Major Changes in dbCCP4i

Changes in Version 0.4.11

DBviewer and applications

• dbviewer: the menu of available projects is now split into columns of 30 project names, to ensure that projects at the end of the menu are still accessible and don't fall off the bottom of the screen.
• dbviewer: fix bug whereby zooming out too far caused the display to begin zooming back in.

DB handler

• Minor optimisation for reading def files for directories and project database data.
• Bug fix: in certain situations the handler could erroneously discard client requests, with the effect that the client might end up waiting for the requests to timeout. This is now fixed.

Client API

• dbClientAPI.tcl: the time interval for polling the handler lock file has been made much shorter, which should hopefully lead to quicker start up times for Tcl client applications.

Changes in Version 0.4.10

DBviewer and applications

• None.

DB handler

• Bug fix: using Python 2.4.4 under Linux, backgrounding a client application (e.g. CCP4i) using control-Z and the "bg" command was causing dbccp4i to disconnect the client. This should now be fixed.

Client API

• None.

Changes in Version 0.4.9

DBviewer and applications

• None.

DB handler

• OpenProject command could get confused if a request was made to open a non-existent project; if a request was made subsequently to create a real project then the attempt would fail even though it was valid. This is now fixed.

Client API

• None.

Changes in Version 0.4.8

DBviewer and applications

• Python unit tests now include basic tests for the history class in ccp4i.py.
• test_dbsocket.py and test_addfiles.py now added to the run_tests.tcl script
• test_ccp4i.py: fixed not to leave "test_directories.def.copy" lying around in test directory after completing.
• New test script "test_directories_client.tcl" added to test "GetDirectoriesData" command via the Tcl client API.

DB handler

• ccp4i.py: all classes and methods should now have doc strings for improved Python documentation.
• Fixed bugs which meant that the -debug and -shutdown options of dbccp4i didn't work in earlier versions.
• dbccp4i returns a non-zero exit status in the event that one of the modules that it needs fails to load.
• New handler API command "GetDirectoriesData" allows multiple data items to be retrieved for project and data dir information in a single request.
• Minor fix to GetDataDir command, which should be quicker as it doesn't check whether the supplied alias is a project before attempting to look it up as a data directory; the return status should now correctly be ERROR if the alias is not found.

Client API

• Updated the "Communication Protocols" documentation (communications.html) with more information about broadcast messages from the handler.
• Added "GetDirectoriesData" commands to the Tcl and Python client APIs, corresponding to the new handler API command with the same name.

Changes in Version 0.4.7.2 / 0.4.7.1

DBviewer and applications

• Various updates to test scripts to improve robustness.

DB handler

• Implemented changes to try and improve performance on systems where file access operations become expensive if performed many times (reported for some setups using NFS).

Client API

• dbClientAPI.tcl,.py: fixed to function correctly for installations of dbccp4i which have spaces in the pathname (for example, under Windows).

Changes in Version 0.4.6

DBviewer and applications

• test_directories_mr.py: removed the dependence on PYTHONPATH to locate the required Python modules.
• dbitem_client.tcl: new test script checks that the data items available in the database are consistent with that in database.def.
• dbviewer: the "Output Tracking XML" option was broken under Windows if the output XML filename contained spaces - should now be fixed.
• reaper: new client application that can be used to analyse a project database to extract information for data harvesting. Reaper can be run from the command line or by selecting the appropriate option in dbviewer when right-clicking on a job.
• Demonstration SQLite crystallographic database: files for an example CCP4i task interface are provided in the "tasks" subdirectory (bioxhit_db.tcl and bioxhit_db.def) which allows interaction with an existing SQLite database associated with a project. The files must be copied to $CCP4/ccp4i/tasks and then the interface can be launched using "ccp4i -t bioxhit_db", or via the option from the viewer (under the "File" menu).
• Tests will only run if an existing handler instance isn't already running for the user running the test suite.

DB handler

• dbccp4i.setup-dist,-bash: no longer adds paths to the PYTHONPATH environment variable - applications should explicitly specify the location of the required modules.
• Fixed bug in handler which meant that dbccp4i ran forever under Windows, and could only be stopped by killing the python process.

Client API

• New data items added to the database: MACHINE and USER_AGENT; also, USER_AGENT is now automatically stored by the handler for new jobs and subjobs, and takes its value as the name supplied by the client application when it first connected.
• It is now possible to extend the .def file database with new items by adding definitions for those items in the template database.def ($DBCCP4I_TOP/etc/database.def).

Changes in Version 0.4.5

DBviewer and applications

• test_directories_mr.py: new test script added which checks that it possible to connect to a handler with non-standard directories.def file from the Python client API.
• run_tests.tcl: fixed problem that Python unit test always reported failure, even if all unit tests worked.
• dbccp4i_test_client.tcl: added a simple test for subjob addition.
• dbviewer: a number of changes:
  • Options to view the "annotated" logfile and to run "plugins" such as Coot and CCP4mg have been added to the job options menus.
  • A number of small bugs with selection and filtering have been fixed as a result of refactoring the code. The viewer should now also be a little more stable.
• starKey: fixed a number of issues:
  • Now possible to run starKey in an environment where PYTHONPATH doesn't include the appropriate directories for the client API and other modules (previously failed with an ImportError).
  • Previously would fail to generate XML file if it encountered a logfile which contained unrecognised program output (e.g. from programs that don't follow the CCP4 logfile conventions recognised by smartie) - now fixed.
  • smartie: updated to version 0.0.14.

DB handler

• Fixed bug where attempting start up of a handler with non standard directories.def from the Python client API would always fail to create a handler instance.
• Control-C to kill a client application that started the handler in background should not now also kill the handler process. (In fact it should not be possible to kill the handler process using Control-C at all.)
• Fixed some bugs when running the handler with Python 2.5.2: on Linux, suspending and backgrounding the client that started the handler no longer results in the connection being dropped.

Client API

• AddSubJob command (dbClientAPI.tcl, dbClientAPI.py): the "taskname" and "title" arguments supplied to the AddSubJob commands have been reversed (essentially correcting an old bug in the handler). Also, a bug in the Tcl client API (whereby only the first word in the title was actually used) has been corrected.
• HasJobs command (dbClientAPI.tcl): now returns zero if the handler returns an error, rather than an empty string.

Changes in Version 0.4.4

DBviewer and applications

• dbccp4i_test_client.tcl: added tests for set/get of data for a single job.
• dbccp4i_test_client.py and dbsocket_crash.py: now explicitly appends the ClientAPI and dbccp4i directories to the module search path, so that the tests will run in environments where these directories are not part of the PYTHONPATH.

DB handler

• Fixed DbGetData command which was broken in 0.4.3 (would always generate a handler exception warning if multiple data items were requested in a single request to the handler).
• Trap for existence of directories.def or database.def file before attempting to check modification status, which should prevent errors if .CCP4 area or project directory is removed while handler is running.

Client API

• dbClientAPI.tcl: missing .CCP4 directory in user's home area no longer crashes the client API due to being unable to make a logging file there.

Changes in Version 0.4.3

DBviewer and applications

• No changes.

DB handler

• The "operation" reported in broadcast messages has been updated for NewProject, DeleteProject, ImportProject, AddDataDirRef and DeleteDataDirRef.
• Warnings are now suppressed if a project is opened which has mismatching header information for the project name or directories.
• DbGetData command: better handling of cases when requested job id and/or data item(s) don't exist. Note that if several data items are requested, if even one doesn't exist then the request as a whole will fail and return an error.
• DbSetData command: better handling of cases when requested job id and/or data item(s) don't exist. Note that if several data items are requested, if one doesn't exist then the returned status will be ambiguious.
• AddOutputFile command: better handling of case when requested job id doesn't exist.

Client API

• Tcl client API: the default timeout has been increased to 30 seconds. This should be sufficient to deal with large projects.

Changes in Version 0.4.2

DBviewer and applications

• tests: new platform-independent script run_tests.tcl, which runs all test scripts and reports outcomes (replaces run_tests.sh, which has been withdrawn).
• tests: new diagnostic test script dbccp4i_diagnose.tcl has been added, which attempts to characterise the interactions with the handler.

DB handler

• DbInfo: now includes information on the Python interpreter that the handler is running under, as well as the handler version.

Client API

• dbClientAPI.tcl: Fixed bug in "namespace exists" workaround which stopped the API from working properly if sourced more than once.

Changes in Version 0.4.1

DBviewer and applications

• New command line option for DBviewer: -title allows custom text to be added to the title bar, e.g.
  dbviewer -title "viewing MrBUMP"
• Python dbconsole: new -directories option allows the user to specify a non-default directories.def file to user on start-up.

DB handler

Client API

• dbClientAPI.py: Connect command supports -directories option, to specify a non-default directories.def file to user on start-up.

Changes in Version 0.4

DBviewer

• New command line options:
  • -directories: allows an arbitrary non-default directories.def file to be specified on start-up.
  • -remote: allows the specification of a remote handler that the viewer should use instead of one on localhost (the default).
• Updated to work with CCP4 6.1 as well as CCP4 6.0.2.

DB handler

• Implemented -directories option, to specify an arbitrary non-default directories.def file to use on start-up.
• Fixed bug in the DeleteProject command: now it is not possible to delete a reference to a project while it is open.
• Fixed bug in the ImportProject command: now it is not possible to import a project unless it has a unique name and directory path. Also the import will fail if the directory is not a valid project directory.
• Fixed bug when adding projects, that project database directory path would be left blank if not explicitly specified (caused problems if CCP4i subsquently tried opening the project directly).

Client API

• dbClientAPI.tcl: DbHandlerConnect command supports -directories option, to specify a non-default directories.def file to user on start-up.
• dbClientAPI.tcl: Fixed bugs in db_client_error which meant that no error messages were ever retrieved, and added a new command called db_client_response_data which allows the status and result from the last handler interaction to be returned

Changes in Version 0.3

DBviewer

• Add an icon on the job node. If a job has subjobs, in the upper left side, a star '*' is shown.
• Add an up arrow, allow to go from subjob view to top lever job view.
• Replaced textual buttons on tool bar with a set of icons e.g. for zooming in/zooming out etc.
• Uses colour scheme from CCP4i if user has specified custom colours in CCP4i.

DB handler

• Added support for subjobs: it is possible to create jobs within jobs, to represent substeps of a larger process (for example, automated pipeline).
• Added implementation of demonstration SQLite knowledge base.
• Large number of bugs addressed.

Client API

• Added namespacing to Tcl client API: prepend ::dbClientAPI:: to commands or use namespace import.
• Fixed bug where Tcl client API failed if sourced more than once.
• Tcl and Python client APIs updated with commands for interacting with subjobs.
• Tcl client API has functions for interacting with generic SQLite tables, plus additional functions for interacting with demonstration knowledge base.

Changes in Version 0.2

General

• Tested on Windows.
• Installation/setup: the GRAPHVIZ_BIN environment variable is no longer required by dbviewer and has been removed.

DBviewer

• Added 'view Files' feature. Now files including log file, input files, output files and notebook can be viewed from the menu when right click over the job node.
• Added 'select related jobs'. Now any job node, you can select all jobs that directly or in-directly related to the job, including all children and parents.
• Added user's preferences. Now it is possible to save the changes in appearance menu.
• Added 'scale' menu. It is possible to enlarge or shrink the graph by selecting different scale.
• Added 'node' menu. It is allowed to choose to show 'title' or 'taskname' in the job node.
• Add an icon at lower right hand side on job node. If the 'JobQuality' is 1, the icon is a tick; if the 'JobQuality' is -1, the icon is a cross; if the 'JobQuality' is 0, the icon is a question mark.
• Add Zoom in(+)/Zoom out(-) button.

DB handler

• Added 'AddInputFile', 'AddOutputFile', 'ListInputFiles','ListOutputFiles', 'DbReadable', 'DbWriteable', 'DbReacquire' commands.
• Make major command name changes. (see also name changes in API.
• Add a SQLite backend for each project to store JobQuality data.
• Change the broadcast message. Now the xml tags for broadcast message is:

  <db_broadcast>
  <message></message>
  <project></project>
  <jobid></jobid>
  <operation></operation>
  <agent></agent>
  </db_broadcast>
  

• Add 'GetDbItems' command.
• Replace 'database' class with 'ProjectDB' class.
• Add 'AddSubJob','SelectSubJobs','HasSubJobs' commands.

Client API

• Major changes in python API. Now if handler response is 'OK', API returns the actural result. If handler response is 'ERROR', API raises 'DBError' exception.
• In python API,Change DbRegister, now it takes two arguments, user_agent and broadcast flag.
• In python API, changes in handler connection: Remove 'DbStartHander' & 'DbRegister'. HandlerConnection initialisation takes two arguments: user agent and broadcast flag. There are major changes in the name of the methods/procedures. The following table show the changes names in both python & tcl API. tr>

  Old Name	New Name
  handlerconnection	HandlerConnection (only in python)
  OpenDatabase	OpenProject
  CreateDatabase	CreateProject
  CloseDatabase	CloseProject
  NewRecord	NewJob
  DeleteRecord	DeleteJob
  DbReadable	ProjectReadable
  DbWriteable	ProjectWriteable
  DbReacquire	ReacquireProject
  GetAllLinks	GetAllFileLinks
  GetLinks	GetFileLinks
  ListDefDirs	ListDataDirs
  AddDefDirRef	AddDataDirRef
  DeleDefDirRef	DeleteDataDirRef
  GetDefDir	GetDataDir

• In Tcl API, change DbHandlerConnect, add two arguments: userAgent and broadcastFlag.
• In Tcl API, add four procedures:
  • cacheProject: This stores a project data in a database array for use. This can be called from client application when open a project.
  • updateCachedJob: This updates a job in cache. This procedure is called within Client API when receives broadcast message.
  • deleteCachedJob: This deletes a job from cache. This procedure is called within Client API when receives broadcast message.
  • getCachedData: retrives data from the cached project.
  • Add 'AddSubJob','SelectSubJobs','HasSubJobs' commands in both Tcl & python API..

Last Update: $Date: 2008/09/19 08:42:59 $