See
<https://builds.apache.org/job/ctakes-trunk-package/534/display/redirect?page=changes>
Changes:
[james-masanz] CTAKES-39 Update LVG, which uses a more recent version of hsqldb
so also update that.
[seanfinan] Initial commit of ctakes-gui
[seanfinan] PipeBitInfo update
------------------------------------------
[...truncated 668.10 KB...]
init:
umls.check.mrconso:
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[sql] Executing commands
[sql] 1 of 1 SQL statements executed successfully
[echo] mrconso.out = 0
[echo]
[delete] Deleting: /tmp/mrconso-check.txt
[echo] mrconso.exists = ${mrconso.exists}
umls.all:
[echo] mrconso.exists = ${mrconso.exists}
init:
umls.drop.view:
[echo] drop v_snomed_fword_lookup table
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/./umls/drop_view.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex355375018.sql
[sql] Executing resource: /tmp/ytex355375018.sql
[sql] 3 of 3 SQL statements executed successfully
[delete] Deleting: /tmp/ytex355375018.sql
[delete] Deleting: /tmp/ytex2072494679use.sql
init.conn:
[copy] Copying 1 file to /tmp
umls.create.view:
[echo] create the v_snomed_fword_lookup table
jdbc.sqlcmd:
[echo] db.schemaPUBLIC
[echo] umls.schema ${db.schema}
[echo] umls.catalog
[echo] execute ./hsql/./umls/create_view.sql
[copy] Copying 1 file to /tmp
[echo] executing /tmp/ytex2134363557.sql
[sql] Executing resource: /tmp/ytex2134363557.sql
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex2134363557.sql
[delete] Deleting: /tmp/ytex851534116use.sql
umls.import.view:
[echo] import v_snomed_fword_lookup from
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/data/umls/v_snomed_fword_lookup.txt.>
Be patient, this can take a while.
jdl:
[echo] jdl.format
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/data/umls/v_snomed_fword_lookup.xml>
[echo] jdl.data
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/data/umls/v_snomed_fword_lookup.txt>
[echo] umls.prefix
[copy] Copying 1 file to /tmp
[java] Exception in thread "main" java.lang.NoSuchMethodError:
org.hsqldb.DatabaseURL.parseURL(Ljava/lang/String;ZZ)Lorg/hsqldb/persist/HsqlProperties;
[java] at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source)
[java] at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Sou2017-03-28
11:52:15,228 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9
encapsulator 65534
[java] 2017-03-28 11:52:15,239 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into
PUBLIC.v_snomed_fword_lookup (cui,tui,fword,fstem,tok_str,stem_str) values
(?,?,?,?,?,?)
[java] rce)
[java] at java.sql.DriverManager.getConnection(DriverManager.java:664)
[java] at java.sql.DriverManager.getConnection(DriverManager.java:247)
[java] at
org.apache.ctakes.jdl.data.base.JdlConnection.openConnection(JdlConnection.java:77)
[java] at
org.apache.ctakes.jdl.data.base.JdlConnection.getOpenConnection(JdlConnection.java:93)
[java] at
org.apache.ctakes.jdl.data.loader.CsvLoader.dataInsert(CsvLoader.java:133)
[java] at org.apache.ctakes.jdl.AppJdl.execute(AppJdl.java:90)
[java] at org.apache.ctakes.jdl.AppMain.main(AppMain.java:88)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] Apache cTAKES ..................................... SUCCESS [4.466s]
[INFO] Apache cTAKES common type system .................. SUCCESS [10.374s]
[INFO] Apache cTAKES utils ............................... SUCCESS [7.388s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [3.778s]
[INFO] Apache cTAKES core ................................ SUCCESS [10.560s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [2.217s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [3.843s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [3.201s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [2.802s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [1.484s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [12.938s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [4.377s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [1.226s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [32.244s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [5.485s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [1.172s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [1.694s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [3.922s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [2.054s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [6.034s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [0.686s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [25.708s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [5.048s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [6.814s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [2.900s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [7.402s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [2.160s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res SUCCESS [1.610s]
[INFO] Apache cTAKES dictionary lookup fast .............. SUCCESS [3.272s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [1:10.778s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [8.231s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [0.622s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [5.292s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [1.108s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [6.500s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [0.679s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [6.612s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [1.014s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [1.668s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [0.644s]
[INFO] Apache cTAKES YTEX ................................ SUCCESS [42.154s]
[INFO] Apache cTAKES YTEX UIMA ........................... FAILURE [18.444s]
[INFO] ctakes-clinical-pipeline-res ...................... SKIPPED
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SKIPPED
[INFO] ctakes-examples-res ............................... SKIPPED
[INFO] ctakes-examples ................................... SKIPPED
[INFO] Apache cTAKES YTEX Web ............................ SKIPPED
[INFO] Apache cTAKES Distribution ........................ SKIPPED
[INFO] Apache cTAKES Regression-test ..................... SKIPPED
[INFO] Apache cTAKES template filler ..................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 6:44.426s
[INFO] Finished at: Tue Mar 28 11:52:17 UTC 2017
[INFO] Final Memory: 109M/911M
[INFO] ------------------------------------------------------------------------
Waiting for Jenkins to finish collecting data
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-antrun-plugin:1.6:run (generate-test-config) on
project ctakes-ytex-uima: An Ant BuildException has occured: The following
error occurred while executing this line:
[ERROR]
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/build-setup.xml>:149:
The following error occurred while executing this line:
[ERROR]
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/data/build.xml>:148:
The following error occurred while executing this line:
[ERROR]
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/data/build.xml>:295:
The following error occurred while executing this line:
[ERROR]
<https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/scripts/data/build.xml>:456:
Java returned: 1
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please
read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR] mvn <goals> -rf :ctakes-ytex-uima
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