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TASK-4770 Error running migration calculate_pedigree_graph #2314

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merged 3 commits into from
Oct 4, 2023
Merged

TASK-4770 Error running migration calculate_pedigree_graph #2314

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36027f2
app: use the full qualified names for study IDs when calculating pedi…
jtarraga Jul 18, 2023
cb4d77b
migration: update pedigree graph migration, #TASK-4770
jtarraga Oct 2, 2023
56b67e1
Merge branch 'release-2.8.x' into TASK-4770
jtarraga Oct 4, 2023
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25 changes: 20 additions & 5 deletions ...ava/org/opencb/opencga/app/migrations/v2_8_0/catalog/CalculatePedigreeGraphMigration.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,14 +34,28 @@ public class CalculatePedigreeGraphMigration extends MigrationTool {
protected void run() throws Exception {
MigrationRun migrationRun = getMigrationRun();

// Map study studyFqn -> job
Map<String, Job> jobs = new HashMap<>();
for (JobReferenceParam jobReference : migrationRun.getJobs()) {
Job job = catalogManager.getJobManager().get(jobReference.getStudyId(), jobReference.getId(), new QueryOptions(), token)
.first();
logger.info("Registering job {} for study {} to migrate", job.getId(), job.getStudy().getId());
logger.info("Reading already executed job '{}' for study '{}' with status '{}'",
job.getId(),
job.getStudy().getId(),
job.getInternal().getStatus().getId());
jobs.put(job.getStudy().getId(), job);
}
for (String study : getStudies()) {

Set<String> studies = new LinkedHashSet<>(getStudies());
logger.info("Study IDs (num. total = {}) to initialize pedigree graphs: {}", studies.size(), StringUtils.join(studies, ", "));

// Ensure that studies with already executed jobs are included in the migration run
getMigrationRun().getJobs().forEach(j -> studies.add(j.getStudyId()));

logger.info("Study IDs (num. total = {}) after adding studies from migration jobs: {}", studies.size(),
StringUtils.join(studies, ", "));

for (String study : studies) {
Job job = jobs.get(study);
if (job != null) {
String status = job.getInternal().getStatus().getId();
Expand All @@ -61,8 +75,9 @@ protected void run() throws Exception {
logger.info("Adding new job to migrate/initialize pedigree graph for study {}", study);
ObjectMap params = new ObjectMap()
.append(ParamConstants.STUDY_PARAM, study);
getMigrationRun().addJob(catalogManager.getJobManager().submit(study, PedigreeGraphInitAnalysis.ID, Enums.Priority.MEDIUM,
params, null, null, null, new ArrayList<>(), token).first());
Job newJob = catalogManager.getJobManager().submit(study, PedigreeGraphInitAnalysis.ID, Enums.Priority.MEDIUM,
params, null, null, null, new ArrayList<>(), token).first();
getMigrationRun().addJob(newJob);
}
}

Expand All @@ -73,7 +88,7 @@ public List<String> getStudies() throws CatalogException {
for (Project project : catalogManager.getProjectManager().search(new Query(), projectOptions, token).getResults()) {
if (CollectionUtils.isNotEmpty(project.getStudies())) {
for (Study study : project.getStudies()) {
String id = project.getId() + ":" + study.getId();
String id = study.getFqn();
for (Family family : catalogManager.getFamilyManager().search(id, new Query(), familyOptions, token).getResults()) {
if (PedigreeGraphUtils.hasMinTwoGenerations(family)
&& (family.getPedigreeGraph() == null || StringUtils.isEmpty(family.getPedigreeGraph().getBase64()))) {
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