See <
https://ci.eclipse.org/ice/job/ice-next/831/display/redirect?page=changes>
Changes:
[smithrw] Fixed target
[anara.ornl] Update the licence reference
[smithrw] Fixed target
[smithrw] Updated build for changes in target
[Jay Jay Billings] Deleted everything except the original framework. Mostly.
[Jay Jay Billings] Fixed other things preventing target resolution in the build.
[Jay Jay Billings] Cleaned up minor things, but build is still broken.
[Jay Jay Billings] Pushing some basic III changes.
[Jay Jay Billings] Added initial Identifiable OWL schema and instance.
[Jay Jay Billings] Added Component and most of Composite to ontology.
[Jay Jay Billings] Intermediate progress on OWL ontology.
[Jay Jay Billings] Added most of the component list and associated baggage.
[Jay Jay Billings] Renamed and moved the project directory.
[Jay Jay Billings] Added test files.
[Jay Jay Billings] Reorganized files and combined the projects.
[Jay Jay Billings] Further cleanup.
[Jay Jay Billings] Fixed test structure and build paths.
[Jay Jay Billings] Figured out basic Jena operations with the ICE ontology.
[Jay Jay Billings] Minor changes based on the static constants.
[Jay Jay Billings] Finished first implementation of ComponentBuilder and its test.
[Jay Jay Billings] Finished the first complete implementation of ComponentBuilder and test.
[Jay Jay Billings] Finished ICEModelFactory basic implementation.
[Jay Jay Billings] Added stubs for the next set of data classes and tests.
[Jay Jay Billings] Started Fuseki connection testing.
[Jay Jay Billings] Minor cleanup of FusekiTest.
[Jay Jay Billings] I have a working example of dataset creation wired up in FusekiTest.
[Jay Jay Billings] Minor changes ahead of migrating this to BATS.
[Jay Jay Billings] Minor preferences update.
[Jay Jay Billings] Added ReadWrite import and uncommented some parts.
[Jay Jay Billings] Renamed data OWL file. Added workflows project.
[Jay Jay Billings] Capturing a few lines of notes.
[Jay Jay Billings] Renamed/scoped the ICE data ontology namespace to be more precise.
[Jay Jay Billings] Added some notes. Removed tracked target files.
[Jay Jay Billings] Fixed some errors in the data ontology, continued on workflows.
[Jay Jay Billings] Reworked some of this using Protege.
[Jay Jay Billings] Added more to the workflow ontology. Started making tests.
[Jay Jay Billings] Fixed action types and added subclasses.
[Jay Jay Billings] Changed "Bash Script" to "Shell Script."
[Jay Jay Billings] Added CWLTool to represent Common Workflow Language Tools.
[Jay Jay Billings] Added web service subclasses, reorganized language invocation.
[Jay Jay Billings] Fixed multiple object properties...
[Jay Jay Billings] Fixing project file.
[Jay Jay Billings] Reworked Task.
[Jay Jay Billings] Cleaned up and modified Workflow Description.
[Jay Jay Billings] Finished task model, workflow description, action updates.
[Jay Jay Billings] Added Spring State Machine dependency.
[Jay Jay Billings] Fixed state names and documentation in workflow ontology.
[Jay Jay Billings] Added a simple Spring State Machine for file moving.
[Jay Jay Billings] Fixed some ignores.
[Jay Jay Billings] Added test turtl files for simple move and Pegasus split workflows.
[Jay Jay Billings] Finished pegasus split example. Started on ICE example.
[Jay Jay Billings] Finished ICE and SNS-HFIR workflows.
[Jay Jay Billings] Added commands bundle (no classes).
[Jay Jay Billings] Fixed test package name.
[Jay Jay Billings] Added CommandFactory and test stub. Added junit dependency.
[Jay Jay Billings] Added FileHandler classes for file transfer commands.
[Jay Jay Billings] Added additional stubs for classes and tests.
[osbornjd] Initial commit of some basic classes for API
[osbornjd] Some test classes
[osbornjd] More class commits with associated test classes
[osbornjd] Added some member variables to classes
[osbornjd] Added some member variables to classes
[osbornjd] Pushing new commit message
[osbornjd] Added more member variables and functions
[osbornjd] Developed local commands, started implementing file handler after rebase
[osbornjd] Changed local FileHandler/copy/move command tests to create temp files
[osbornjd] Moved testfile creation into setup functions
[osbornjd] Fixed monitorJob() exitValue bug
[osbornjd] Changed copy/move inheritance structure
[osbornjd] Removed isLocal AtomicBoolean as it is extraneous
[osbornjd] Added some finals in a few method arguments
[osbornjd] Changed fixExecutableName function name
[osbornjd] Delete test files after creation, check file creation in FileHandler
[osbornjd] Moved execute() outside of constructor to be called by user
[osbornjd] Removed System.exit(1) calls from CommandFactory
[osbornjd] Trying to add logger, still debugging
[osbornjd] Added default log4j properties file so that logger actually prints stuff
[osbornjd] Cleaned up command test, cleaned up CommandStatus options
[osbornjd] Ran eclipse formatter on everything. Will do in the future by default
[osbornjd] Removed some (to date) unimplemented test failures so that maven could
[Jay Jay Billings] Cleaned up FileHandler.
[osbornjd] Cleaned up FileHandler.
[osbornjd] Committing some remote command functionality
[osbornjd] Reconfigured much of CommandConfiguration, Command, etc.
[osbornjd] Overhaul of Command design
[osbornjd] Removed static declaration from CommandFactory class
[osbornjd] Removed CommandConfiguration constructor and not accessing with get/set
[osbornjd] Move setConfiguration to Command, delete useless test class
[osbornjd] Constructed some tests for getting the executable name in CommandConfig
[osbornjd] Re-added fails to unimplemented tests, added CommandStatus documentation
[osbornjd] Added comments to all getter/setter pairs
[osbornjd] Committing to save changes made to FileHandler
[osbornjd] Separated comments in CommandConfiguration get/set, small improvements
[osbornjd] Beginning overhaul of FileHandler framework - more to work on
[osbornjd] Overhaul of FileHandler design
[Jay Jay Billings] Fixed the name of FileHandlerFactory.
[Jay Jay Billings] Changed method name to FileHandlerFactory.getFileHandler.
[Jay Jay Billings] Hooked FileHandler up to the workflow code.
[Jay Jay Billings] Fixed paths in test.
[osbornjd] Committing to pull
[osbornjd] Added examples showing the command API
[osbornjd] Changed FileHandler design to use default constructors and accessors
[osbornjd] Removed unnecessary ConnectionConfigurations
[osbornjd] Fixed up comments
[osbornjd] Committing some intermediate work while breaking to merge Jay's changes.
[Jay Jay Billings] Added tests/resources folder to fix Maven build.
[osbornjd] Added test and code to address bug of changing file names
[osbornjd] Moved file extension logic into own function
[osbornjd] Moved copy/move functionality into base class
[osbornjd] Added some things to Command as asked by Ross/Jean
[osbornjd] Put OS back in command config
[osbornjd] Changed command configuration function name
[osbornjd] Added os test in CommandConfiguration
[osbornjd] Committing two days of work on remote commands
[osbornjd] Adjusted remote password collection, fixed a test or two
[osbornjd] Adjusted some tests and username/hostname grabbing. Also reformatted
[osbornjd] Put JSch in pom instead of classpath
[osbornjd] Committing work from yesterday on remote commands
[osbornjd] Execute remote command test successful
[osbornjd] Finishing up Remote Commands functionality
[osbornjd] Adjusted some of Command's design, added a few other things
[osbornjd] Added a console eraser class and function to mask password input
[osbornjd] Condensed some Command functionality
[osbornjd] Added some more tests, refactored a few things
[osbornjd] Cleaned up several tests, unified path/script settings
[osbornjd] Fixed file permission bug
[osbornjd] Moved remote working directory to command configuration
[osbornjd] First pass at remote file handling tests, start development next
[osbornjd] Wrote tests for remote file handling, need to write source code now
[osbornjd] Committing changes requested by Jay, some more tests, and remote file
[osbornjd] Dummy change since git password was rejected for some reason
[osbornjd] Git config was messed up, trying again
[osbornjd] Updated connection list to hash map instead of array list
[osbornjd] Adjusted protected/private member variables as needed
[osbornjd] Removed requirement of an inputfile
[osbornjd] Edited CommandConfiguration etc. to handle multiple input files
[osbornjd] Eclipse didn't pick up the additional input file
[osbornjd] Changed format of inputfiles to have the option to match Robert's
[osbornjd] Updated JRE
[osbornjd] Added test for null connection from getConnection
[osbornjd] Changed key set to values in close all connections iteration
[osbornjd] Updated comment
[osbornjd] Started implementing multi-hop functionality
[osbornjd] Started remote file handling api
[osbornjd] Made ConnectionManager local
[osbornjd] Adjusted input file naming format to hashmap
[osbornjd] Whoops, uncommented the tests
[osbornjd] Added more tests, also added a build script
[osbornjd] Added some file handling source code, more work to do
[osbornjd] Lots of work on remote file handling. Created static ConnManagerFactory
[osbornjd] Updated ConnectionManagerFactory, implemented functioning remote file
[osbornjd] Added remote copy test
[osbornjd] Checked file handler factory source code and tests
[osbornjd] All FileHandlerFactoryTests now independent
[osbornjd] Added ability to create multiple subdirectories remotely
[osbornjd] Cleaned up some tests, added file removal. formatted all files
[osbornjd] Fixed up some tests and put file handler api into remote commands
[osbornjd] Cleaned up some tests
[osbornjd] Fixed local move bug, added test to check for it
[osbornjd] Updated some tests, added source code to the examples in demo
[osbornjd] Refactored comments
[osbornjd] Formatted all setter functions the same
[osbornjd] Added comments to get password function
[osbornjd] Moved exception catching to the publicly called functions
[osbornjd] Checked that all exceptions were properly logged
[osbornjd] Removed all cases of else with return
[osbornjd] Checked that all exceptions were properly handled or logged
[osbornjd] Altered try/catch logic for channel connection in running remote cmd
[osbornjd] Removed all print stack traces, changed checkStatus to return bool
[osbornjd] Added some file handling log statements
[osbornjd] Added functionality to run python scripts, including test and example
[osbornjd] Initial commit of password authorization design
[osbornjd] Implemented console and SWT password functionality, with tests
[osbornjd] Commented out tests since they aren't automated
[osbornjd] Added option to get password from an input text file
[osbornjd] Committing note on password factory
[osbornjd] Moved SWT authorization to its own package to remove extra dependencies
[osbornjd] Eclipse missed .project
[osbornjd] Changed class names, reorganizing password collection in ConnManager
[osbornjd] Complete overhaul of password authorization design and implementation
[osbornjd] Added settings directory to swt package
[osbornjd] Added short README
[osbornjd] Updated string output to add line by line
[osbornjd] Fixed examples to contain new password authorization API
[osbornjd] Fixed remote command ls bug. added corresponding test
[osbornjd] Removed absolute directory reference
[osbornjd] Added hello world windows powershell script
[osbornjd] Working on profiling remote commands, haven't made much progress
[osbornjd] Minimum working example of a remote ls command
[osbornjd] Updated README to include comment on double dependencies discovered
[osbornjd] Majorly revamped the file handling connections
[osbornjd] Continued speed improvements
[osbornjd] Fixed bug in connection manager test, uncommented remote command tests
[osbornjd] Remote commands connection management changes
[osbornjd] Fixed bug that required working directory to end in /
[osbornjd] Removed some excessive log statements
[osbornjd] Session management
[osbornjd] Commit for windows local command testing
[osbornjd] Altered functionality to include remote scripts and local input files
[osbornjd] Cleaned up test file clean up
[osbornjd] Implemented changes requested by Jay
[osbornjd] Added git ignore files, modified swt build script name
[osbornjd] Fixed examples
[osbornjd] Fixed local command test for windows
[osbornjd] Commit updated README after discussion with Lance
[osbornjd] Testing git commit on desktop
[osbornjd] Some improved tests for windows
[osbornjd] Fixed bug
[osbornjd] Added test for exceptional grep exit value case, added code for
[osbornjd] Switched outfile names
[osbornjd] Removed exit value exception logic
[osbornjd] Fixed test for Windows
[osbornjd] LocalFileHandler windows tests pass
[osbornjd] Updated ConnectionManager test for windows
[osbornjd] Remote file transfer windows tests
[osbornjd] Typo in cred file name
[osbornjd] Fixed remote dummy host file deletion
[osbornjd] Remote file handling windows tests
[osbornjd] Fix IFileHandlerFactoryTests for windows
[osbornjd] Added stack trace
[osbornjd] Added stack traces to logging statements for debugging
[osbornjd] Forgot to add script
[osbornjd] Comment this out for now, need to return to it with robert
[osbornjd] Fixed up remote command tests for windows
[osbornjd] Remote Command test bug fixed
[osbornjd] Fixed up command and command factory tests for windows
[osbornjd] Committing minor changes to connection in file handling
[osbornjd] Separated sftp and exec channels. Reformatted code with eclipse format
[osbornjd] Added some comments
[osbornjd] Added argument variable and associated test for fix executable
[osbornjd] Committing first pass at (nonfunctional) file browsing tests
[osbornjd] Commit to switch branches
[osbornjd] Added test with argument and input files
[osbornjd] Committing work from yesterday on file browsing
[osbornjd] Implemented remote file walking, refactored names
[osbornjd] Fixed file creation bug windows
[osbornjd] Always delete remote file browsing tree structure
[osbornjd] Windows testing for remote file browser and tests
[osbornjd] windows testing
[osbornjd] Added some code to increase security of ssh connection
[osbornjd] Set strict host checking to no for tests
[osbornjd] Updated readme with blurb about public key in known_hosts
[osbornjd] Removed the StrictHostKeyChecking in tests, setup a setter for users
[osbornjd] Trying to fix CI connection
[osbornjd] Added some more detail to commands use readme
[osbornjd] Fix exception
[osbornjd] Committing spaces for ci test
[osbornjd] Added enum to explicitly set transfer type
[osbornjd] Changed FileBrower logger class name
[osbornjd] Altered design for FileHandler to return a FileBrowser and for...
[osbornjd] updated readme
[osbornjd] Updated command manager known_hosts default location for windows
[osbornjd] Committing some gitignores
[osbornjd] Removed a few simple TODOs, formatted each class
[osbornjd] Added private key authentication possibility in ConnectionManager
[osbornjd] Removed duplicate code for key authorization, cleaned up manager
[osbornjd] Created a Basic connection authorization to take uname/hname/pwd
[osbornjd] Change key paths to system default
[osbornjd] Adjusted some comments, a few connection related clean ups
[osbornjd] Remove unnecessary line
[osbornjd] Trying to make file browser more efficient
[osbornjd] updated readme with keygen test info
[osbornjd] Delete remote files made in test
[osbornjd] Fixed file deletion test error
[osbornjd] Fixed tests to run appropriately on any arbitrary remote host (i.e. not
[osbornjd] Add all ssh authentication methods from known_hosts
[osbornjd] Adjusted authorization type to a list for easy additions
[osbornjd] Added statements in to check for job cancellation in job monitoring
[osbornjd] Updated README with connection manager info
[osbornjd] Fixed comment
[osbornjd] Reformatted
[osbornjd] Merging
[osbornjd] Removed redundant code
[osbornjd] Added getter/setter for ConnectionManager
[osbornjd] Made set connection public, streamlined keypath tests, removed todo
[osbornjd] hack fix for jsch threading issue for now
[osbornjd] Removed log statements
[osbornjd] Committing hello world modeling project
[Jay Jay Billings] Added initial prototype files.
[Jay Jay Billings] Added cleanup task lists.
[smithrw] Changed package name for inclusion in ICE
[smithrw] Added copyright statements
[smithrw] Created org.eclipse.ice.tests.renderer package
[smithrw] Moved DataElement to its own file
[Jay Jay Billings] Class path and preference changes.
[Jay Jay Billings] Fixed other classpath issues (maven eclipse:clean & maven
[Jay Jay Billings] Fixed renderer project structure to match the Maven standard.
[Jay Jay Billings] Finished the first complete implementation of DataElement.
[Jay Jay Billings] Added an slf4j logger.
[Jay Jay Billings] Finished some cleanup and first cut of the _javascript_Validator.
[Jay Jay Billings] Updated the class documentation and fixed missing equals() docs.
[Jay Jay Billings] Fixing project structure, classpath, and build issues.
[Jay Jay Billings] Fixed class paths and build.
[Jay Jay Billings] Cleaned up POM file and fixed release version to 11.
[Jay Jay Billings] Switched to Dagger 2 for dependency injection.
[Jay Jay Billings] Added some classes and a dependency to play with annotations.
[Jay Jay Billings] Added annotations bundle.
[Jay Jay Billings] Added .gitignore
[Jay Jay Billings] Added .gitignore
[Jay Jay Billings] Added annotations to the annotations.
[Jay Jay Billings] Fixed bug where annotations were not registered.
[Jay Jay Billings] Fixed bug where annotation processes were not called.
[Jay Jay Billings] Set version back to Java 11 after fixing processors.
[bluhmdj] Exclude logback-classic
[bluhmdj] Basic processing in place with template
[bluhmdj] Refine processor, write to JavaFileObject
[bluhmdj] Cleanup
[bluhmdj] Remove duplicate logback-classic exclusion
[bluhmdj] Clean up formatting
[bluhmdj] Skip annotations not of type DataField
[bluhmdj] Only visit DataFields
[bluhmdj] Correctly handle single and many DataField Annotations
[bluhmdj] Ensure auto service is working
[bluhmdj] Simplify annotation value retrieval method
[bluhmdj] Split inner classes out to separate files
[bluhmdj] Document body of process and writeClass
[bluhmdj] Drop main from DataElement.vm
[bluhmdj] stackTracetoString -> stackTraceToString
[bluhmdj] Return false from DataElementProcessor
[bluhmdj] More documentation
[bluhmdj] Remove @DataElement from HTMLView
[bluhmdj] Avoid using hardcoded strings, move to enums
[bluhmdj] Add elements from property map as fields
[bluhmdj] Add properties from DataElement<T>
[bluhmdj] Initial tests for @DataElement
[bluhmdj] Create DefaultFields helper
[bluhmdj] Add failing tests back in
[bluhmdj] Update template to pass tests
[bluhmdj] Refine DefaultFields
[bluhmdj] Add more documentation to DefaultFields, Fields, Tests
[bluhmdj] Documentation and refinements on Field
[bluhmdj] Load Fields from JSON file with @DataFieldJson
[bluhmdj] Set annotation version to 11
[bluhmdj] Generate comments for the default fields
[bluhmdj] Make matches() less branch-tastic
[bluhmdj] Fill out IDataElement with accessors for DefaultFields
[bluhmdj] Add documentation to Fields
[bluhmdj] Rework DataFieldsVisitor
[bluhmdj] Add deserialization methods for recently added fields
[bluhmdj] Use ObjectMapper in DataFieldsVisitor
[bluhmdj] Use one ObjectMapper in DataElementProcessor
[bluhmdj] Remove intermediate value
[bluhmdj] No longer need to escape JSON defaultValues
[bluhmdj] Fix setter template
[bluhmdj] Fix defaultValue escaping and add tests
[bluhmdj] Add JUnit dependency to dev.annotations
[bluhmdj] Fix eclipse settings to target Java 11
[bluhmdj] Simplify retrieving AnnotationMirrors by class
[bluhmdj] Initial Persistence interface and annotation
[bluhmdj] ContextProperty -> DataElementTemplateProperty
[bluhmdj] Add DataElementRoot class
[bluhmdj] Add fromJSON(T) where T extends Map<String,Object>
[bluhmdj] Add initial PersistenceHandler template
[bluhmdj] Generate Persistence Find methods by fields
[bluhmdj] Remove FieldAlias and just use Field
[bluhmdj] Generate find methods for aliases
[bluhmdj] Add docs to PersistenceHandler interface and impl
[bluhmdj] Custom filter methods to handle UUID special case
[bluhmdj] Remove asMap
[bluhmdj] Rework generics in IPersistenceHandler
[bluhmdj] Manually include methods generated by DataElement
[bluhmdj] Persisted Annotation docs.
[bluhmdj] Rename find() -> findAll()
------------------------------------------
Started by an SCM change
Running as SYSTEM
Building in workspace <
https://ci.eclipse.org/ice/job/ice-next/ws/>
No credentials specified
Cloning the remote Git repository
Cloning repository
https://github.com/eclipse/ice
> /usr/local/bin/git init <
https://ci.eclipse.org/ice/job/ice-next/ws/ice> # timeout=10
Fetching upstream changes from
https://github.com/eclipse/ice
> /usr/local/bin/git --version # timeout=10
> /usr/local/bin/git fetch --tags --progress --
https://github.com/eclipse/ice +refs/heads/*:refs/remotes/origin/* # timeout=10
> /usr/local/bin/git config remote.origin.url
https://github.com/eclipse/ice # timeout=10
> /usr/local/bin/git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
> /usr/local/bin/git config remote.origin.url
https://github.com/eclipse/ice # timeout=10
Fetching upstream changes from
https://github.com/eclipse/ice
> /usr/local/bin/git fetch --tags --progress --
https://github.com/eclipse/ice +refs/heads/*:refs/remotes/origin/* # timeout=10
> /usr/local/bin/git rev-parse origin/next^{commit} # timeout=10
Checking out Revision 298e97c434beceda7bd747fb6ec259121790d0de (origin/next)
> /usr/local/bin/git config core.sparsecheckout # timeout=10
> /usr/local/bin/git checkout -f 298e97c434beceda7bd747fb6ec259121790d0de # timeout=10
Commit message: "Pulled in annotation engine from GitLab"
> /usr/local/bin/git rev-list --no-walk efe1924122aa43cc4c5e4c349675a5e75cf832d0 # timeout=10
$ pkill Xvnc
$ pkill Xrealvnc
$ sh -c "rm -f /tmp/.X*-lock /tmp/.X11-unix/X*"
Starting xvnc
[workspace] $ Xvnc :1522 -geometry 1024x768 -depth 24 -ac -SecurityTypes none -noreset
Xvnc TigerVNC 1.4.1 - built ??? ?? ???? ??:??:??
Copyright (C) 1999-2013 TigerVNC Team and many others (see README.txt)
See
http://www.tigervnc.org for information on TigerVNC.
Underlying X server release 11502000, The X.Org Foundation
Initializing built-in extension VNC-EXTENSION
Initializing built-in extension Generic Event Extension
Initializing built-in extension SHAPE
Initializing built-in extension MIT-SHM
Initializing built-in extension XInputExtension
Initializing built-in extension XTEST
Initializing built-in extension BIG-REQUESTS
Initializing built-in extension SYNC
Initializing built-in extension XKEYBOARD
Initializing built-in extension XC-MISC
Initializing built-in extension XFIXES
Initializing built-in extension RENDER
Initializing built-in extension RANDR
Initializing built-in extension COMPOSITE
Initializing built-in extension DAMAGE
Initializing built-in extension MIT-SCREEN-SAVER
Initializing built-in extension DOUBLE-BUFFER
Initializing built-in extension RECORD
Initializing built-in extension DPMS
Initializing built-in extension Present
Initializing built-in extension X-Resource
Initializing built-in extension XVideo
Initializing built-in extension XVideo-MotionCompensation
Initializing built-in extension GLX
Sat Jun 20 10:35:18 2020
vncext: VNC extension running!
vncext: Listening for VNC connections on all interface(s), port 7422
vncext: created VNC server for screen 0
[dix] Could not init font path element /usr/share/fonts/TTF/, removing from list!
[dix] Could not init font path element /usr/share/fonts/OTF/, removing from list!
[workspace] $ /bin/sh -xe /tmp/genie.ice/jenkins8857151775926956891.sh
+ cd /opt/public/hipp/homes/genie.ice
+ rm -rf ICETests
+ git clone git@xxxxxxxxxx:jayjaybillings/ICETests.git
Cloning into 'ICETests'...
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
Build step 'Execute shell' marked build as failure
Taking screenshot.
[workspace] $ echo $XAUTHORITY
<
https://ci.eclipse.org/ice/job/ice-next/ws/.Xauthority-2962878022813792140>
[workspace] $ ls -l $XAUTHORITY
-rw-rw-r-- 1 genie.ice 8303 0 Jun 20 10:35 <
https://ci.eclipse.org/ice/job/ice-next/ws/.Xauthority-2962878022813792140>
[workspace] $ import -window root -display :1522 screenshot.jpg
Terminating xvnc.
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