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organizations: start removal of organization from public api, TASK-4389
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@pfurio
pfurio committed Sep 20, 2023
1 parent 0bff62f commit 9844259
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Showing 136 changed files with 3,093 additions and 2,572 deletions.
12 changes: 6 additions & 6 deletions opencga-analysis/src/main/java/org/opencb/opencga/analysis/AnalysisUtils.java
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Expand Up @@ -33,7 +33,7 @@ public static File getBamFileBySampleId(String sampleId, String studyId, FileMan
Query query = new Query(FileDBAdaptor.QueryParams.FORMAT.key(), File.Format.BAM)
.append(FileDBAdaptor.QueryParams.SAMPLE_IDS.key(), sampleId);
try {
fileQueryResult = fileManager.search(organizationId, studyId, query, QueryOptions.empty(), token);
fileQueryResult = fileManager.search(studyId, query, QueryOptions.empty(), token);
} catch (CatalogException e) {
throw new ToolException(e);
}
Expand All @@ -55,7 +55,7 @@ public static File getBamFile(String filename, String sampleId, String studyId,

query.put(FileDBAdaptor.QueryParams.SAMPLE_IDS.key(), sampleId);
try {
fileQueryResult = fileManager.search(organizationId, studyId, query, queryOptions, token);
fileQueryResult = fileManager.search(studyId, query, queryOptions, token);
} catch (CatalogException e) {
throw new ToolException(e);
}
Expand All @@ -81,7 +81,7 @@ public static File getCatalogFile(String file, String studyId, FileManager fileM

Query query = new Query(FileDBAdaptor.QueryParams.ID.key(), file);

fileQueryResult = fileManager.search(organizationId, studyId, query, QueryOptions.empty(), token);
fileQueryResult = fileManager.search(studyId, query, QueryOptions.empty(), token);

// Sanity check
if (fileQueryResult.getNumResults() == 0) {
Expand Down Expand Up @@ -124,7 +124,7 @@ public static Map<String, Map<String, Float>> parseRelatednessThresholds(Path th

public static boolean waitFor(String jobId, String study, JobManager jobManager, String token) throws ToolException, CatalogException {
Query query = new Query("id", jobId);
OpenCGAResult<Job> result = jobManager.search(organizationId, study, query, QueryOptions.empty(), token);
OpenCGAResult<Job> result = jobManager.search(study, query, QueryOptions.empty(), token);
Job job = result.first();
String status = job.getInternal().getStatus().getId();

Expand All @@ -134,7 +134,7 @@ public static boolean waitFor(String jobId, String study, JobManager jobManager,
try {
// Sleep for 30 seconds
Thread.sleep(30000);
result = jobManager.search(organizationId, study, query, QueryOptions.empty(), token);
result = jobManager.search(study, query, QueryOptions.empty(), token);
job = result.first();
} catch (CatalogException | InterruptedException e) {
new ToolException("Error waiting for job '" + jobId + "': " + e.getMessage());
Expand All @@ -146,7 +146,7 @@ public static boolean waitFor(String jobId, String study, JobManager jobManager,

public static Job getJob(String jobId, String study, JobManager jobManager, String token) throws ToolException, CatalogException {
Query query = new Query("id", jobId);
OpenCGAResult<Job> result = jobManager.search(organizationId, study, query, QueryOptions.empty(), token);
OpenCGAResult<Job> result = jobManager.search(study, query, QueryOptions.empty(), token);
Job job = result.first();
if (job == null) {
new ToolException("Error getting job '" + jobId + "' from study '" + study + "'.");
Expand Down
2 changes: 1 addition & 1 deletion ...rc/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentFastQcMetricsAnalysis.java
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Expand Up @@ -67,7 +67,7 @@ protected void check() throws Exception {

Query query = new Query(FileDBAdaptor.QueryParams.ID.key(), analysisParams.getFile());
query.put(FileDBAdaptor.QueryParams.FORMAT.key(), File.Format.BAM);
OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(organizationId, getStudy(), query, QueryOptions.empty(), token);
OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(getStudy(), query, QueryOptions.empty(), token);
if (fileResult.getNumResults() != 1) {
throw new ToolException("File " + analysisParams.getFile() + " must be a BAM file in study " + getStudy());
}
Expand Down
2 changes: 1 addition & 1 deletion ...is/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentFlagStatsAnalysis.java
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Expand Up @@ -72,7 +72,7 @@ protected void check() throws Exception {

Query query = new Query(FileDBAdaptor.QueryParams.ID.key(), analysisParams.getFile());
query.put(FileDBAdaptor.QueryParams.FORMAT.key(), File.Format.BAM);
OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(organizationId, getStudy(), query, QueryOptions.empty(), token);
OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(getStudy(), query, QueryOptions.empty(), token);
if (fileResult.getNumResults() != 1) {
throw new ToolException("File " + analysisParams.getFile() + " must be a BAM file in study " + getStudy());
}
Expand Down
6 changes: 3 additions & 3 deletions ...-analysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentQcAnalysis.java
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Expand Up @@ -240,7 +240,7 @@ private boolean waitFor(String jobId) throws ToolException {
Query query = new Query("id", jobId);
OpenCGAResult<Job> result = null;
try {
result = catalogManager.getJobManager().search(organizationId, study, query, QueryOptions.empty(), token);
result = catalogManager.getJobManager().search(study, query, QueryOptions.empty(), token);
} catch (CatalogException e) {
new ToolException("Error waiting for job '" + jobId + "': " + e.getMessage());
}
Expand All @@ -253,7 +253,7 @@ private boolean waitFor(String jobId) throws ToolException {
// Sleep for 1 minute
try {
Thread.sleep(60000);
result = catalogManager.getJobManager().search(organizationId, study, query, QueryOptions.empty(), token);
result = catalogManager.getJobManager().search(study, query, QueryOptions.empty(), token);
job = result.first();
} catch (CatalogException | InterruptedException e) {
new ToolException("Error waiting for job '" + jobId + "': " + e.getMessage());
Expand All @@ -268,7 +268,7 @@ private Job getJob(String jobId) {
Job job = null;
try {
Query query = new Query("id", jobId);
OpenCGAResult<Job> result = catalogManager.getJobManager().search(organizationId, study, query, QueryOptions.empty(), token);
OpenCGAResult<Job> result = catalogManager.getJobManager().search(study, query, QueryOptions.empty(), token);
job = result.first();
} catch (CatalogException e) {
new ToolException("Error getting job '" + jobId + "' from catalog: " + e.getMessage());
Expand Down
2 changes: 1 addition & 1 deletion ...alysis/src/main/java/org/opencb/opencga/analysis/alignment/qc/AlignmentStatsAnalysis.java
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Expand Up @@ -73,7 +73,7 @@ protected void check() throws Exception {

Query query = new Query(FileDBAdaptor.QueryParams.ID.key(), analysisParams.getFile());
query.put(FileDBAdaptor.QueryParams.FORMAT.key(), File.Format.BAM);
OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(organizationId, getStudy(), query, QueryOptions.empty(), token);
OpenCGAResult<File> fileResult = catalogManager.getFileManager().search(getStudy(), query, QueryOptions.empty(), token);
if (fileResult.getNumResults() != 1) {
throw new ToolException("File " + analysisParams.getFile() + " must be a BAM file in study " + getStudy());
}
Expand Down
6 changes: 3 additions & 3 deletions ...sis/src/main/java/org/opencb/opencga/analysis/clinical/ClinicalInterpretationManager.java
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Expand Up @@ -165,7 +165,7 @@ public DataResult<ClinicalVariant> index(String token) {

public DataResult<ClinicalVariant> index(String study, String token) throws IOException, ClinicalVariantException, CatalogException {
DBIterator<ClinicalAnalysis> clinicalAnalysisDBIterator =
clinicalAnalysisManager.iterator(organizationId, study, new Query(), QueryOptions.empty(), token);
clinicalAnalysisManager.iterator(study, new Query(), QueryOptions.empty(), token);

while (clinicalAnalysisDBIterator.hasNext()) {
ClinicalAnalysis clinicalAnalysis = clinicalAnalysisDBIterator.next();
Expand Down Expand Up @@ -885,7 +885,7 @@ private Query checkQueryPermissions(Query query, String token) throws ClinicalVa
if (studyIds.size() == 1) {
// This checks that the user has permission to the clinical analysis, family, sample or individual
DataResult<ClinicalAnalysis> clinicalAnalysisQueryResult = catalogManager.getClinicalAnalysisManager()
.search(organizationId, studyIds.get(0), query, QueryOptions.empty(), token);
.search(studyIds.get(0), query, QueryOptions.empty(), token);

if (clinicalAnalysisQueryResult.getResults().isEmpty()) {
throw new ClinicalVariantException("Either the ID does not exist or the user does not have permissions to view it");
Expand Down Expand Up @@ -953,7 +953,7 @@ private void checkInterpretationPermissions(String study, long interpretationId,
// This checks that the user has permission to this interpretation
Query query = new Query(ClinicalAnalysisDBAdaptor.QueryParams.INTERPRETATION_ID.key(), interpretationId);
DataResult<ClinicalAnalysis> clinicalAnalysisQueryResult = catalogManager.getClinicalAnalysisManager()
.search(organizationId, studyId, query, QueryOptions.empty(), token);
.search(studyId, query, QueryOptions.empty(), token);

if (clinicalAnalysisQueryResult.getResults().isEmpty()) {
throw new ClinicalVariantException("Either the interpretation ID (" + interpretationId + ") does not exist or the user does"
Expand Down
2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/cohort/CohortIndexTask.java
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Expand Up @@ -90,7 +90,7 @@ private void indexCohort(CatalogSolrManager catalogSolrManager, Study study) thr
.append(DBAdaptor.INCLUDE_ACLS, true)
.append(ParamConstants.FLATTEN_ANNOTATIONS, true);

catalogSolrManager.insertCatalogCollection(catalogManager.getCohortManager().iterator(organizationId, study.getFqn(), query,
catalogSolrManager.insertCatalogCollection(catalogManager.getCohortManager().iterator(study.getFqn(), query,
cohortQueryOptions, token), new CatalogCohortToSolrCohortConverter(study), CatalogSolrManager.COHORT_SOLR_COLLECTION);
}
}
2 changes: 1 addition & 1 deletion ...-analysis/src/main/java/org/opencb/opencga/analysis/cohort/CohortTsvAnnotationLoader.java
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Expand Up @@ -31,7 +31,7 @@ public class CohortTsvAnnotationLoader extends TsvAnnotationLoader {

@Override
public int count(Query query) throws CatalogException {
return catalogManager.getCohortManager().count(organizationId, study, query, token).getNumResults();
return catalogManager.getCohortManager().count(study, query, token).getNumResults();
}

@Override
Expand Down
2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/FamilyIndexTask.java
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Expand Up @@ -89,7 +89,7 @@ private void indexFamily(CatalogSolrManager catalogSolrManager, Study study) thr
.append(DBAdaptor.INCLUDE_ACLS, true)
.append(ParamConstants.FLATTEN_ANNOTATIONS, true);

catalogSolrManager.insertCatalogCollection(catalogManager.getFamilyManager().iterator(organizationId, study.getFqn(), query,
catalogSolrManager.insertCatalogCollection(catalogManager.getFamilyManager().iterator(study.getFqn(), query,
familyQueryOptions, token), new CatalogFamilyToSolrFamilyConverter(study), CatalogSolrManager.FAMILY_SOLR_COLLECTION);
}
}
Expand Down
2 changes: 1 addition & 1 deletion ...-analysis/src/main/java/org/opencb/opencga/analysis/family/FamilyTsvAnnotationLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ public class FamilyTsvAnnotationLoader extends TsvAnnotationLoader {

@Override
public int count(Query query) throws CatalogException {
return catalogManager.getFamilyManager().count(organizationId, study, query, token).getNumResults();
return catalogManager.getFamilyManager().count(study, query, token).getNumResults();
}

@Override
Expand Down
2 changes: 1 addition & 1 deletion ...-analysis/src/main/java/org/opencb/opencga/analysis/family/PedigreeGraphInitAnalysis.java
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Expand Up @@ -69,7 +69,7 @@ protected void run() throws ToolException {
step(getId(), () -> {
// Get all families from that study
QueryOptions queryOptions = new QueryOptions(QueryOptions.INCLUDE, Arrays.asList("id", "members", "pedigreeGraph"));
OpenCGAResult<Family> results = catalogManager.getFamilyManager().search(organizationId, study, new Query(), queryOptions, token);
OpenCGAResult<Family> results = catalogManager.getFamilyManager().search(study, new Query(), queryOptions, token);

// Get families to update by filtering
List<Family> familiesToUpdate = results.getResults().stream().filter(family -> PedigreeGraphUtils.hasMinTwoGenerations(family)
Expand Down
2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcAnalysis.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,7 @@ protected void check() throws Exception {
try {
Study study = catalogManager.getStudyManager().get(organizationId, studyId, QueryOptions.empty(), token).first();
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
catalogManager.getAuthorizationManager().checkStudyPermission(study.getUid(), userId, WRITE_FAMILIES);
catalogManager.getAuthorizationManager().checkStudyPermission(organizationId, study.getUid(), userId, WRITE_FAMILIES);
} catch (CatalogException e) {
throw new ToolException(e);
}
Expand Down
2 changes: 1 addition & 1 deletion ...is/src/main/java/org/opencb/opencga/analysis/family/qc/FamilyQcLocalAnalysisExecutor.java
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Expand Up @@ -85,7 +85,7 @@ private void runRelatedness() throws ToolException {

List<String> sampleIds = new ArrayList<>();
try {
OpenCGAResult<Individual> individualResult = catalogManager.getIndividualManager().search(organizationId, getStudyId(), query, queryOptions,
OpenCGAResult<Individual> individualResult = catalogManager.getIndividualManager().search(getStudyId(), query, queryOptions,
getToken());
for (Individual individual : individualResult.getResults()) {
if (CollectionUtils.isNotEmpty(individual.getSamples())) {
Expand Down
2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FetchAndRegisterTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ protected void check() throws Exception {
String userId = catalogManager.getUserManager().getUserId(organizationId, token);
// Check write permissions over the path
catalogManager.getAuthorizationManager()
.checkFilePermission(study.getUid(), parents.first().getUid(), userId, FilePermissions.WRITE);
.checkFilePermission(organizationId, study.getUid(), parents.first().getUid(), userId, FilePermissions.WRITE);
} catch (CatalogException e) {
throw new ToolException(e);
}
Expand Down
6 changes: 3 additions & 3 deletions opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileDeleteTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -132,13 +132,13 @@ protected void run() throws Exception {
Query query = new Query()
.append(FileDBAdaptor.QueryParams.INTERNAL_STATUS_ID.key(), FileStatus.PENDING_DELETE)
.append(FileDBAdaptor.QueryParams.TAGS.key(), randomMark);
try (DBIterator<File> iterator = fileManager.iterator(organizationId, studyFqn, query, FileManager.EXCLUDE_FILE_ATTRIBUTES, token)) {
try (DBIterator<File> iterator = fileManager.iterator(studyFqn, query, FileManager.EXCLUDE_FILE_ATTRIBUTES, token)) {
while (iterator.hasNext()) {
File file = iterator.next();
try {
logger.info("Deleting file '{}'...", file.getPath());
QueryOptions params = new QueryOptions(Constants.SKIP_TRASH, skipTrash);
fileManager.delete(organizationId, studyFqn, Collections.singletonList(file.getUuid()), params, token);
fileManager.delete(studyFqn, Collections.singletonList(file.getUuid()), params, token);
} catch (Exception e) {
logger.error("Error deleting file '{}': {}", file.getPath(), e.getMessage(), e);
logger.info("Restoring status of file '{}'", file.getPath());
Expand Down Expand Up @@ -172,7 +172,7 @@ private void recoverFromFatalCrash() {
query.put(FileDBAdaptor.QueryParams.INTERNAL_STATUS_ID.key(), FileStatus.DELETING);
OpenCGAResult<File> fileResult = null;
try {
fileResult = catalogManager.getFileManager().search(organizationId, studyFqn, query, FileManager.EXCLUDE_FILE_ATTRIBUTES,
fileResult = catalogManager.getFileManager().search(studyFqn, query, FileManager.EXCLUDE_FILE_ATTRIBUTES,
token);
} catch (CatalogException e) {
logger.error("Critical: Could not check if there are any inconsistent files", e);
Expand Down
2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileIndexTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ private void indexFile(CatalogSolrManager catalogSolrManager, Study study) throw
.append(DBAdaptor.INCLUDE_ACLS, true)
.append(ParamConstants.FLATTEN_ANNOTATIONS, true);

catalogSolrManager.insertCatalogCollection(catalogManager.getFileManager().iterator(organizationId, study.getFqn(), query,
catalogSolrManager.insertCatalogCollection(catalogManager.getFileManager().iterator(study.getFqn(), query,
fileQueryOptions, token), new CatalogFileToSolrFileConverter(study), CatalogSolrManager.FILE_SOLR_COLLECTION);
}
}
2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileTsvAnnotationLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ public class FileTsvAnnotationLoader extends TsvAnnotationLoader {

@Override
public int count(Query query) throws CatalogException {
return catalogManager.getFileManager().count(organizationId, study, query, token).getNumResults();
return catalogManager.getFileManager().count(study, query, token).getNumResults();
}

@Override
Expand Down
2 changes: 1 addition & 1 deletion opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/FileUnlinkTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ protected void run() throws Exception {
Query query = new Query()
.append(FileDBAdaptor.QueryParams.INTERNAL_STATUS_ID.key(), FileStatus.PENDING_DELETE)
.append(FileDBAdaptor.QueryParams.TAGS.key(), randomMark);
try (DBIterator<File> iterator = fileManager.iterator(organizationId, studyFqn, query, FileManager.EXCLUDE_FILE_ATTRIBUTES, token)) {
try (DBIterator<File> iterator = fileManager.iterator(studyFqn, query, FileManager.EXCLUDE_FILE_ATTRIBUTES, token)) {
while (iterator.hasNext()) {
File file = iterator.next();
try {
Expand Down
6 changes: 3 additions & 3 deletions ...ga-analysis/src/main/java/org/opencb/opencga/analysis/file/PostLinkSampleAssociation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ protected void run() throws Exception {
OpenCGAResult<File> fileResult;
if (files == null) {
// We need to associate all non-associated files
fileResult = catalogManager.getFileManager().search(organizationId, study, fileQuery, options, token);
fileResult = catalogManager.getFileManager().search(study, fileQuery, options, token);
if (fileResult.getNumResults() == 0) {
break;
}
Expand Down Expand Up @@ -126,7 +126,7 @@ protected void run() throws Exception {
if (!sampleExists(sampleId)) {
try {
// Sample still doesn't exist, so we create it
OpenCGAResult<Sample> sampleResult = catalogManager.getSampleManager().create(organizationId, study, new Sample().setId(sampleId),
OpenCGAResult<Sample> sampleResult = catalogManager.getSampleManager().create(study, new Sample().setId(sampleId),
QueryOptions.empty(), token);
if (sampleResult.getNumResults() != 1) {
throw new CatalogException("Could not create sample '" + sampleId + "'");
Expand Down Expand Up @@ -218,7 +218,7 @@ protected void run() throws Exception {

private boolean sampleExists(String sampleId) throws CatalogException {
Query sampleQuery = new Query(SampleDBAdaptor.QueryParams.ID.key(), sampleId);
OpenCGAResult<Sample> sampleResult = catalogManager.getSampleManager().search(organizationId, study, sampleQuery,
OpenCGAResult<Sample> sampleResult = catalogManager.getSampleManager().search(study, sampleQuery,
SampleManager.INCLUDE_SAMPLE_IDS, token);

return sampleResult.getNumResults() == 1;
Expand Down
2 changes: 1 addition & 1 deletion ...ga-analysis/src/main/java/org/opencb/opencga/analysis/individual/IndividualIndexTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@ private void indexIndividual(CatalogSolrManager catalogSolrManager, Study study)
.append(DBAdaptor.INCLUDE_ACLS, true)
.append(ParamConstants.FLATTEN_ANNOTATIONS, true);

catalogSolrManager.insertCatalogCollection(catalogManager.getIndividualManager().iterator(organizationId, study.getFqn(), query,
catalogSolrManager.insertCatalogCollection(catalogManager.getIndividualManager().iterator(study.getFqn(), query,
individualQueryOptions, token), new CatalogIndividualToSolrIndividualConverter(study),
CatalogSolrManager.INDIVIDUAL_SOLR_COLLECTION);
}
Expand Down
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