See
<https://builds.apache.org/job/ctakes-trunk-package/536/display/redirect?page=changes>
Changes:
[james-masanz] update URL of Supplementary Guidelines for ETTB 2.0 (Addendum
2009)
[tmill] Minor fixes to thyme reader to enable qa anafora reading. Switched to
using TemporalTypeRelation from Binary
[seanfinan] dependencies : reverting to hsqldb 1.8
------------------------------------------
[...truncated 654.47 KB...]
[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/ytex2029570364.sql
[sql] Executing resource: /tmp/ytex2029570364.sql
[sql] 3 of 3 SQL statements executed successfully
[delete] Deleting: /tmp/ytex2029570364.sql
[delete] Deleting: /tmp/ytex1120717829use.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/ytex1973651204.sql
[sql] Executing resource: /tmp/ytex1973651204.sql
[sql] 2 of 2 SQL statements executed successfully
[delete] Deleting: /tmp/ytex1973651204.sql
[delete] Deleting: /tmp/ytex1466786827use.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] 2017-03-30 11:59:46,385 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534
[java] 2017-03-30 11:59:46,397 INFO
org.apache.ctakes.jdl.data.loader.CsvLoader - insert into
PUBLIC.v_snomed_fword_lookup (cui,tui,fword,fstem,tok_str,sException in thread
"main" java.lang.NoSuchMethodError:
org.hsqldb.DatabaseURL.parseURL(Ljava/lang/String;ZZ)Lorg/hsqldb/persisttem_str)
values (?,?,?,?,?,?)
[java] /HsqlProperties;
[java] at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source)
[java] at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source)
[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 [5.560s]
[INFO] ctakes-gui-res .................................... SUCCESS [3.253s]
[INFO] Apache cTAKES Resources core ...................... SUCCESS [1.990s]
[INFO] Apache cTAKES common type system .................. SUCCESS [10.731s]
[INFO] Apache cTAKES utils ............................... SUCCESS [7.232s]
[INFO] Apache cTAKES core ................................ SUCCESS [11.463s]
[INFO] ctakes-gui ........................................ SUCCESS [8.381s]
[INFO] Apache cTAKES Resources pos-tagger ................ SUCCESS [8.144s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [3.459s]
[INFO] Apache cTAKES Resources ctakes-chunker-res ........ SUCCESS [3.177s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [4.475s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [3.228s]
[INFO] Apache cTAKES Resources dictionary-lookup ......... SUCCESS [15.090s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [10.530s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [13.804s]
[INFO] Apache cTAKES Resources lvg ....................... SUCCESS [41.733s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [10.171s]
[INFO] Apache cTAKES Resources ne-contexts ............... SUCCESS [13.769s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [2.941s]
[INFO] Apache cTAKES Resources constituency-parser ....... SUCCESS [16.254s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [12.425s]
[INFO] Apache cTAKES Resources coreference ............... SUCCESS [18.930s]
[INFO] Apache cTAKES Resources relation-extractor ........ SUCCESS [10.075s]
[INFO] Apache cTAKES Resources dependency-parser ......... SUCCESS [30.788s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [12.355s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [12.610s]
[INFO] Apache cTAKES Resources assertion ................. SUCCESS [14.272s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [20.745s]
[INFO] Apache cTAKES Resources temporal .................. SUCCESS [10.643s]
[INFO] Apache cTAKES Resources dictionary-lookup-fast-res SUCCESS [13.509s]
[INFO] Apache cTAKES dictionary lookup fast .............. SUCCESS [14.416s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [1:17.108s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [18.301s]
[INFO] Apache cTAKES Resources drug-ner .................. SUCCESS [6.766s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [10.685s]
[INFO] Apache cTAKES Resources side-effect ............... SUCCESS [6.102s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [26.080s]
[INFO] Apache cTAKES Resources smoking-status ............ SUCCESS [3.538s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [9.282s]
[INFO] Apache cTAKES Resources assertion-zoner ........... SUCCESS [1.153s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [7.336s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ........... SUCCESS [5.595s]
[INFO] Apache cTAKES YTEX ................................ SUCCESS [53.820s]
[INFO] Apache cTAKES YTEX UIMA ........................... FAILURE [27.431s]
[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: 16:24.448s
[INFO] Finished at: Thu Mar 30 12:00:05 UTC 2017
[INFO] Final Memory: 111M/915M
[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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[JENKINS] Archiving
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[JENKINS] Archiving
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Compressed 123.84 MB of artifacts by 99.0% relative to #535
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Compressed 12.16 MB of artifacts by 99.7% relative to #535
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[JENKINS] Archiving
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