BUG:Figure generation PDF

[omero-qa]

​http://qa.openmicroscopy.org.uk/qa/feedback/9286/

Comment: Either this .figure PDF, or one created at the same time, by a CLS user is causing the Indexer to crash with the following:

14:26:35 Exception in thread "Thread-70" Exception in thread "Thread-71" java.lang.NullPointerException?

at org.pdfbox.pdmodel.PDPageNode.getAllKids(PDPageNode.java:194)
at org.pdfbox.pdmodel.PDPageNode.getAllKids(PDPageNode.java:182)
at org.pdfbox.pdmodel.PDDocumentCatalog.getAllPages(PDDocumentCatalog.java:226)
at org.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:216)
at ome.services.fulltext.PdfThread?.run(PdfParser?.java:92)

java.lang.NullPointerException?

at org.pdfbox.pdmodel.PDPageNode.getAllKids(PDPageNode.java:194)
at org.pdfbox.pdmodel.PDPageNode.getAllKids(PDPageNode.java:182)
at org.pdfbox.pdmodel.PDDocumentCatalog.getAllPages(PDDocumentCatalog.java:226)
at org.pdfbox.util.PDFTextStripper.writeText(PDFTextStripper.java:216)
at ome.services.fulltext.PdfThread?.run(PdfParser?.java:92)

File submitted with permission from content owner Amy Gerc.

[wmoore]

Tried to repeat locally, and didn't see the errors above, but saw other errors and warnings.
Tricky to tell where these are coming from - adding a file annotation can trigger re-indexing that includes a bunch of files that failed for the indexer earlier, not necessarily for the file you're adding.

2015-03-26 21:09:35,942 WARN  [         ome.services.fulltext.PdfThread] ( Thread-18) Error reading pdf file
java.io.IOException: Unknown encoding for 'SymbolEncoding'
        at org.pdfbox.encoding.EncodingManager.getEncoding(EncodingManager.java:82) ~[pdfbox.jar:na]
        at org.pdfbox.pdmodel.font.PDFont.getEncoding(PDFont.java:612) ~[pdfbox.jar:na]



2015-03-26 21:10:18,838 INFO  [   ome.services.fulltext.FullTextIndexer] (2-thread-2) INDEXED  151 objects in batch#1      [  53775 ms.]  ~100% done (267928 of 267928)
2015-03-26 21:10:18,843 ERROR [        ome.services.util.ServiceHandler] (2-thread-2) Method interface ome.services.util.Executor$Work.doWork invocation took 53796
2015-03-26 21:13:26,340 ERROR [org.hibernate.util.JDBCExceptionReporter] (2-thread-4) ERROR: cached plan must not change result type
2015-03-26 21:13:26,389 WARN  [        ome.services.util.ServiceHandler] (2-thread-4) Unknown exception thrown.


2015-03-26 21:13:26,390 ERROR [             org.quartz.core.JobRunShell] (2-thread-4) Job DEFAULT.fullTextThreadRun threw an unhandled Exception: 
org.springframework.scheduling.quartz.JobMethodInvocationFailedException: Invocation of method 'run' on target class [class ome.services.fulltext.FullTextThread] failed; nested exception is ome.conditions.InternalException:  Wrapped Exception: (org.springframework.jdbc.UncategorizedSQLException):
Hibernate operation: could not initialize a collection: [ome.model.meta.ExperimenterGroup.config#4]; uncategorized SQLException for SQL [select config0_.experimentergroup_id as experime1_34_0_, config0_.name as name0_, config0_.value as value0_, config0_.index as index0_ from experimentergroup_config config0_ where config0_.experimentergroup_id=?]; SQL state [0A000]; error code [0]; ERROR: cached plan must not change result type; nested exception is org.postgresql.util.PSQLException: ERROR: cached plan must not change result type

[wmoore]

Anyone know how to tell which file is generating Indexing errors?

[jamoore]

If you can get the EventLog? from Indexer-0.log, then a query will tell you.

[jamoore]

Splitting 5.1.4 due to milestone decoupling

[sbesson]

As discussed with Will earlier today, pushing the non-critical Web tickets out of 5.1.4