jdbc PGCopyOutputStream close() v. endCopy()

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lup
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jdbc PGCopyOutputStream close() v. endCopy()

lup

As is often the case, I'm unsure of which of these methods to use, or if I'm using them correctly.

PG10.5, jooq-3.10.8, postgresql-42.1.4, linux (redhat 6.9) and logback to a file.

I have been using close() for a while but thought I would make use of either the returned long from endCopy() or perhaps getHandledRowCount().

Both work perfectly, but when I use endCopy() I always get the exception shown near the bottom of this log excerpt. The COPY is on its own thread from the same connection as the direct jooq writes also listed.  Again, the data is all saved but I am worried that I'm not closing properly even if I use close(). The data here doesn't warrent bulk copy but it's just a quick example to repeat.

13:32:55.785 [pool-1-thread-1] DEBUG edu.utah.camplab.jx.PayloadFromMux - STAGING TABLE CREATED: bulk."flk_g16-forcing very long name to trigger truncation_22_8045c0"
13:32:55.786 [pool-1-thread-1] INFO  edu.utah.camplab.jx.PayloadFromMux - 8045c057-99ec-490b-90c1-85875269afee: started COPY work at 1546979575786
13:32:55.789 [pool-1-thread-1] INFO  edu.utah.camplab.jx.PayloadFromMux - 8045c057-99ec-490b-90c1-85875269afee: Total segment save took 22 ms
13:32:55.790 [pool-1-thread-1] INFO  edu.utah.camplab.jx.AbstractPayload - 8045c057-99ec-490b-90c1-85875269afee: closing process 8045c057-99ec-490b-90c1-85875269afee
13:32:55.790 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulk."flk_g16-forcing very long name to trigger truncation_22_8045c0": Begin bulk copy segment
13:32:55.793 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 89, maybe?
13:32:55.793 [pool-1-thread-1] DEBUG org.jooq.tools.LoggerListener - Executing batch query    : insert into "process_input" ("id", "process_id", "input_type", "input_ref") values (?, ?, ?, ?)
13:32:55.795 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 197, maybe?
13:32:55.797 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 318, maybe?
13:32:55.798 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 393, maybe?
13:32:55.799 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - 393/393 segments delivered in 9 ms
13:32:55.799 [8045c057-99ec-490b-90c1-85875269afee] DEBUG e.u.camplab.jx.PayloadWriterThread - staged in 9 ms
13:32:55.800 [pool-1-thread-1] DEBUG org.jooq.tools.LoggerListener - Executing batch query    : insert into "process_output" ("id", "process_id", "output_type", "output_ref") values (?, ?, ?, ?)
13:32:55.805 [8045c057-99ec-490b-90c1-85875269afee] ERROR e.u.camplab.jx.PayloadWriterThread - bulk."flk_g16-forcing very long name to trigger truncation_22_8045c0": i/o trouble
java.io.IOException: Ending write to copy failed.
    at org.postgresql.copy.PGCopyOutputStream.close(PGCopyOutputStream.java:107) ~[postgresql-42.1.4.jar:42.1.4]
    at edu.utah.camplab.jx.PayloadWriterThread.run(PayloadWriterThread.java:75) ~[transport/:na]
Caused by: org.postgresql.util.PSQLException: Tried to write to an inactive copy operation
    at org.postgresql.core.v3.QueryExecutorImpl.writeToCopy(QueryExecutorImpl.java:978) ~[postgresql-42.1.4.jar:42.1.4]
    at org.postgresql.core.v3.CopyInImpl.writeToCopy(CopyInImpl.java:35) ~[postgresql-42.1.4.jar:42.1.4]
    at org.postgresql.copy.PGCopyOutputStream.endCopy(PGCopyOutputStream.java:166) ~[postgresql-42.1.4.jar:42.1.4]
    at org.postgresql.copy.PGCopyOutputStream.close(PGCopyOutputStream.java:105) ~[postgresql-42.1.4.jar:42.1.4]
    ... 1 common frames omitted
13:32:55.810 [pool-1-thread-1] DEBUG org.jooq.tools.LoggerListener - Executing batch query    : insert into "process_arg" ("id", "process_id", "argname", "argvalue_int", "argvalue_float", "argvalue_text") values (?, ?, ?, ?, ?, ?)

The class doing the bulk work, PayloadWriterThread extends Thread, the thread name is set from the caller and the critical parts are as follows:

    @Override
    public void run() {
        try (PGCopyOutputStream writer = new PGCopyOutputStream(copyIn)) {
            long startAt = System.currentTimeMillis();
            deliverSegments(writer);
            long postDeliver = System.currentTimeMillis();
            logger.debug("staged in {} ms", postDeliver - startAt);
        }
        catch (SQLException sqle) {
            sqle.printStackTrace();
            logger.error("{}: sql trouble", tableName, sqle);
            throw new RuntimeException("Bulk copy failed on sql", sqle);
        }
        catch (IOException ioe) {
            ioe.printStackTrace();
            logger.error("{}: i/o trouble", tableName, ioe);
            throw new RuntimeException("Bulk copy failed on i/o", ioe);
        }
    }
    private void deliverSegments(PGCopyOutputStream writer) throws IOException, SQLException {
        logger.info("{}: Begin bulk copy segment", tableName);

        long counter = 0;
        long copied = 0;
        //These had better end up the same number
        long st = System.currentTimeMillis();
        for (Map.Entry<String, List<Segment>> seglistME : segmentListMap.entrySet()) {
            String pbsCSV = seglistME.getKey();
            UUID currentPbsId = probandsetIdMap.get(pbsCSV);
            if (currentPbsId == null) {
                throw new RuntimeException("Could not find pbsId by " + pbsCSV);
            }
            counter += seglistME.getValue().size();
            for (Segment segment : seglistME.getValue()) {
                String segmentCSV = makeCSV(segment, currentPbsId);
                writer.write(segmentCSV.getBytes());
            }
            logger.info("bulked up to {}, maybe?", counter);
        }
        copied = writer.endCopy();
        logger.info("{}/{} segments delivered in {} ms", copied, counter, System.currentTimeMillis() - st);
    }

Also, the stack trace always references the line of the closing brace of the try-with-resources and not on the call to endCopy. Because it's a caught exception? Or it's closing a closed writer?


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Re: jdbc PGCopyOutputStream close() v. endCopy()

Dave Cramer-8
Hi Rob,

Interesting. I've not looked too much into the copy implementation. 
The JDBC list or the jdbc github repo https://github.com/pgjdbc/pgjdbc might be a better place to report this. I know Lukas Edar monitors it as well

On Tue, 8 Jan 2019 at 16:29, Rob Sargent <[hidden email]> wrote:

As is often the case, I'm unsure of which of these methods to use, or if I'm using them correctly.

PG10.5, jooq-3.10.8, postgresql-42.1.4, linux (redhat 6.9) and logback to a file.

I have been using close() for a while but thought I would make use of either the returned long from endCopy() or perhaps getHandledRowCount().

Both work perfectly, but when I use endCopy() I always get the exception shown near the bottom of this log excerpt. The COPY is on its own thread from the same connection as the direct jooq writes also listed.  Again, the data is all saved but I am worried that I'm not closing properly even if I use close(). The data here doesn't warrent bulk copy but it's just a quick example to repeat.

13:32:55.785 [pool-1-thread-1] DEBUG edu.utah.camplab.jx.PayloadFromMux - STAGING TABLE CREATED: bulk."flk_g16-forcing very long name to trigger truncation_22_8045c0"
13:32:55.786 [pool-1-thread-1] INFO  edu.utah.camplab.jx.PayloadFromMux - 8045c057-99ec-490b-90c1-85875269afee: started COPY work at 1546979575786
13:32:55.789 [pool-1-thread-1] INFO  edu.utah.camplab.jx.PayloadFromMux - 8045c057-99ec-490b-90c1-85875269afee: Total segment save took 22 ms
13:32:55.790 [pool-1-thread-1] INFO  edu.utah.camplab.jx.AbstractPayload - 8045c057-99ec-490b-90c1-85875269afee: closing process 8045c057-99ec-490b-90c1-85875269afee
13:32:55.790 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulk."flk_g16-forcing very long name to trigger truncation_22_8045c0": Begin bulk copy segment
13:32:55.793 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 89, maybe?
13:32:55.793 [pool-1-thread-1] DEBUG org.jooq.tools.LoggerListener - Executing batch query    : insert into "process_input" ("id", "process_id", "input_type", "input_ref") values (?, ?, ?, ?)
13:32:55.795 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 197, maybe?
13:32:55.797 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 318, maybe?
13:32:55.798 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 393, maybe?
13:32:55.799 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - 393/393 segments delivered in 9 ms
13:32:55.799 [8045c057-99ec-490b-90c1-85875269afee] DEBUG e.u.camplab.jx.PayloadWriterThread - staged in 9 ms
13:32:55.800 [pool-1-thread-1] DEBUG org.jooq.tools.LoggerListener - Executing batch query    : insert into "process_output" ("id", "process_id", "output_type", "output_ref") values (?, ?, ?, ?)
13:32:55.805 [8045c057-99ec-490b-90c1-85875269afee] ERROR e.u.camplab.jx.PayloadWriterThread - bulk."flk_g16-forcing very long name to trigger truncation_22_8045c0": i/o trouble
java.io.IOException: Ending write to copy failed.
    at org.postgresql.copy.PGCopyOutputStream.close(PGCopyOutputStream.java:107) ~[postgresql-42.1.4.jar:42.1.4]
    at edu.utah.camplab.jx.PayloadWriterThread.run(PayloadWriterThread.java:75) ~[transport/:na]
Caused by: org.postgresql.util.PSQLException: Tried to write to an inactive copy operation
    at org.postgresql.core.v3.QueryExecutorImpl.writeToCopy(QueryExecutorImpl.java:978) ~[postgresql-42.1.4.jar:42.1.4]
    at org.postgresql.core.v3.CopyInImpl.writeToCopy(CopyInImpl.java:35) ~[postgresql-42.1.4.jar:42.1.4]
    at org.postgresql.copy.PGCopyOutputStream.endCopy(PGCopyOutputStream.java:166) ~[postgresql-42.1.4.jar:42.1.4]
    at org.postgresql.copy.PGCopyOutputStream.close(PGCopyOutputStream.java:105) ~[postgresql-42.1.4.jar:42.1.4]
    ... 1 common frames omitted
13:32:55.810 [pool-1-thread-1] DEBUG org.jooq.tools.LoggerListener - Executing batch query    : insert into "process_arg" ("id", "process_id", "argname", "argvalue_int", "argvalue_float", "argvalue_text") values (?, ?, ?, ?, ?, ?)

The class doing the bulk work, PayloadWriterThread extends Thread, the thread name is set from the caller and the critical parts are as follows:

    @Override
    public void run() {
        try (PGCopyOutputStream writer = new PGCopyOutputStream(copyIn)) {
            long startAt = System.currentTimeMillis();
            deliverSegments(writer);
            long postDeliver = System.currentTimeMillis();
            logger.debug("staged in {} ms", postDeliver - startAt);
        }
        catch (SQLException sqle) {
            sqle.printStackTrace();
            logger.error("{}: sql trouble", tableName, sqle);
            throw new RuntimeException("Bulk copy failed on sql", sqle);
        }
        catch (IOException ioe) {
            ioe.printStackTrace();
            logger.error("{}: i/o trouble", tableName, ioe);
            throw new RuntimeException("Bulk copy failed on i/o", ioe);
        }
    }
    private void deliverSegments(PGCopyOutputStream writer) throws IOException, SQLException {
        logger.info("{}: Begin bulk copy segment", tableName);

        long counter = 0;
        long copied = 0;
        //These had better end up the same number
        long st = System.currentTimeMillis();
        for (Map.Entry<String, List<Segment>> seglistME : segmentListMap.entrySet()) {
            String pbsCSV = seglistME.getKey();
            UUID currentPbsId = probandsetIdMap.get(pbsCSV);
            if (currentPbsId == null) {
                throw new RuntimeException("Could not find pbsId by " + pbsCSV);
            }
            counter += seglistME.getValue().size();
            for (Segment segment : seglistME.getValue()) {
                String segmentCSV = makeCSV(segment, currentPbsId);
                writer.write(segmentCSV.getBytes());
            }
            logger.info("bulked up to {}, maybe?", counter);
        }
        copied = writer.endCopy();
        logger.info("{}/{} segments delivered in {} ms", copied, counter, System.currentTimeMillis() - st);
    }

Also, the stack trace always references the line of the closing brace of the try-with-resources and not on the call to endCopy. Because it's a caught exception? Or it's closing a closed writer?


lup
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Re: jdbc PGCopyOutputStream close() v. endCopy()

lup
Ok I’ll repost there. Thanks

On Jan 10, 2019, at 6:09 AM, Dave Cramer <[hidden email]> wrote:

Hi Rob,

Interesting. I've not looked too much into the copy implementation. 
The JDBC list or the jdbc github repo https://github.com/pgjdbc/pgjdbc might be a better place to report this. I know Lukas Edar monitors it as well

On Tue, 8 Jan 2019 at 16:29, Rob Sargent <[hidden email]> wrote:

As is often the case, I'm unsure of which of these methods to use, or if I'm using them correctly.

PG10.5, jooq-3.10.8, postgresql-42.1.4, linux (redhat 6.9) and logback to a file.

I have been using close() for a while but thought I would make use of either the returned long from endCopy() or perhaps getHandledRowCount().

Both work perfectly, but when I use endCopy() I always get the exception shown near the bottom of this log excerpt. The COPY is on its own thread from the same connection as the direct jooq writes also listed.  Again, the data is all saved but I am worried that I'm not closing properly even if I use close(). The data here doesn't warrent bulk copy but it's just a quick example to repeat.

13:32:55.785 [pool-1-thread-1] DEBUG edu.utah.camplab.jx.PayloadFromMux - STAGING TABLE CREATED: bulk."flk_g16-forcing very long name to trigger truncation_22_8045c0"
13:32:55.786 [pool-1-thread-1] INFO  edu.utah.camplab.jx.PayloadFromMux - 8045c057-99ec-490b-90c1-85875269afee: started COPY work at 1546979575786
13:32:55.789 [pool-1-thread-1] INFO  edu.utah.camplab.jx.PayloadFromMux - 8045c057-99ec-490b-90c1-85875269afee: Total segment save took 22 ms
13:32:55.790 [pool-1-thread-1] INFO  edu.utah.camplab.jx.AbstractPayload - 8045c057-99ec-490b-90c1-85875269afee: closing process 8045c057-99ec-490b-90c1-85875269afee
13:32:55.790 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulk."flk_g16-forcing very long name to trigger truncation_22_8045c0": Begin bulk copy segment
13:32:55.793 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 89, maybe?
13:32:55.793 [pool-1-thread-1] DEBUG org.jooq.tools.LoggerListener - Executing batch query    : insert into "process_input" ("id", "process_id", "input_type", "input_ref") values (?, ?, ?, ?)
13:32:55.795 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 197, maybe?
13:32:55.797 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 318, maybe?
13:32:55.798 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - bulked up to 393, maybe?
13:32:55.799 [8045c057-99ec-490b-90c1-85875269afee] INFO  e.u.camplab.jx.PayloadWriterThread - 393/393 segments delivered in 9 ms
13:32:55.799 [8045c057-99ec-490b-90c1-85875269afee] DEBUG e.u.camplab.jx.PayloadWriterThread - staged in 9 ms
13:32:55.800 [pool-1-thread-1] DEBUG org.jooq.tools.LoggerListener - Executing batch query    : insert into "process_output" ("id", "process_id", "output_type", "output_ref") values (?, ?, ?, ?)
13:32:55.805 [8045c057-99ec-490b-90c1-85875269afee] ERROR e.u.camplab.jx.PayloadWriterThread - bulk."flk_g16-forcing very long name to trigger truncation_22_8045c0": i/o trouble
java.io.IOException: Ending write to copy failed.
    at org.postgresql.copy.PGCopyOutputStream.close(PGCopyOutputStream.java:107) ~[postgresql-42.1.4.jar:42.1.4]
    at edu.utah.camplab.jx.PayloadWriterThread.run(PayloadWriterThread.java:75) ~[transport/:na]
Caused by: org.postgresql.util.PSQLException: Tried to write to an inactive copy operation
    at org.postgresql.core.v3.QueryExecutorImpl.writeToCopy(QueryExecutorImpl.java:978) ~[postgresql-42.1.4.jar:42.1.4]
    at org.postgresql.core.v3.CopyInImpl.writeToCopy(CopyInImpl.java:35) ~[postgresql-42.1.4.jar:42.1.4]
    at org.postgresql.copy.PGCopyOutputStream.endCopy(PGCopyOutputStream.java:166) ~[postgresql-42.1.4.jar:42.1.4]
    at org.postgresql.copy.PGCopyOutputStream.close(PGCopyOutputStream.java:105) ~[postgresql-42.1.4.jar:42.1.4]
    ... 1 common frames omitted
13:32:55.810 [pool-1-thread-1] DEBUG org.jooq.tools.LoggerListener - Executing batch query    : insert into "process_arg" ("id", "process_id", "argname", "argvalue_int", "argvalue_float", "argvalue_text") values (?, ?, ?, ?, ?, ?)

The class doing the bulk work, PayloadWriterThread extends Thread, the thread name is set from the caller and the critical parts are as follows:

    @Override
    public void run() {
        try (PGCopyOutputStream writer = new PGCopyOutputStream(copyIn)) {
            long startAt = System.currentTimeMillis();
            deliverSegments(writer);
            long postDeliver = System.currentTimeMillis();
            logger.debug("staged in {} ms", postDeliver - startAt);
        }
        catch (SQLException sqle) {
            sqle.printStackTrace();
            logger.error("{}: sql trouble", tableName, sqle);
            throw new RuntimeException("Bulk copy failed on sql", sqle);
        }
        catch (IOException ioe) {
            ioe.printStackTrace();
            logger.error("{}: i/o trouble", tableName, ioe);
            throw new RuntimeException("Bulk copy failed on i/o", ioe);
        }
    }
    private void deliverSegments(PGCopyOutputStream writer) throws IOException, SQLException {
        logger.info("{}: Begin bulk copy segment", tableName);

        long counter = 0;
        long copied = 0;
        //These had better end up the same number
        long st = System.currentTimeMillis();
        for (Map.Entry<String, List<Segment>> seglistME : segmentListMap.entrySet()) {
            String pbsCSV = seglistME.getKey();
            UUID currentPbsId = probandsetIdMap.get(pbsCSV);
            if (currentPbsId == null) {
                throw new RuntimeException("Could not find pbsId by " + pbsCSV);
            }
            counter += seglistME.getValue().size();
            for (Segment segment : seglistME.getValue()) {
                String segmentCSV = makeCSV(segment, currentPbsId);
                writer.write(segmentCSV.getBytes());
            }
            logger.info("bulked up to {}, maybe?", counter);
        }
        copied = writer.endCopy();
        logger.info("{}/{} segments delivered in {} ms", copied, counter, System.currentTimeMillis() - st);
    }

Also, the stack trace always references the line of the closing brace of the try-with-resources and not on the call to endCopy. Because it's a caught exception? Or it's closing a closed writer?