[phenotips-notifications] Build failed in Jenkins: PhenoTips-pull-requests #986

ci at phenotips.org ci at phenotips.org
Sun Oct 25 01:29:14 EDT 2015


See <https://ci.phenotips.org/job/PhenoTips-pull-requests/986/changes>

Changes:

[Sergiu Dumitriu] Initial commit

[marta.girdea] generated keywords for indexing

[marta.girdea] replaced dashes with underscores in fields names

[marta.girdea] fixed field name (for consistency). added "not_keywords" field only if negative phenotypes exist.

[Sergiu Dumitriu] Adjusted boost values

[Sergiu Dumitriu] Index the actual specified symptoms separately

[marta.girdea] More fields indexed

[Sergiu Dumitriu] [misc] Use org.phenotips as the package name / groupId

[j.kereliuk] Initial commit of some setup

[j.kereliuk] Added test deps and changed min coverage for dev

[j.kereliuk] Set up getting instances of injected classes

[deanway93] Changed POM to include wiki test component dependency

[deanway93] Added Test for ConfigureISODatesInJson OnEvent method

[deanway93] Added Test for object contruction of ConfigureISODatesInJson class

[deanway93] Added javax.servlet dependancy

[deanway93] DefaultPatientResourceImpl tests

[deanway93] completed test coverage of DefaultPatientResourceImplTest

[deanway93] changed minimum coverage to avoid build failure

[deanway93] Added comment header to DefaultPatientResourceImplTest class

[deanway93] Removed a few unused statements

[deanway93] changed Reflections to getInstance for mocking of injected fields

[deanway93] added static imports for Mockito.when and Mockito.verify

[deanway93] Added test for new logger message in deletePatient

[deanway93] hasAccess now checks for real DocumentReferences instead of null values

[deanway93] Removed ReflectionUtils.setFieldValue calls in deletePatient tests

[j.kereliuk] changed set up and added another test

[deanway93] Whitespace/formating changes

[deanway93] Removed unnecessary URI field

[deanway93] Make use of XWikiContext.TYPE_PROVIDER field

[deanway93] Use getInstance() instead of calling constructor

[j.kereliuk] added test for getting patient properly

[j.kereliuk] Added test for getting a patient that isn't found

[j.kereliuk] Added test for not finding a patient while updating

[j.kereliuk] Added test for updating patient with no access

[j.kereliuk] test for json not having id feild when updating

[j.kereliuk] fixed typo

[j.kereliuk] removed useless test

[j.kereliuk] test for throwing exception while updating from json

[j.kereliuk] fixed typo

[j.kereliuk] test successful update of patient

[j.kereliuk] merge

[j.kereliuk] clean up

[j.kereliuk] added test for private checking multiple method

[j.kereliuk] clean up variables

[j.kereliuk] test for checkMultiplePatients throwing QueryException

[deanway93] Updated tests for throws changes

[tarang] initial addPatient and listPatient tests

[tarang] added exception status checks

[tarang] added exception checking

[tarang] completed listPatientsDefaultBehaviour test

[tarang] license added

[tarang] listPatients error handling

[tarang] removed throws XWikiRestException

[tarang] removed unused classes

[tarang] improved exception status checking

[j.kereliuk] uses real document reference now

[deanway93] Improved method for checking that and ApplicationStartedEvent is added by ConfigureISODatesInJson

[deanway93] Improved test method names

[deanway93] Expanded tests on normal Behavior of DefaultPatientResourceImpl methods

[j.kereliuk] changed method name to make more sense

[j.kereliuk] private method checks for when it is called on all other public methods

[j.kereliuk] removed XWikiException

[deanway93] fixed imports

[deanway93] Verify use of DomainObjectFactory

[tarang] added user access test for listPatients

[deanway93] Check for initial logger message only once

[deanway93] Reordered tests for readability(Tests for the same method grouped together)

[tarang] additonal user access test

[tarang] improved listPatientsNoUserAccess

[deanway93] Added test for PatientDeathdateUpdater

[deanway93] Minor edit to PatientDeathdateUpdater

[deanway93] License header added

[deanway93] Remove unnecessary cast

[tarang] number of record tests

[tarang] fixed array Object lengths

[tarang] edge cases for record lookup

[mjshepherd] Issue #1769: Moved dashboard gadgets into UIX extensions in separate file

[mjshepherd] Issue #1769: Added UIX extension point to homepage

[mjshepherd] Issue #1769: Removed original gadgets from data.WebHome

[mjshepherd] Issue #1769: Added parent to PhenoTips.DashboardGadgets and titles will not be displayed if empty

[deanway93] Changed test class based on changes to PatientDeathDateUpdater class on master

[asm] Issue #1877: HGNC vocabulary does not properly search genes by alternative IDs.

[mjshepherd] Issue #1769: Addressing comment in WebHome

[mjshepherd] Issue #1769: Moved individual gadgets to their own documents

[mjshepherd] Issue #1769: Welcome message is configurable from admin, gadget title are now specified in document titles

[mjshepherd] Issue #1769: minor typo fix

[mjshepherd] Issue #1769: Removed welcome message gadget

[mjshepherd] Issue #1870: Use RequireJS to load the pedigree files

[mjshepherd] Issue #1870: Errors in commit

[mjshepherd] Issue: Minify Pedigree

[mjshepherd] Issue #1769: Fixed build failure. Added parent to new xml files

[mjshepherd] PT-2007: Minify Pedigree -- Minified pedigree will not be created in src directory

[mjshepherd] PT-2022: ABiolity to add notes to cancers in the pedigree

[mjshepherd] PT-2022: Ability to add notes to cancers in pedigree -- addressing comments

[mjshepherd] PT-2022: Fixing bugs

[Sergiu Dumitriu] PT-1828: New Perinatal questions: maternal and paternal age at birth

[Sergiu Dumitriu] [cleanup] Better performance + fixed wrong javadoc

[Sergiu Dumitriu] PT-2033: Add support for using different XClasses than PatientClass in the AbstractComplexController

[Sergiu Dumitriu] [cleanup] Fixed wrong indentation

[Sergiu Dumitriu] PT-1828: New Perinatal questions: maternal and paternal age at birth

[Sergiu Dumitriu] PT-1944: PatientDataControllers send logger error messages when a new patient is created

[Sergiu Dumitriu] [cleanup] Fixed typo

[Sergiu Dumitriu] Issue #1853: Upgrade to XWiki 7.1.1

[Sergiu Dumitriu] PT-2045: Add support for recording mother's obstetric history

[Sergiu Dumitriu] PT-2048: When using dd-MM-yyyy as the date format in the pedigree, the day selector wrongly preserves the selected value between different individuals

[Sergiu Dumitriu] [misc] Documented some methods

[veronika.koltunov] PT-2049: Remove yellow on-hover row highlight of a table. Fixed

[Sergiu Dumitriu] [release] Update the HPO index

[Sergiu Dumitriu] [misc] Fixed a recent bug which caused some fields not to be displayed

[Sergiu Dumitriu] PT-1837: Phenotype configuration preview is broken

[Sergiu Dumitriu] PT-2050: Display more prenatal, neonatal and perinatal phenotypes

[Sergiu Dumitriu] PT-2050: Display more prenatal, neonatal and perinatal phenotypes

[antonkats] [bug fix] wiki syntax caused  to be removed in the JSON

[Sergiu Dumitriu] PT-2050: Display more prenatal, neonatal and perinatal phenotypes

[Sergiu Dumitriu] PT-2050: Display more prenatal, neonatal and perinatal phenotypes

[Sergiu Dumitriu] PT-2055: Selecting two distant "Assisted reproduction" options will display a large space in view mode

[Sergiu Dumitriu] PT-2056: Add "Intrauterine insemination (IUI)" as an "Assisted reproduction" option

[Sergiu Dumitriu] [misc] Sync xobjects with their xclass

[Sergiu Dumitriu] [maven-release-plugin] prepare branch stable-1.2.x

[Sergiu Dumitriu] [maven-release-plugin] prepare for next development iteration

[Sergiu Dumitriu] [release] Update current and previous version after switching master to 1.3-SNAPSHOT

[antonkats] [misc] Fixed incorrect JavaDoc

[Sergiu Dumitriu] [cleanup] Applied codestyle

[Sergiu Dumitriu] PT-2065: JS errors related to bad CSS selectors triggered when editing patient records

[Sergiu Dumitriu] [cleanup] Applied codestyle

[Sergiu Dumitriu] [cleanup] Improved method names

[Sergiu Dumitriu] [cleanup] Removed unnecessary tests

[Sergiu Dumitriu] PT-2066: Add support for recording which twin (A/B) the current patient is

[Sergiu Dumitriu] [cleanup] Sync xobjects with their xclasses

[veronika.koltunov] PT-2049: Remove yellow on-hover row highlight of a table. Removed commented code.

[Sergiu Dumitriu] PT-2074: Inconsistent indentation in the Allergies list

[Sergiu Dumitriu] PT-1917: Updated cancer section in the pedigre editor (some rewordings, added "none of the above" button).

[Sergiu Dumitriu] PT-2077: The ability to push patients to another server is no longer available

[Sergiu Dumitriu] [cleanup] Applied codestyle

[Sergiu Dumitriu] [misc] Fixed bad test

[Sergiu Dumitriu] [cleanup] Applied codestyle

[Sergiu Dumitriu] [misc] Rewrite test so that it doesn't alter the Restlet engine, since other tests require a valid engine

[Sergiu Dumitriu] [misc] Re-commit changes lost when rewriting the pedigree using require.js

[Sergiu Dumitriu] [cleanup] Fixed indentation + typos

[mjshepherd] PT-2059: "Enter" should accept first phenotype suggestion

[mjshepherd] PT-2058: Phenotype search should regain focus after selecting suggestion

[mjshepherd] PT-2080: Unable to add notes on "affected" cancer after reload if notes field was blank before reload

[Sergiu Dumitriu] PT-2083: Upgrade to Solr 5.3.1

[Sergiu Dumitriu] PT-2084: Enter should accept the selected suggestion

[Sergiu Dumitriu] [misc] Update dependencies

[Sergiu Dumitriu] [misc] Update main class declaration after changing packages

[Sergiu Dumitriu] [misc] Added git configuration files

[Sergiu Dumitriu] [misc] Update data files

[Sergiu Dumitriu] [misc] Start bringing the omim indexer closer to being merged with the main PhenoTips codebase

[Sergiu Dumitriu] [cleanup] Use try-with-resources

[Sergiu Dumitriu] [cleanup] Applied codestyle

[Sergiu Dumitriu] [cleanup] Removed unneeded method

[Sergiu Dumitriu] [cleanup] Removed unused class

[Sergiu Dumitriu] [cleanup] Removed classes already present in a dependency

[Sergiu Dumitriu] [cleanup] Added license headers

[asm] PT-2089: In pedigree BOADICEA export non-monozyg. twins are exported as siblings

[Sergiu Dumitriu] [cleanup] Improved codestyle

[asm] PT-2087: In pedigree editor comments box appears on all tabs of a node's menu

[Sergiu Dumitriu] [cleanup] Improve build configuration codestyle

[Sergiu Dumitriu] PT-2007: Minify Pedigree

[Sergiu Dumitriu] PT-2087: The comments box should appear in all tabs of a node's menu

[tarang] initial ObstetricHistoryController test

[tarang] updated dependencies, corrected initial test

[Sergiu Dumitriu] [misc] Use online resources for indexing

[tarang] changed test

[Sergiu Dumitriu] [cleanup] Removed legacy sources

[tarang] PT-2046: default behaviour test

[Sergiu Dumitriu] [misc] store the full link to genereviews for backwards compatibility

[Sergiu Dumitriu] [cleanup] Define more constants

[Sergiu Dumitriu] [cleanup] Use commons-csv for parsing mim2gene instead of a custom class

[Sergiu Dumitriu] [misc] Fixed dependencies

[Sergiu Dumitriu] [misc] Move all loading code into one class

[Sergiu Dumitriu] [cleanup] Removed code duplication

[Sergiu Dumitriu] [misc] Removed local data

[Sergiu Dumitriu] [cleanup] Applied codestyle, use a proper logger

[Sergiu Dumitriu] [misc] Move classes in the right place

[Sergiu Dumitriu] [misc] Prepare for merging: deleted files that won't be needed anymore

[Sergiu Dumitriu] [misc] Declared the used dependencies

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] [cleanup] Added javadoc

[Sergiu Dumitriu] [cleanup] Don't expose more information than needed

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] [cleanup] Moved class in the right package

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] [cleanup] Removed unneeded whitespace

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] [misc] Always ignore Solr locks

[Sergiu Dumitriu] PT-497: Add the possibility to reindex OMIM from the administration

[Sergiu Dumitriu] PT-2097: Display only the official title for OMIM diseases

[tarang] exception catching test

[asm] PT-1917: Fix cancer notes icon clickable when it should not be; minor UI update

[root] Issue PT-1619: ExportFilter count does not reflect number of patients that will be exported.

[Sergiu Dumitriu] [misc] Various Maven plugin updates

[Sergiu Dumitriu] PT-1827: Make the homepage easily extensible

[Sergiu Dumitriu] [cleanup] Improved codestyle

[Sergiu Dumitriu] [misc] Sync xobjects with their xclasses

[Sergiu Dumitriu] PT-2112: Add a VocabularyInputTerm interface

[Sergiu Dumitriu] PT-2105: Add a VocabularyExtension @Role

[Sergiu Dumitriu] PT-2105: Add a VocabularyExtension @Role

[Sergiu Dumitriu] PT-2120: When allowing guests to view data, many styles, scripts and UI elements are broken

[Sergiu Dumitriu] [misc] Sync xobjects with their xclass

[Sergiu Dumitriu] [cleanup] Cleanup whitespace

[Sergiu Dumitriu] PT-2122: The TranslationManager component cannot be used

[Sergiu Dumitriu] [misc] Mark new role as unstable API

[Sergiu Dumitriu] PT-2122: The TranslationManager component cannot be used

[Sergiu Dumitriu] [misc] Use the new TranslationManager instead of XWiki's LocalizationManager

[Sergiu Dumitriu] [misc] Use the new TranslationManager instead of XWiki's LocalizationManager

[marta.girdea] PT-2132: Requesting raster export of pedigree images fails

[tarang] initial save tests

[tarang] saveDefaultBehaviourTest

[tarang] initial writejson test

[tarang] completed writejson tests

[tarang] readJSON tests

[tarang] corrected pom files

[Sergiu Dumitriu] PT-2110: Validation for date of death should not display anything if valid

[Sergiu Dumitriu] PT-2147: Move the Identifier column to the second place of the All patient record page

[Sergiu Dumitriu] [misc] Sync xobjects with their current xclass

[orion.buske] PT-2144: Added controller tests for deletion bug

[orion.buske] [misc] Return null instead of empty gene list

[orion.buske] PT-2143: Fixed deletion bug in ListControllers

[Sergiu Dumitriu] [cleanup] Revert wrong change

[Sergiu Dumitriu] [cleanup] Applied codestyle, fixed compiler warnings

[Sergiu Dumitriu] PT-2046: Add unit tests for the Obstetric History controller

[Sergiu Dumitriu] PT-2151: Placeholder text in "Other" term search box gets saved

[veronika-koltunov] PT-2023: One unified gene section with variants (Issue #1280). Final commit for codefeview

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[INFO] Building PhenoTips - DMG Distribution 1.3-SNAPSHOT
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[INFO] --- maven-clean-plugin:2.6.1:clean (default-clean) @ phenotips-rpm ---
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[INFO] Reactor Summary:
[INFO] 
[INFO] PhenoTips - Parent POM ............................ SUCCESS [1.241s]
[INFO] PhenoTips - Resource packages ..................... SUCCESS [0.195s]
[INFO] PhenoTips - Jetty ................................. SUCCESS [0.042s]
[INFO] PhenoTips - Jetty Lifecycle Listener - Log Writer . SUCCESS [0.023s]
[INFO] PhenoTips - Jetty Lifecycle Listener - Open Browser  SUCCESS [0.110s]
[INFO] PhenoTips - Jetty Resources ....................... SUCCESS [0.047s]
[INFO] PhenoTips - Solr configuration files .............. SUCCESS [0.231s]
[INFO] PhenoTips - Various Java components ............... SUCCESS [0.007s]
[INFO] PhenoTips - Default administrative account and default rights  SUCCESS [0.090s]
[INFO] PhenoTips - Joda Time Script Service .............. SUCCESS [0.036s]
[INFO] PhenoTips - UI Widgets ............................ SUCCESS [0.020s]
[INFO] PhenoTips - UI Widgets - Documents providing various widgets  SUCCESS [0.011s]
[INFO] PhenoTips - Skin .................................. SUCCESS [0.022s]
[INFO] PhenoTips - Skin - Documents providing the custom Skin  SUCCESS [0.048s]
[INFO] PhenoTips - General navigation .................... SUCCESS [0.024s]
[INFO] PhenoTips - Navigation - Java APIs ................ SUCCESS [0.021s]
[INFO] PhenoTips - OBO to Solr conversion ................ SUCCESS [0.016s]
[INFO] PhenoTips - Data model constants .................. SUCCESS [0.035s]
[INFO] XWiki Platform - Core - Users - Parent POM ........ SUCCESS [0.064s]
[INFO] XWiki Platform - Core - Users - API ............... SUCCESS [0.055s]
[INFO] PhenoTips - Patient data .......................... SUCCESS [0.032s]
[INFO] PhenoTips - Patient data - Java APIs .............. SUCCESS [0.062s]
[INFO] PhenoTips - Vocabularies .......................... SUCCESS [0.034s]
[INFO] PhenoTips - Vocabularies - APIs ................... SUCCESS [0.047s]
[INFO] PhenoTips - Vocabularies - Human Phenotype Ontology integration  SUCCESS [0.030s]
[INFO] PhenoTips - Vocabularies - Human Phenotype Ontology integration - APIs  SUCCESS [0.059s]
[INFO] PhenoTips - Vocabularies - Human Phenotype Ontology integration - Documents providing HPO services  SUCCESS [0.046s]
[INFO] PhenoTips - Vocabularies - Online Mendelian Inheritance in Man integration  SUCCESS [0.006s]
[INFO] PhenoTips - Vocabularies - Online Mendelian Inheritance in Man integration - APIs  SUCCESS [0.016s]
[INFO] PhenoTips - Vocabularies - Online Mendelian Inheritance in Man integration - Documents providing services  SUCCESS [0.009s]
[INFO] PhenoTips - Vocabularies - HUGO Gene Nomenclature Committee (GeneNames) integration  SUCCESS [0.030s]
[INFO] PhenoTips - Vocabularies - HUGO Gene Nomenclature Committee (GeneNames) integration - APIs  SUCCESS [0.021s]
[INFO] PhenoTips - Vocabularies - HUGO Gene Nomenclature Committee (GeneNames) integration - Documents providing services  SUCCESS [0.037s]
[INFO] PhenoTips - Solr Access Service ................... SUCCESS [0.006s]
[INFO] PhenoTips - Solr Access Service - Java code ....... SUCCESS [0.021s]
[INFO] PhenoTips - Solr Access Service - Documents providing phenotype and disease suggestions  SUCCESS [0.070s]
[INFO] PhenoTips - Component Manager Registry ............ SUCCESS [0.018s]
[INFO] PhenoTips - Application configuration ............. SUCCESS [0.035s]
[INFO] PhenoTips - Application configuration - Java APIs . SUCCESS [0.045s]
[INFO] PhenoTips - Patient data - Default implementation for the Java APIs  SUCCESS [0.082s]
[INFO] XWiki Translation Manager ......................... SUCCESS [0.047s]
[INFO] PhenoTips - Various Tools ......................... SUCCESS [0.083s]
[INFO] PhenoTips - Patient data - Documents providing the patient class, sheet and display code  SUCCESS [0.018s]
[INFO] PhenoTips - Users and Groups ...................... SUCCESS [0.006s]
[INFO] PhenoTips - Users and Groups - Wiki Documents ..... SUCCESS [0.040s]
[INFO] PhenoTips - Application configuration - Documents providing the configuration classes and their display code  SUCCESS [0.050s]
[INFO] PhenoTips - Patient access rules .................. SUCCESS [0.006s]
[INFO] PhenoTips - Patient access rules - Wiki Documents . SUCCESS [0.031s]
[INFO] PhenoTips - Navigation - Documents providing the homepage and the All Data page  SUCCESS [0.046s]
[INFO] PhenoTips - User - Profile - UI ................... SUCCESS [0.043s]
[INFO] PhenoTips - Data export ........................... SUCCESS [0.007s]
[INFO] PhenoTips - Data export - Spreadsheet Export APIs . SUCCESS [0.174s]
[INFO] PhenoTips - Data export - Documents providing the Export functionality  SUCCESS [0.011s]
[INFO] PhenoTips - Patient measurements .................. SUCCESS [0.039s]
[INFO] PhenoTips - Patient measurements - Java APIs ...... SUCCESS [0.122s]
[INFO] PhenoTips - Patient measurements - Documents providing the measurements functionality in the UI  SUCCESS [0.008s]
[INFO] PhenoTips - Studies ............................... SUCCESS [0.006s]
[INFO] PhenoTips - Studies - Java APIs ................... SUCCESS [0.057s]
[INFO] PhenoTips - Studies - Wiki Documents .............. SUCCESS [0.074s]
[INFO] PhenoTips - Vocabularies - Documents providing the patient class, sheet and display code  SUCCESS [0.047s]
[INFO] PhenoTips - Patient data sharing .................. SUCCESS [0.006s]
[INFO] PhenoTips - Patient data sharing - Communication Protocol Details  SUCCESS [0.033s]
[INFO] PhenoTips - Patient data sharing - Secure data storage API  SUCCESS [0.014s]
[INFO] PhenoTips - Patient data sharing - Push Java APIs . SUCCESS [0.096s]
[INFO] PhenoTips - Patient data sharing - Push Configuration UI  SUCCESS [0.008s]
[INFO] PhenoTips - Specificity Meter ..................... SUCCESS [0.006s]
[INFO] PhenoTips - Specificity Meter - Documents providing the UI  SUCCESS [0.040s]
[INFO] PhenoTips - Diagnosis Suggestion Service .......... SUCCESS [0.006s]
[INFO] PhenoTips - Diagnosis Suggestion Java Code ........ SUCCESS [0.108s]
[INFO] PhenoTips - Diagnosis Suggestion- Documents providing phenotype and disease suggestions  SUCCESS [0.022s]
[INFO] PhenoTips - Pedigree .............................. SUCCESS [0.006s]
[INFO] PhenoTips - Pedigree - Application Documents ...... SUCCESS [0.009s]
[INFO] PhenoTips - Application interface ................. SUCCESS [0.013s]
[INFO] PhenoTips - Pedigree - JS and CSS Resources ....... SUCCESS [0.124s]
[INFO] PhenoTips - Base War package ...................... SUCCESS [1.196s]
[INFO] PhenoTips - Widget - Java APIs .................... SUCCESS [0.056s]
[INFO] PhenoTips - Skin - Java APIs ...................... SUCCESS [0.032s]
[INFO] PhenoTips - Patient data - Page Objects ........... SUCCESS [0.042s]
[INFO] PhenoTips - Navigation - Testing Page Objects ..... SUCCESS [0.046s]
[INFO] PhenoTips - Navigation - Functional Tests ......... SUCCESS [0.005s]
[INFO] PhenoTips - Vocabularies - Chemical Entities of Biological Interest  SUCCESS [0.010s]
[INFO] PhenoTips - Vocabularies - Chemical Entities of Biological Interest integration - APIs  SUCCESS [0.025s]
[INFO] PhenoTips - Vocabularies - Ethnicity Ontology integration  SUCCESS [0.016s]
[INFO] PhenoTips - Vocabularies - Ethnicity Ontology integration - APIs  SUCCESS [0.014s]
[INFO] PhenoTips - Patient data - Data migrations ........ SUCCESS [0.027s]
[INFO] PhenoTips - Patient Data - REST services .......... SUCCESS [0.218s]
[INFO] PhenoTips - Users and Groups - Java APIs .......... SUCCESS [0.029s]
[INFO] PhenoTips - Patient access rules - Java APIs ...... SUCCESS [0.063s]
[INFO] PhenoTips - Patient data - Solr indexing .......... SUCCESS [0.086s]
[INFO] PhenoTips - Patient data - Functional Tests ....... SUCCESS [0.005s]
[INFO] PhenoTips - Extra fields for patient data ......... SUCCESS [0.014s]
[INFO] PhenoTips - Extra fields for patient data - Medication  SUCCESS [0.006s]
[INFO] PhenoTips - Extra fields for patient data - Medication - Java APIs  SUCCESS [0.043s]
[INFO] PhenoTips - Extra fields for patient data - Medication - Documents providing the medication data class and display code  SUCCESS [0.016s]
[INFO] PhenoTips - Security .............................. SUCCESS [0.005s]
[INFO] PhenoTips - Security - Authorization APIs ......... SUCCESS [0.042s]
[INFO] PhenoTips - Security - Bridge between the old XWiki security interfaces and the new security components  SUCCESS [0.017s]
[INFO] PhenoTips - Patient access rules - Migrations ..... SUCCESS [0.048s]
[INFO] PhenoTips - Patient data sharing - Receiver Java APIs  SUCCESS [0.018s]
[INFO] PhenoTips - Patient data sharing - Receiver UI .... SUCCESS [0.007s]
[INFO] PhenoTips - Patient measurements - Data migrations  SUCCESS [0.119s]
[INFO] XWiki Platform - Core - Users - Wiki .............. SUCCESS [0.036s]
[INFO] PhenoTips - Application configuration - Data migrations  SUCCESS [0.032s]
[INFO] PhenoTips - Storage migrator ...................... SUCCESS [0.012s]
[INFO] PhenoTips - Storage migrators - Java APIs ......... SUCCESS [0.025s]
[INFO] PhenoTips - Storage migrators - Attachments ....... SUCCESS [0.006s]
[INFO] PhenoTips - Storage migrators - Attachments - DataBase store  SUCCESS [0.034s]
[INFO] PhenoTips - Storage migrators - Attachments - Filesystem store  SUCCESS [0.021s]
[INFO] PhenoTips - Storage migrators - Attachments - Generic migrator  SUCCESS [0.013s]
[INFO] PhenoTips - NCBI eUtils Services .................. SUCCESS [0.017s]
[INFO] PhenoTips - NCBI eUtils Services - Java APIs ...... SUCCESS [0.020s]
[INFO] PhenoTips - NCBI eUtils Services - Documents providing PubMed relevant articles suggestions  SUCCESS [0.007s]
[INFO] PhenoTips - Specificity Meter - Java APIs ......... SUCCESS [0.086s]
[INFO] PhenoTips - MedSavant Integration - Java APIs ..... SUCCESS [0.024s]
[INFO] PhenoTips - Pedigree - Java APIs .................. SUCCESS [0.032s]
[INFO] PhenoTips - Misc - Support for proxy authentication  SUCCESS [0.032s]
[INFO] PhenoTips - Record Locking ........................ SUCCESS [0.005s]
[INFO] PhenoTips - Record Locking - API .................. SUCCESS [0.039s]
[INFO] PhenoTips - Record Locking - UI - Documents providing record locking functionality  SUCCESS [0.008s]
[INFO] PhenoTips - Distribution packages ................. SUCCESS [0.005s]
[INFO] PhenoTips - HSQLDB Database ....................... SUCCESS [7.089s]
[INFO] PhenoTips - War package ........................... SUCCESS [0.765s]
[INFO] PhenoTips - Standalone Distribution ............... SUCCESS [0.008s]
[INFO] PhenoTips - DMG Distribution ...................... SUCCESS [0.003s]
[INFO] PhenoTips - RPM Distribution ...................... SUCCESS [0.040s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 32.806s
[INFO] Finished at: Sun Oct 25 01:27:59 EDT 2015
[INFO] Final Memory: 35M/308M
[INFO] ------------------------------------------------------------------------
Setting status of 4e72b3547036f6763c15b8a8480610a3e47726a8 to FAILURE with url https://ci.phenotips.org/job/PhenoTips-pull-requests/986/ and message: 'Build finished.'
Could not update commit status of the Pull Request on GitHub.
java.net.ConnectException: Connection timed out
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:579)
	at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:625)
	at sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:160)
	at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)
	at sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:275)
	at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:371)
	at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:933)
	at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177)
	at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(HttpURLConnection.java:1092)
	at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(HttpsURLConnectionImpl.java:250)
	at org.kohsuke.github.Requester.buildRequest(Requester.java:299)
	at org.kohsuke.github.Requester._to(Requester.java:221)
	at org.kohsuke.github.Requester.to(Requester.java:191)
	at org.kohsuke.github.GHRepository.createCommitStatus(GHRepository.java:780)
	at org.jenkinsci.plugins.ghprb.extensions.status.GhprbSimpleStatus.createCommitStatus(GhprbSimpleStatus.java:91)
	at org.jenkinsci.plugins.ghprb.extensions.status.GhprbSimpleStatus.onBuildComplete(GhprbSimpleStatus.java:76)
	at org.jenkinsci.plugins.ghprb.GhprbBuilds.onCompleted(GhprbBuilds.java:145)
	at org.jenkinsci.plugins.ghprb.GhprbBuildListener.onCompleted(GhprbBuildListener.java:27)
	at org.jenkinsci.plugins.ghprb.GhprbBuildListener.onCompleted(GhprbBuildListener.java:12)
	at hudson.model.listeners.RunListener.fireCompleted(RunListener.java:201)
	at hudson.model.Run.execute(Run.java:1789)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:537)
	at hudson.model.ResourceController.execute(ResourceController.java:98)
	at hudson.model.Executor.run(Executor.java:374)
ERROR: Unable to send to address: asm at asm.(none)
javax.mail.internet.AddressException: Domain ends with dot in string ``asm at asm.''
	at javax.mail.internet.InternetAddress.checkAddress(InternetAddress.java:1277)
	at javax.mail.internet.InternetAddress.parse(InternetAddress.java:1091)
	at javax.mail.internet.InternetAddress.parse(InternetAddress.java:633)
	at javax.mail.internet.InternetAddress.<init>(InternetAddress.java:111)
	at hudson.tasks.Mailer.StringToAddress(Mailer.java:180)
	at jenkins.plugins.mailer.tasks.MimeMessageBuilder.toNormalizedAddress(MimeMessageBuilder.java:262)
	at jenkins.plugins.mailer.tasks.MimeMessageBuilder.addRecipients(MimeMessageBuilder.java:141)
	at jenkins.plugins.mailer.tasks.MimeMessageBuilder.addRecipients(MimeMessageBuilder.java:133)
	at hudson.tasks.MailSender.createEmptyMail(MailSender.java:380)
	at hudson.tasks.MailSender.createFailureMail(MailSender.java:260)
	at hudson.tasks.MailSender.createMail(MailSender.java:178)
	at hudson.tasks.MailSender.run(MailSender.java:107)
	at hudson.tasks.MailSender.execute(MailSender.java:101)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.cleanUp(MavenModuleSetBuild.java:1071)
	at hudson.model.Run.execute(Run.java:1791)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:537)
	at hudson.model.ResourceController.execute(ResourceController.java:98)
	at hudson.model.Executor.run(Executor.java:374)
ERROR: Unable to send to address: root at ravi-K53SV.(none)
javax.mail.internet.AddressException: Domain ends with dot in string ``root at ravi-K53SV.''
	at javax.mail.internet.InternetAddress.checkAddress(InternetAddress.java:1277)
	at javax.mail.internet.InternetAddress.parse(InternetAddress.java:1091)
	at javax.mail.internet.InternetAddress.parse(InternetAddress.java:633)
	at javax.mail.internet.InternetAddress.<init>(InternetAddress.java:111)
	at hudson.tasks.Mailer.StringToAddress(Mailer.java:180)
	at jenkins.plugins.mailer.tasks.MimeMessageBuilder.toNormalizedAddress(MimeMessageBuilder.java:262)
	at jenkins.plugins.mailer.tasks.MimeMessageBuilder.addRecipients(MimeMessageBuilder.java:141)
	at jenkins.plugins.mailer.tasks.MimeMessageBuilder.addRecipients(MimeMessageBuilder.java:133)
	at hudson.tasks.MailSender.createEmptyMail(MailSender.java:380)
	at hudson.tasks.MailSender.createFailureMail(MailSender.java:260)
	at hudson.tasks.MailSender.createMail(MailSender.java:178)
	at hudson.tasks.MailSender.run(MailSender.java:107)
	at hudson.tasks.MailSender.execute(MailSender.java:101)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.cleanUp(MavenModuleSetBuild.java:1071)
	at hudson.model.Run.execute(Run.java:1791)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:537)
	at hudson.model.ResourceController.execute(ResourceController.java:98)
	at hudson.model.Executor.run(Executor.java:374)


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