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Merge branch 'TASK-6089' of github.com:opencb/opencga into TASK-6089
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@j-coll
j-coll committed Jul 3, 2024
2 parents 3fa655b + d3f69e7 commit dc3546f
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Showing 61 changed files with 1,840 additions and 1,831 deletions.
20 changes: 10 additions & 10 deletions ...app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomStudiesCommandOptions.java
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Original file line number Diff line number Diff line change
Expand Up @@ -54,25 +54,25 @@ public class RunTemplatesCommandOptions {
@Parameter(names = {"--resume"}, description = "Resume study metadata ingestion.", arity = 0)
public boolean resume;

@Parameter(names = {"--jobId"}, description = "Job id.", arity = 1)
@Parameter(names = {"--job-id", "--jobId"}, description = "Job id.", arity = 1)
public String jobId;

@Parameter(names = {"--jobDependsOn"}, description = "Job depends on.", arity = 1)
@Parameter(names = {"--job-depends-on", "--jobDependsOn"}, description = "Job depends on.", arity = 1)
public String jobDependsOn;

@Parameter(names = {"--jobDescription"}, description = "Job description.", arity = 1)
@Parameter(names = {"--job-description", "--jobDescription"}, description = "Job description.", arity = 1)
public String jobDescription;

@Parameter(names = {"--jobTags"}, description = "Job tags.", arity = 1)
@Parameter(names = {"--job-tags", "--jobTags"}, description = "Job tags.", arity = 1)
public String jobTags;

@Parameter(names = {"--jobScheduledStartTime"}, description = "Job scheduled start time.", arity = 1)
public String scheduledStartTime;
@Parameter(names = {"--job-scheduled-start-time"}, description = "Job scheduled start time.", arity = 1)
public String jobScheduledStartTime;

@Parameter(names = {"--jobPriority"}, description = "Job priority.", arity = 1)
public String priority;
@Parameter(names = {"--job-priority"}, description = "Job priority.", arity = 1)
public String jobPriority;

@Parameter(names = {"--jobDryRun"}, description = "Job dry-run mode.", arity = 1)
public Boolean dryRun;
@Parameter(names = {"--job-dry-run"}, description = "Job dry-run mode.", arity = 1)
public Boolean jobDryRun;
}
}
54 changes: 27 additions & 27 deletions ...main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -121,9 +121,9 @@ private RestResponse<Job> runBwa() throws Exception {
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -165,9 +165,9 @@ private RestResponse<Job> runCoverageIndex() throws Exception {
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -206,9 +206,9 @@ private RestResponse<Job> coverageQcGeneCoverageStatsRun() throws Exception {
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -304,9 +304,9 @@ private RestResponse<Job> runDeeptools() throws Exception {
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -345,9 +345,9 @@ private RestResponse<Job> runFastqc() throws Exception {
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -386,9 +386,9 @@ private RestResponse<Job> runIndex() throws Exception {
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -426,9 +426,9 @@ private RestResponse<Job> runPicard() throws Exception {
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -467,9 +467,9 @@ private RestResponse<Job> runQc() throws Exception {
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -541,9 +541,9 @@ private RestResponse<Job> runSamtools() throws Exception {
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down
42 changes: 21 additions & 21 deletions .../main/java/org/opencb/opencga/app/cli/main/executors/AnalysisClinicalCommandExecutor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -518,9 +518,9 @@ private RestResponse<Job> runInterpreterCancerTiering() throws Exception {
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -559,9 +559,9 @@ private RestResponse<Job> runInterpreterExomiser() throws Exception {
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -598,9 +598,9 @@ private RestResponse<Job> runInterpreterTeam() throws Exception {
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -640,9 +640,9 @@ private RestResponse<Job> runInterpreterTiering() throws Exception {
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -682,9 +682,9 @@ private RestResponse<Job> runInterpreterZetta() throws Exception {
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -771,9 +771,9 @@ private RestResponse<Job> load() throws Exception {
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
}
Expand Down Expand Up @@ -925,9 +925,9 @@ private RestResponse<Job> runRgaIndex() throws Exception {
queryParams.putIfNotEmpty("jobDescription", commandOptions.jobDescription);
queryParams.putIfNotEmpty("jobDependsOn", commandOptions.jobDependsOn);
queryParams.putIfNotEmpty("jobTags", commandOptions.jobTags);
queryParams.putIfNotEmpty("scheduledStartTime", commandOptions.scheduledStartTime);
queryParams.putIfNotEmpty("priority", commandOptions.priority);
queryParams.putIfNotNull("dryRun", commandOptions.dryRun);
queryParams.putIfNotEmpty("jobScheduledStartTime", commandOptions.jobScheduledStartTime);
queryParams.putIfNotEmpty("jobPriority", commandOptions.jobPriority);
queryParams.putIfNotNull("jobDryRun", commandOptions.jobDryRun);
queryParams.putIfNotNull("auxiliarIndex", commandOptions.auxiliarIndex);
if (queryParams.get("study") == null && OpencgaMain.isShellMode()) {
queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
Expand Down
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