Loading unicode text file for FASTQ names fails

[jdeck88]

In the FASTQ loader, if the filetype is unicode then the loader fails, e.g.:

sample.txt

>file sample.txt
sample: Little-endian UTF-16 Unicode text, with CRLF line terminators

As a work-around, run the following command to convert to ascii (tested on Mac OS, should work on any linux):

>iconv -f UTF-16 -t ASCII//TRANSLIT//IGNORE 1904_MS_fastq_files.txt > 1904_MS_fastq_files.ascii.txt

The following is the system error that is generated.... this needs to be fixed (or at least tell the user to convert their file to ASCII).

 ERROR: invalid byte sequence for encoding "UTF8": 0x00; nested exception is org.postgresql.util.PSQLException: ERROR: invalid byte sequence for encoding "UTF8": 0x00
	at org.springframework.jdbc.support.SQLStateSQLExceptionTranslator.doTranslate(SQLStateSQLExceptionTranslator.java:102)
	at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:73)
	at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:82)
	at org.springframework.jdbc.support.AbstractFallbackSQLExceptionTranslator.translate(AbstractFallbackSQLExceptionTranslator.java:82)
	at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:655)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:690)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:717)
	at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:767)
	at org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate.query(NamedParameterJdbcTemplate.java:192)
	at org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate.query(NamedParameterJdbcTemplate.java:199)
	at biocode.fims.fastq.PostgresFastqRepository.getRecords(PostgresFastqRepository.java:36)
	at jdk.internal.reflect.GeneratedMethodAccessor2300.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy1156.getRecords(Unknown Source)
	at biocode.fims.fastq.reader.FastqConverter.getExistingRecords(FastqConverter.java:164)
	at biocode.fims.fastq.reader.FastqConverter.convertRecordSet(FastqConverter.java:65)
	at biocode.fims.run.DatasetBuilder.runDataConverters(DatasetBuilder.java:400)
	at biocode.fims.run.DatasetBuilder.build(DatasetBuilder.java:131)
	at biocode.fims.run.DatasetProcessor.validate(DatasetProcessor.java:101)
	at biocode.fims.rest.services.DatasetController.lambda$validate$0(DatasetController.java:220)
	at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java:1700)
	... 1 more
Caused by: org.postgresql.util.PSQLException: ERROR: invalid byte sequence for encoding "UTF8": 0x00
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2422)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2167)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:306)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:441)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:365)
	at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:155)
	at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:118)
	at org.springframework.jdbc.core.JdbcTemplate$1.doInPreparedStatement(JdbcTemplate.java:698)
	at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:639)
	... 26 more