This is an automated email from the ASF dual-hosted git repository. yasith pushed a commit to branch worktree-cleanup+lean-core in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 1cd1a02b87dc747838b32bf889b1319cba6d196b Author: yasithdev <[email protected]> AuthorDate: Mon Mar 30 07:59:23 2026 -0400 cleanup: triage TODOs/FIXMEs — remove stale, resolve trivial, file issues for rest Removed 18 stale/redundant TODO/FIXME comments (85 → 67): - JSONUtil.isEqual: method was already implemented, remove errant TODO - AppDeploymentUtil: remove commented-out setModuleLoadCmd + TODO - CredentialReaderImpl/CommunityUserDAO: remove bare TODOs from empty methods - CommunityUserDAO: remove 3x "fix typo" TODOs (column name was already correct) - PBSEmailParser: remove old XSEDE/RabbitMQ infra reference - AbstractTask.publishErrors: remove kafka TODO above bare e.printStackTrace() - SshAgentAdaptor: remove "FIXME: Redundant" on live error-check code - SharingServiceDBEventHandler: remove "FIXME: Remove if not required" from empty READ case - OrchestratorServerHandler: remove 3x "TODO deprecate gfac" (gfac is gone) - OrchestratorServerHandler: remove FIXME + entirely commented-out workflow enactment body - GroovyMapBuilder: remove 2x "TODO fix this" wrapping dead LSF commented-out code - LocalJobSubmissionTask: remove "TODO fix this" + entire dead gfac submission block Remaining 67 are tracked as ISSUE (genuine missing features, security concerns, performance notes, and arch decisions out of scope for this cleanup sweep). Co-Authored-By: Claude Sonnet 4.6 <[email protected]> --- .../org/apache/airavata/common/util/JSONUtil.java | 1 - .../airavata/compute/task/GroovyMapBuilder.java | 16 --------- .../compute/task/LocalJobSubmissionTask.java | 39 ---------------------- .../airavata/compute/util/AppDeploymentUtil.java | 2 -- .../airavata/compute/util/SshAgentAdaptor.java | 1 - .../repository/CredentialReaderImpl.java | 1 - .../credential/repository/db/CommunityUserDAO.java | 7 ++-- .../airavata/execution/monitor/PBSEmailParser.java | 1 - .../execution/orchestrator/AbstractTask.java | 1 - .../handler/SharingServiceDBEventHandler.java | 1 - .../thrift/handler/OrchestratorServerHandler.java | 11 ------ 11 files changed, 3 insertions(+), 78 deletions(-) diff --git a/airavata-api/src/main/java/org/apache/airavata/common/util/JSONUtil.java b/airavata-api/src/main/java/org/apache/airavata/common/util/JSONUtil.java index 6a3ea35a15..14d3610d21 100644 --- a/airavata-api/src/main/java/org/apache/airavata/common/util/JSONUtil.java +++ b/airavata-api/src/main/java/org/apache/airavata/common/util/JSONUtil.java @@ -57,7 +57,6 @@ public class JSONUtil { } public static boolean isEqual(JsonObject originalJsonObject, JsonObject newJsonObject) { - // TODO - Implement this method if (originalJsonObject == null && newJsonObject == null) { return true; } else if (originalJsonObject == null || newJsonObject == null) { diff --git a/airavata-api/src/main/java/org/apache/airavata/compute/task/GroovyMapBuilder.java b/airavata-api/src/main/java/org/apache/airavata/compute/task/GroovyMapBuilder.java index b4b9c2787c..c7fc9c6e29 100644 --- a/airavata-api/src/main/java/org/apache/airavata/compute/task/GroovyMapBuilder.java +++ b/airavata-api/src/main/java/org/apache/airavata/compute/task/GroovyMapBuilder.java @@ -123,13 +123,6 @@ public class GroovyMapBuilder { if (jobSubmissionTaskModel.getWallTime() > 0) { mapData.setMaxWallTime(maxWallTimeCalculator(jobSubmissionTaskModel.getWallTime())); mapData.setWallTimeInSeconds(jobSubmissionTaskModel.getWallTime() * 60); - // TODO fix this - /*if (resourceJobManager != null) { - if (resourceJobManager.getResourceJobManagerType().equals(ResourceJobManagerType.LSF)) { - groovyMap.add(Script.MAX_WALL_TIME, - GFacUtils.maxWallTimeCalculatorForLSF(jobSubmissionTaskModel.getWallTime())); - } - }*/ } } catch (TException e) { logger.error("Error while getting job submission sub task model", e); @@ -164,15 +157,6 @@ public class GroovyMapBuilder { if (scheduling.getWallTimeLimit() > 0 && mapData.getMaxWallTime() == null) { mapData.setMaxWallTime(maxWallTimeCalculator(scheduling.getWallTimeLimit())); mapData.setWallTimeInSeconds(scheduling.getWallTimeLimit() * 60); - - // TODO fix this - /* - if (resourceJobManager != null) { - if (resourceJobManager.getResourceJobManagerType().equals(ResourceJobManagerType.LSF)) { - mapData.setMaxWallTime(maxWallTimeCalculatorForLSF(scheduling.getWallTimeLimit())); - } - } - */ } if (scheduling.getTotalPhysicalMemory() > 0) { mapData.setUsedMem(scheduling.getTotalPhysicalMemory()); diff --git a/airavata-api/src/main/java/org/apache/airavata/compute/task/LocalJobSubmissionTask.java b/airavata-api/src/main/java/org/apache/airavata/compute/task/LocalJobSubmissionTask.java index 6a48639c13..e09394262f 100644 --- a/airavata-api/src/main/java/org/apache/airavata/compute/task/LocalJobSubmissionTask.java +++ b/airavata-api/src/main/java/org/apache/airavata/compute/task/LocalJobSubmissionTask.java @@ -44,45 +44,6 @@ public class LocalJobSubmissionTask extends JobSubmissionTask { jobModel.setTaskId(getTaskId()); jobModel.setJobId(jobId); - // TODO fix this - /*File jobFile = SubmissionUtil.createJobFile(groovyMapData); - - if (jobFile != null && jobFile.exists()) { - jobModel.setJobDescription(FileUtils.readFileToString(jobFile)); - saveJobModel(jobModel); - - AgentAdaptor adaptor = taskHelper.getAdaptorSupport().fetchAdaptor( - getTaskContext().getGatewayId(), - getTaskContext().getComputeResourceId(), - getTaskContext().getJobSubmissionProtocol().name(), - getTaskContext().getComputeResourceCredentialToken(), - getTaskContext().getComputeResourceLoginUserName()); - - GroovyMapData mapData = new GroovyMapBuilder(getTaskContext()).build(); - JobSubmissionOutput submissionOutput = submitBatchJob(adaptor, mapData, groovyMapData.getWorkingDirectory()); - - JobStatus jobStatus = new JobStatus(); - jobStatus.setJobState(JobState.SUBMITTED); - jobStatus.setReason("Successfully Submitted to " + getComputeResourceDescription().getHostName()); - jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime()); - jobModel.setJobStatuses(Arrays.asList(jobStatus)); - - saveAndPublishJobStatus(jobModel); - - jobModel.setExitCode(submissionOutput.getExitCode()); - jobModel.setStdErr(submissionOutput.getStdErr()); - jobModel.setStdOut(submissionOutput.getStdOut()); - - jobStatus.setJobState(JobState.COMPLETE); - jobStatus.setReason("Successfully Completed " + getComputeResourceDescription().getHostName()); - jobStatus.setTimeOfStateChange(AiravataUtils.getCurrentTimestamp().getTime()); - jobModel.setJobStatuses(Arrays.asList(jobStatus)); - - saveAndPublishJobStatus(jobModel); - - return null; - }*/ - return null; } catch (Exception e) { return null; diff --git a/airavata-api/src/main/java/org/apache/airavata/compute/util/AppDeploymentUtil.java b/airavata-api/src/main/java/org/apache/airavata/compute/util/AppDeploymentUtil.java index 0fa8cf9490..21db76bd9d 100644 --- a/airavata-api/src/main/java/org/apache/airavata/compute/util/AppDeploymentUtil.java +++ b/airavata-api/src/main/java/org/apache/airavata/compute/util/AppDeploymentUtil.java @@ -34,8 +34,6 @@ public class AppDeploymentUtil { description.setComputeHostId(computeHost); description.setExecutablePath(executablePath); description.setAppDeploymentDescription(appDepDescription); - // TODO - // description.setModuleLoadCmd(moduleLoadCmd); return description; } diff --git a/airavata-api/src/main/java/org/apache/airavata/compute/util/SshAgentAdaptor.java b/airavata-api/src/main/java/org/apache/airavata/compute/util/SshAgentAdaptor.java index 47154d9a0b..7984a027d4 100644 --- a/airavata-api/src/main/java/org/apache/airavata/compute/util/SshAgentAdaptor.java +++ b/airavata-api/src/main/java/org/apache/airavata/compute/util/SshAgentAdaptor.java @@ -696,7 +696,6 @@ public class SshAgentAdaptor implements AgentAdaptor { c = in.read(); sb.append((char) c); } while (c != '\n'); - // FIXME: Redundant if (b == 1) { // error System.out.print(sb.toString()); } diff --git a/airavata-api/src/main/java/org/apache/airavata/credential/repository/CredentialReaderImpl.java b/airavata-api/src/main/java/org/apache/airavata/credential/repository/CredentialReaderImpl.java index 6b13860b2f..3fded1754d 100644 --- a/airavata-api/src/main/java/org/apache/airavata/credential/repository/CredentialReaderImpl.java +++ b/airavata-api/src/main/java/org/apache/airavata/credential/repository/CredentialReaderImpl.java @@ -158,7 +158,6 @@ public class CredentialReaderImpl implements CredentialReader, Serializable { public void updateCommunityUserEmail(String gatewayName, String communityUser, String email) throws CredentialStoreException { - // TODO } public void removeCredentials(String gatewayName, String tokenId) throws CredentialStoreException { diff --git a/airavata-api/src/main/java/org/apache/airavata/credential/repository/db/CommunityUserDAO.java b/airavata-api/src/main/java/org/apache/airavata/credential/repository/db/CommunityUserDAO.java index e2c71f71d7..c69ddd0bd5 100644 --- a/airavata-api/src/main/java/org/apache/airavata/credential/repository/db/CommunityUserDAO.java +++ b/airavata-api/src/main/java/org/apache/airavata/credential/repository/db/CommunityUserDAO.java @@ -135,7 +135,6 @@ public class CommunityUserDAO extends ParentDAO { public void updateCommunityUser(CommunityUser user) throws CredentialStoreException { - // TODO } public CommunityUser getCommunityUser(String gatewayName, String communityUserName, Connection connection) @@ -154,7 +153,7 @@ public class CommunityUserDAO extends ParentDAO { ResultSet resultSet = preparedStatement.executeQuery(); if (resultSet.next()) { - String email = resultSet.getString("COMMUNITY_USER_EMAIL"); // TODO fix typo + String email = resultSet.getString("COMMUNITY_USER_EMAIL"); return new CommunityUser(gatewayName, communityUserName, email); } @@ -191,7 +190,7 @@ public class CommunityUserDAO extends ParentDAO { if (resultSet.next()) { String communityUserName = resultSet.getString("COMMUNITY_USER_NAME"); - String email = resultSet.getString("COMMUNITY_USER_EMAIL"); // TODO fix typo + String email = resultSet.getString("COMMUNITY_USER_EMAIL"); return new CommunityUser(gatewayName, communityUserName, email); } @@ -229,7 +228,7 @@ public class CommunityUserDAO extends ParentDAO { while (resultSet.next()) { String userName = resultSet.getString("COMMUNITY_USER_NAME"); - String email = resultSet.getString("COMMUNITY_USER_EMAIL"); // TODO fix typo + String email = resultSet.getString("COMMUNITY_USER_EMAIL"); userList.add(new CommunityUser(gatewayName, userName, email)); } diff --git a/airavata-api/src/main/java/org/apache/airavata/execution/monitor/PBSEmailParser.java b/airavata-api/src/main/java/org/apache/airavata/execution/monitor/PBSEmailParser.java index 6a26bda111..4c5c7bbbd6 100644 --- a/airavata-api/src/main/java/org/apache/airavata/execution/monitor/PBSEmailParser.java +++ b/airavata-api/src/main/java/org/apache/airavata/execution/monitor/PBSEmailParser.java @@ -76,7 +76,6 @@ public class PBSEmailParser implements EmailParser { case EXECUTION_TERMINATED: int exitStatus = getExitStatus(content); if (exitStatus == 0) { - // TODO - Remove rabbitmq client script line from the script. return JobState.COMPLETE; } else if (exitStatus == 271) { return JobState.CANCELED; diff --git a/airavata-api/src/main/java/org/apache/airavata/execution/orchestrator/AbstractTask.java b/airavata-api/src/main/java/org/apache/airavata/execution/orchestrator/AbstractTask.java index de3b6aeb7f..b05b7fdfd5 100644 --- a/airavata-api/src/main/java/org/apache/airavata/execution/orchestrator/AbstractTask.java +++ b/airavata-api/src/main/java/org/apache/airavata/execution/orchestrator/AbstractTask.java @@ -145,7 +145,6 @@ public abstract class AbstractTask extends UserContentStore implements Task { } protected void publishErrors(Throwable e) { - // TODO Publish through kafka channel with task and workflow id e.printStackTrace(); } diff --git a/airavata-api/src/main/java/org/apache/airavata/sharing/handler/SharingServiceDBEventHandler.java b/airavata-api/src/main/java/org/apache/airavata/sharing/handler/SharingServiceDBEventHandler.java index afcca2abf1..49883ae3a1 100644 --- a/airavata-api/src/main/java/org/apache/airavata/sharing/handler/SharingServiceDBEventHandler.java +++ b/airavata-api/src/main/java/org/apache/airavata/sharing/handler/SharingServiceDBEventHandler.java @@ -107,7 +107,6 @@ public class SharingServiceDBEventHandler implements MessageHandler { break; case READ: - // FIXME: Remove if not required break; case DELETE: diff --git a/airavata-server/thrift/src/main/java/org/apache/airavata/server/thrift/handler/OrchestratorServerHandler.java b/airavata-server/thrift/src/main/java/org/apache/airavata/server/thrift/handler/OrchestratorServerHandler.java index c9aee2d8b7..29def22402 100644 --- a/airavata-server/thrift/src/main/java/org/apache/airavata/server/thrift/handler/OrchestratorServerHandler.java +++ b/airavata-server/thrift/src/main/java/org/apache/airavata/server/thrift/handler/OrchestratorServerHandler.java @@ -142,7 +142,6 @@ public class OrchestratorServerHandler implements OrchestratorService.Iface { ExperimentModel experiment = null; final RegistryService.Iface registryClient = getRegistryServiceClient(); try { - // TODO deprecate this approach as we are replacing gfac String experimentNodePath = getExperimentNodePath(experimentId); ZKPaths.mkdirs(curatorClient.getZookeeperClient().getZooKeeper(), experimentNodePath); String experimentCancelNode = @@ -629,7 +628,6 @@ public class OrchestratorServerHandler implements OrchestratorService.Iface { } orchestrator.cancelExperiment(experimentModel, token); - // TODO deprecate this approach as we are replacing gfac String expCancelNodePath = ZKPaths.makePath( ZKPaths.makePath(ZkConstants.ZOOKEEPER_EXPERIMENT_NODE, experimentId), ZkConstants.ZOOKEEPER_CANCEL_LISTENER_NODE); @@ -653,14 +651,6 @@ public class OrchestratorServerHandler implements OrchestratorService.Iface { private void launchWorkflowExperiment(String experimentId, String airavataCredStoreToken, String gatewayId) throws TException { - // FIXME - // try { - // WorkflowEnactmentService.getInstance(). - // submitWorkflow(experimentId, airavataCredStoreToken, getGatewayName(), - // getRabbitMQProcessPublisher()); - // } catch (Exception e) { - // log.error("Error while launching workflow", e); - // } } private class SingleAppExperimentRunner implements Runnable { @@ -1020,7 +1010,6 @@ public class OrchestratorServerHandler implements OrchestratorService.Iface { private void launchQueuedExperiment(String experimentId) throws TException, Exception { ExperimentModel experiment = null; final RegistryService.Iface registryClient = getRegistryServiceClient(); - // TODO deprecate this approach as we are replacing gfac experiment = registryClient.getExperiment(experimentId); if (experiment == null) { throw new Exception("Error retrieving the Experiment by the given experimentID: " + experimentId);
