W2H: History

Version 4.1 (December, 2002)
General changes in W2H:
- Show all outputs after the execution of an application and not just the first one and skip empty output files.
- Graphics device chooser in the application page.
- Working directory chooser in the advanced mode
- Remote host execution: Remember if a job has been started from a batch queue. Now it is no problem to let the queueing system start the job on a remote host.
- New Edit selected feature in the advanced mode without working-lists.
- Use project colours for the output column in the advanced results manager, too.
- Enabled "select all" in the file manager.
  Use "en bloc" selection of many files, that belong to one job (results manager).
- (e)seqinfo.pl: less strict behaviour when unknown file types are encountered.
- w2h.delfiles/-ppdel: Pre-processors on deletion. When application result files are deleted from W2H's result managers, W2H can call a pre-processor on that file prior to this file's deletion. This allows other resources (e.g. files) unknown to W2H to be freed. W2H looks for these delete pre-processers in the W2H post-processor directory and expects the filename to be "file-extension" + "-ppdel", e.g. blastn2-ppdel would be a pre-processor for deletion for BlastN2 outputs.
- Show the waiting clock in all browsers (no 3-5 min. timeout in IE).
- Allow loops in alerts.
- Improved Save in the application page.
- $Cfg'W2H_UMASK allows per user setting of the umask used by W2H's processes.
- Bug fixes:
  - No automatic restart of an application when the browser's Back button was used (Netscape 6/7)
  - Limit the size of HTML <SELECT>s to work arround a bug in modern browsers.
  - Display, saving and command line generation of Menu/Radio parameters
  - Fixed HTTP window-target problem.
  - Saving and restoring environment variables needed more rules.
  - Zooming PNG images.
  - Don't ignore the typed-in sequence name in some cases.
  - Repaired Unix signal detection.
  - Pressing Default->Save in the application page really reverts to the default settings (unlinking personal settings).
  - Reading default graphics device from Cfg.pl.
  - Don't allow the creation of working directories with names, that can't be handled by W2H.
  - Cleanup of unused job files on login (remove unused files, but check for queued jobs, too).
Changes in W2H's EMBOSS mode:
- eseqinfo.pl: (W2H interface to infoseq) Provides information about simple sequence properties to W2H. This program is based on seqinfo.pl and is supposed to replace seqinfo.pl in W2H's EMBOSS mode. eseqinfo.pl supports all seqinfo command-line parameters required by W2H. eseqinfo.pl interfaces to the EMBOSS system by parsing the output of the EMBOSS program infoseq.
- Improved ACDParser.pm: This parser is more stable in reading ACD files and should be less sensitive on future changes in ACD files (EMBOSS upgrades).
  Use ACD "sections" in W2H's application page.
- Better output file names than just outfile
  -ossingle for output sequences allowed.
- Boolean parameters with default:Y are now handled correctly
- Use $Cfg'SITE_DATA to list available databases in W2H.
- Configuration of site-specific graphics devices ($Cfg'SITEDEVICES).
- Propagate begin/end/strand information from W2H to EMBOSS.
- File button in the appliction window uses $Cfg'RUNDATA to find the default browsing directory (EMBOSS' DATA directory).
- $Cfg'KEEP_SEQSETS: If the application has two input sequence qualifiers, where one of them is not just of type sequence but seqset or seqall (e.g. water, needle, est2genome): W2H allows the selection of both input sequences from the main window.
  If you don't want this behavior for some EMBOSS applications, you can specify a list of application names, where W2H should continue to use the old scheme. E.g. Est2Genome seems to work better with the old scheme.
- Use colour for GIF graphics (bug-fix).
- In ACD: Param:Y implies Req:Y.
- Changed some prompts referring to GCG specific topics.
Changes in W2H's GCG mode:
- Use config file rules, when building the command line.
- Don't kill the session of a running background job, when the user clicks on Exit.
- Detect comments in database description files (bug-fix).
- Create better output file names in some bad cases.
- Allow the use of GCG's special variables in graphics-port definitions; quotation mark bug-fixes.
- Evaluation of some more qualifiers before usage (bug-fix).
Known bugs:
- Evaluated limits for ranges of GCG application parameters remain disabled in W2H, because the limits may depend on other parameters, however W2H can not propagate changes in the other parameters correctly to the range limit setting.
Version 4.0 (March, 2001)
Since of this version, W2H can be used not only for GCG-like systems, but also for other command-line driven program packages like EMBOSS. In particular this version contains extensive support to be used with the EMBOSS software suite.
New Features:
- Support for EMBOSS
- W2H Loops: run several instances of an application for each selected sequence file. In the sequence-pair-comparison case: compare each sequence of one listfile with each sequence of a 2nd listfile. Skip a pair if the sequences are identical (just name check) or if this pair has already been compared (maybe in the other order). You can also specify 2 times the same listfile. Instead of 2 listfiles, 1 listfile and a simple sequece file might be specified, too.
- Application piping: This feature is realised via W2H's postprocessing.
- Support for translation of Postscript outputs into PDF format
- Use config-file rules to determine if a certain parameter is allowed to appear on the command line or not (for required and optional parameters)
Feature Updates:
- For GCG 10.2: small updates reading application configurations
- Bring "hidden" browser windows again to front if necessary (using Javascript focus())
- Remember sort preferences of file listings in the File Manager
- Added a (optional) "Save as" text-field for upload in the Main Page of the Simple Mode
- Allow hp2png method if MSIE version >= 5.5
- Tiny HTML corrections for Netscape 6
Bug Fixes:
- create a 2nd scrollbar for very, very long directory listings in the Simple Mode Main Window
- FreeEdit: only try to rename the old working-list if there is/was an old working-list
- added missing Javascript function validInt() in Application Window
- repaired "endPattern" for NetBlast post-processing
- clicking "Restore" in Application Window from Simple Mode did not work properly (wrong reformatting)
- xwindows driver sleep (1) before application action
- allow removal of the last Alert job also on SGI (thanks to Luca Toldo)
- allow removal of jobs from the Results Manager that crashed during their startup
- realize mode changes for displaying the correct help page
- wrong handling of PATH_INFO during REQUEST_METHOD POST if sent from IE
Miscellaneous:
- thorough review of the code of W2H's Setup Window
- increased the size of the DB select box from 3 to 6 in the application window
- increased the width of the Begin/End HTML-form text-fields in the Application Window from 5 to 6
- for the application description, do not only consider the .txt files, but also the .note files.
Version 3.2 (December, 1999)
In this version, we have included a lot of feedback, we got from the rising number of everyday users of W2H. This includes a number of small new features, feature updates and bug-fixes.
New Features:
- New postprocessor for MSF-files (implemented by Artjom Tarasenko): Displays the alignments with different coloring schemes using HTML. Documentation is available.
  A slightly modified version of Michele Clamp's JalView (Java Alignment Viewer/Editor) is included. Modifications:
  - It is possible to save the edited alignment back on the W2H server.
  - Default output format is MSF.
  - Since GCG 9, end gaps in MSF aligments are indicated with "~" (tilde) characters.
  - Editing of nucleotide alignments is supported.
- New: The application output also appears in the Advanced Mode as soon as it is available in the users browser window (like in Simple Mode). Deactivated for user agent MSIE (no Server Push Method).
- New Fetch: The Fetch page has been changed, and now doesn't create invalid files, if the specification gives multiple matches.
- Support for JavaTelnet: W2H can use a Java applet to make a telnet connection. The advantage of using this applet is that users don't need their own telnet application any more. The disadvantage is that some firewalls need a special configuration of telnet applications, which are not provided by this Java Telnet.
  New in Cfg.pl:
```
         
    $TELNET_MODE = 'java';  # Possible values: 'java', 'external'
    	                    # (default: external)
          
```
  Interactive applications like GelEnter, if started via JavaTelnet from the Application Window, are now connected to W2H's GCG session.
- Blast in GCG10: support for multiple selection of databases.
- More JavaScript checks if all required/mandatory arguments to the applications are specified (using the "rules" line in the .config files).
- More environment variables for postprocessing scripts are now available:
```
    $ENV{'W2H_BIN_ROOT'} = $Cfg'BIN_ROOT;
    $ENV{'W2H_YA_ROOT'} = $Cfg'YA_ROOT;
    $ENV{'W2H_DOC_ROOT'} = $Cfg'DOC_ROOT;
    $ENV{'W2H_POSTPROCESS_PATH'} = $Cfg'POSTPROCESS_PATH;
    $ENV{'W2H_FILE_EXTENSION'} = &u'file_ext ($fname);

	
```
Feature Updates:
- New QUEUES_DEFINITION_TABLE: Using Batch Queues doesn't require any more changing the applications .config files. This was necessary, because with GCG 10, .config files with our QUEUES and QUEUEDEFAULT statements were not accepted by Seqlab/Wpi any more. New in Cfg.pl:
```
    $QUEUES_DEFINITION_TABLE = "$YA_ROOT/application.queues";

	     
```
  with example entries in application.queues:
```
    ..
    BLASTN	        QUEUEDEFAULT none
    BLASTN2      	QUEUEDEFAULT none QUEUES short,medium
    BLASTP	        QUEUEDEFAULT short
            
```
  QUEUES and QUEUEDEFAULT in .config files of the individual applications are still understood if they exists. Order: first check .config file, then $Cfg'QUEUES_DEFINITION_TABLE and then for the string in $Cfg'QUEUES.
  Within the distribution: util.extract_queues_from_configs that creates an application.queues file, from the current settings in the application's .config files, allowing W2H-admins to switch to the new scheme with minor effort.
- More reasonable default values in the Application Window for "evaluated" text fields in the case where sequence properties are not available.
- Creating a new working-list always appends .list (or any other extension defined in the settings) to the name of the working-list, if the extension is not already present.
- Because spaces in filenames can cause problems in W2H/GCG, on some places user-typed spaces in filenames are translated into underscores. Special code for handling "'" and "," characters. (Standard users like to use all characters they can find on their keyboard.)
- 1-line application descriptions and SRS hyperlinks for new applications in GCG 10.
- PS to GIF translation can handle more PS dialects.
- More informations in W2H's Log.glob.
Bug Fixes:
- Don't show the "Application Running Time" clock if MSIE is the user agent. (MSIE doesn't understand the Server Push Method)
- Using the File Browser from the Application window did not work in Simple Mode; fixed.
- Remove Selected in Enzyme Chooser did not work; fixed.
- Uploading files from a Mac (i.e. files without newline characters) and their translation into GCG format should work now.
- Don't put -ARG=DUMMY on the command-line (happened if a DUMMY was a member of a MENU structure in the application's config file, e.g. bestfit.config, paupsearch.config).
- Better housekeeping of temporary files.
- Make sure that the selected working-directory has 'r', 'w' and 'x' flag. Otherwise the directory is not usable by W2H.
- extras/w2h.showquota: detect "NOT STARTED" from quota system.
- Less trivial error messages from the File Manager in the httpd server log ("mv: files identical").
Version 3.1 (February, 1999)
This version is mostly bug-fixes, with one major new feature which is support for GCG 10.
- Support for GCG10.
- More improvements of the help system is here, [guess who has done it :-)] including an additional command-line option for nph-w2h.helpapp for generating help pages "viewed best with Lynx instead of Netscape" (see other details in the script "usage").
- Several new configurable options (variables in Cfg.pl file) for W2H administrators:
  
  DISABLED_FOR_ALERTS and ENABLED_FOR_ALERTS
  You can now control which applications can and which cannot be started from cron jobs (regularly repeated jobs, alerts).
  NETBLAST
  It specifies which databases should be visible for the netblast application. By default it is identical with BLAST_REMOTE variable.
  PROTOCOL
  Support for HTTPS/SSL introduced. Next to access of W2H through the HTTP protocol, access through HTTPS can be configured using this new variable.
  USE_W2H_HELP_STYLE
  A possibility to change how the help pages look like.
  
  And there is a new document how to upgrade from W2H 3.0 to W2H 3.1.
- Various bugs fixed
  
  * Renaming in Result Manager fixed that all renamed files now remain displayed
  * In the mode without working lists, sometimes an application page showed in a wrong frame. Fixed.
  * Starting in a selected mode is possible using one of the URL: http://.../w2h.start?MODE=simple or http://.../w2h.start?MODE=advanced. Both work now.
  * Program PileUp produces now correctly two outputs - an .msf file and a graphical one
  * A default graphical driver is correctly chosen (also depending on your Netscape version).
  * A comma separator required for some arguments in LookUp program is now correctly used.
  * Perl 5.004_xx and later is more rigorous so some warnings were produced, and they were fullfilling server log files. Fixed.
  * A crontab (used for regularly repeated jobs) is no any more polluted with W2H comments if there is no W2H job scheduled.
  * Specifying "Save as" in uploading local files works now also for MS Windows platform (problem with different directory separator fixed).
Version 3.0 (October, 1998)
This version brings quite a lot of improvements and changes in GUI. However, we have tried to keep most of the changes backward compatible, so users will be able to use W2H in the same way as before if they prefer. The main goal was to implement simplified ways of usage of W2H (we have heard from users that "...W2H looks, at first glance, like a pilot cockpit...").
- Working without any working list is now supported. In this new mode a user works directly with data from her/his working directory. Easy switching between the original and new modes is supported.
- Another quite new access to applications is provided by the Simple mode. It gives basic functionality in only one window following few basic steps. A user wishing more advanced features can anytime switch to the original (advanced) mode.
- Application menu can show now short application descriptions making navigation easier. A file with one-line descriptions for many GCG and non-GCG programs is provided in distribution (by courtesy of people from DKFZ, Heidelberg).
- Also by courtesy of the same people, W2H is now distributed with the post-processing scripts adding SRS links into some outputs (see details in pp-scripts subdirectory).
- Extra buttons and Extra items. W2H administrator can add her/his own buttons and pieces of HTML code into the Main window. It allows to add links to the site-specific services or pages (one example for showing user disk-quotas is provided). And because any HTMl code can be added it allows you to add even your small Java applets to the Main Window. Peter Ernst not only wrote the code but also documented it in extras.html.
- W2H comes now (optionally) with File Manager functions (Delete/Move/Copy file, create directory) to manage working directories and user data. It is an enhancement of the original Directory Browser (that means that no new window was invented for it).
- Completely new Sequence selector and Search set Builder. These pages seemed to be most confusing - so we decided to change them substantially (but keeping the old versions as well for those who got used to them). I acknowledge very much Peter Ernst who made them available.
- Mechthilde Falkenhahn re-wrote the whole help sytem. Flowers to her...
- seqinfo is a program for finding attributes of sequences. Originally, it was written in C language, using GCG libraries. Because of the new GCG licensing policy, it is not possible to distribute such program anymore. Therefore, Ge Zhang re-wrote this program using only Perl. The result is even faster and you do not need to compile it. W2H is using this program internally and really enjoys it.
- The buttons in the Main Window were slightly re-arranged to reflect new modes (simple mode and mode without using working lists). We hope that this change is the last button-re-arrangement.
- A bit more support for post-processing scripts setting for them some environment variables (see postprocess.html for details).
- With help of UNIX access rights you can set that some programs will be visible only for some users. This is particularly useful for adding non-GCG applications in the phase of their testing. See details in Cfg.pl by variable $APPMENU.
- There is a new button Free edit allowing to edit, or copy&paste, the current working list.
- Remote printing is configurable now. Previously it was possible to disable the access to remote printers only in Intranet mode, but now it is a general feature. (The Intranet users note that the access is now by default enabled - which is different from the previous version.)
- There is now a possibility to rename files in the Result window without actually removing it from there.
- By uploading files, you can now force automatic reformatting into GCG format to consider input as a protein.
- Several new configurable options (variables in Cfg.pl file) for W2H administrators:
  
  TELNET_ALLOWED
  You can forbid now to let your users to start a telnet session from W2H.
  FILEMANAGER_ALLOWED
  Newly introduced file manager functions can be disabled.
  KEEP_OLD_SEQUENCE_SELECTOR
  Just for the backward compatibility if your users want to use it.
  APPDESCRIPTION
  Where application one-line descriptions can be taken from.
  MODE
  What is the default user mode (simple or original).
  APPMENUSIMPLE
  Which aplications should be offered in the simple mode.
  EXTRA_ITEMS and EXTRA_BUTTONS
- Various bugs fixed
  
  * The message I can't create a project directory should not bother you any more.
  * The button Default in application windows restores now properly the last used queue (if any).
  * A Pattern Chooser accepts now character '~'.
  * Uploading local files did not work always correctly in the Intranet mode (nothing was uploaded). It's fixed now.
Version 2.1 (March, 1998)

Due to marvellous (and quickly done) piece of code of Michael Schmitz , a co-author of hp2xx converting software, W2H provides now a graphical output also in PNG format (Portable Network Graphics). This is an additional graphic format, not a replacement of already provided ones. You must have Netscape 4.04 (an later) to display the PNG images.
User projects were added. Users can define their own so-called projects, each of them pointing to the own working directory, having own working list and other properties. A project manager window is provided to easily edit project's properties and to move from project to project. Do not forget to enable this feature in Cfg.pl file if you want to use it.
W2H slowly evolves to some coloring schemes. Different user projects, and queued and not successful results in Result windows are now of different colors. (Which is only a very rudimentary part of what Luca Toldo from Merck KGaA, Darmstadt, suggested and implemented.)
The Upload window has again slightly different layout (functionality is the same) - and I hope that this is finally final, and suitable for most users.
W2H help pages are being improved thanks to effort of Mechthilde Falkenhahn from DKFZ, Heidelberg (see Upload help page, the other will come soon).

Various other bugs fixed

* The exit page caused time to time an error. It's fixed now.
* Batch queues: W2H administrator could not insist on running a program always in a queue if there was only one queue specified. It can be done now.
* Changing from one graphical output format to another could cause that incomplete file names were generated (e.g. only .ps2gif). Fixed now.
* Help page in Setup window has now proper scrollbars, as others.
* You could remove all entries in a working list and let the whole file disappear. But in some situations this working list appears magically again when pressing on Remove again. Fixed now.
Version 2.0 (October, 1997)
This is a major version with important new features (and fixes). A special acknowledgement for many improvements in this release goes to Peter Ernst and Ge Zhang from DKFZ, Heidelberg.

Regularly repeated jobs (Alerts) are supported now. You can let any application to be automatically repeated daily, weekly or monthly (supposing your system allows users's cron jobs). (Thanks to Luca Toldo from Merck KGaA, Darmstadt, for the idea.)
Site-specific documents (Extra buttons) are supported. You can add easily (only by defining it in the configuration file Cfg.pl) new buttons into the main window, pointing to your site-specific documents.
Batch-Queue Jobs are supported now. The applications can be started imediatelly or later depending on the available computer resouces. See a special document about it. There is also a standalone utility reporting on active batches (can be added directly into W2H as a site-specific document described above).
W2H now provides more support and description for the external, non-GCG applications and for user-defined post-processing of the GCG output files. See special documents on external applications and on data post-processing.
A serious licensing problem occured with converting HPGL output into GIF format. We have to ask users to stop using hp2gif program and we do not include it anymore in the W2H distribution (see explanation in a special document). Peter Ernst developed an alternative way for creating GIF files (converting them from a postscript file) and he kept the resulting user interface as similar to the previous one as possible.
A creation of a new directory is available when a new working directory is being chosen.
Bugs in the behaviour of Save/Restore/Defaults buttons were fixed. The GCG default values should be now restored properly in nearly all cases. Also clicking on a toggle box in front of parameters does not destroy parameter's current value (even if it is not used on a command line).
File viewer is now called consistently from all places in the same way (and the corresponding View buttons were renamed to more appropriate Files). Also some Close buttons were put closer to the left upper corner of their frames to occupy more consistent location.

Various other bugs fixed

* Automatic mailing (when a help file was not found) has now also a To: field.
* Help system recognizes properly applications with names containing non-alphanumeric characters.

* Several windows (loading application, add sequence, etc.) had problems under Communicator 4.x. It was fixed.
* On PC: once selected application in the application list could not be deselected without calling a different application. Fixed.
* An error message in the report area of the Upload window is shown only when really appropriate.
* Perl5.004 reported a warning when starting an application. Fixed.
* Applications are not displayed multiple times in the alphabetical list anymore. And the sort order is now without regard to case.
* More of the GCG9 sophisticated constructs in application config files are now understood by W2H (those like default=name (SQ1+.cutters)).
For older versions see older history
The project started on the 1st January 1996.

Peter Ernst
Last modified: Tue Dec 10 17:31:21 2002