[BUG]: PDF extraction fails but still returns success

[dgauldie]

Describe the bug
I ran a document extraction locally. The task returns a success

However, there are no equations extracted and there was an error logged in the equations task-runner.

2024-10-15 14:11:47 [ERROR] Unexpected failure for task 749bd71f-7327-4c9f-b322-42ae02cefe3b [software.uncharted.terarium.taskrunner.service.TaskRunnerService:176]
java.util.concurrent.TimeoutException: Reading from pipe took too long for task 749bd71f-7327-4c9f-b322-42ae02cefe3b
	at software.uncharted.terarium.taskrunner.service.Task.readProgressWithTimeout(Task.java:283)
	at software.uncharted.terarium.taskrunner.service.TaskRunnerService.dispatchSingleInputSingleOutputTask(TaskRunnerService.java:150)
	at software.uncharted.terarium.taskrunner.service.TaskRunnerService.onTaskRequest(TaskRunnerService.java:94)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.springframework.messaging.handler.invocation.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:169)
	at org.springframework.amqp.rabbit.listener.adapter.KotlinAwareInvocableHandlerMethod.doInvoke(KotlinAwareInvocableHandlerMethod.java:45)
	at org.springframework.messaging.handler.invocation.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:119)
	at org.springframework.amqp.rabbit.listener.adapter.HandlerAdapter.invoke(HandlerAdapter.java:75)
	at org.springframework.amqp.rabbit.listener.adapter.MessagingMessageListenerAdapter.invokeHandler(MessagingMessageListenerAdapter.java:277)
	at org.springframework.amqp.rabbit.listener.adapter.MessagingMessageListenerAdapter.invokeHandlerAndProcessResult(MessagingMessageListenerAdapter.java:224)
	at org.springframework.amqp.rabbit.listener.adapter.MessagingMessageListenerAdapter.onMessage(MessagingMessageListenerAdapter.java:149)
	at org.springframework.amqp.rabbit.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:1682)
	at org.springframework.amqp.rabbit.listener.AbstractMessageListenerContainer.actualInvokeListener(AbstractMessageListenerContainer.java:1604)
	at org.springframework.amqp.rabbit.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:1592)
	at org.springframework.amqp.rabbit.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:1583)
	at org.springframework.amqp.rabbit.listener.AbstractMessageListenerContainer.executeListenerAndHandleException(AbstractMessageListenerContainer.java:1528)
	at org.springframework.amqp.rabbit.listener.AbstractMessageListenerContainer.lambda$executeListener$8(AbstractMessageListenerContainer.java:1506)
	at io.micrometer.observation.Observation.observe(Observation.java:499)
	at org.springframework.amqp.rabbit.listener.AbstractMessageListenerContainer.executeListener(AbstractMessageListenerContainer.java:1506)
	at org.springframework.amqp.rabbit.listener.SimpleMessageListenerContainer.doReceiveAndExecute(SimpleMessageListenerContainer.java:1042)
	at org.springframework.amqp.rabbit.listener.SimpleMessageListenerContainer.receiveAndExecute(SimpleMessageListenerContainer.java:989)
	at org.springframework.amqp.rabbit.listener.SimpleMessageListenerContainer$AsyncMessageProcessingConsumer.mainLoop(SimpleMessageListenerContainer.java:1377)
	at org.springframework.amqp.rabbit.listener.SimpleMessageListenerContainer$AsyncMessageProcessingConsumer.run(SimpleMessageListenerContainer.java:1279)
	at java.base/java.lang.Thread.run(Thread.java:840)

This should be fixed 2 ways

1. we should have better error messages from the various tasks that run as part of the extraction process and the notification system should indicate to the user what extractions worked and what did not.
2. there should be a mechanism to retry document extractions since they could have failed due to a transient issue and not a problem with the document or extraction process.

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4. See error

Expected behavior
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