
CatalogManagerTest.clearCatalog(properties);
catalogManager = new CatalogManager(properties);
fileMetadataReader = FileMetadataReader.get(catalogManager);
catalogFileUtils = new CatalogFileUtils(catalogManager);
User user =
catalogManager.createUser(userId, "User", "*****@*****.**", "user", "ACME", null).first();
sessionId = catalogManager.login(userId, "user", "localhost").first().getString("sessionId");
projectId =
catalogManager
.createProject(userId, "p1", "p1", "Project 1", "ACME", null, sessionId)
.first()
.getId();
studyId =
catalogManager
.createStudy(
projectId,
"s1",
"s1",
Study.Type.CASE_CONTROL,
null,
null,
"Study 1",
null,
null,
null,
null,
Collections.singletonMap(File.Bioformat.VARIANT, new DataStore("mongodb", DB_NAME)),
null,
null,
null,
sessionId)
.first()
.getId();
outputId =
catalogManager
.createFolder(studyId, Paths.get("data", "index"), false, null, sessionId)
.first()
.getId();
files.add(
create(
"1-500.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"));
files.add(
create(
"501-1000.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"));
files.add(
create(
"1001-1500.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"));
files.add(
create(
"1501-2000.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"));
files.add(
create(
"2001-2504.filtered.10k.chr22.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz"));
}
