W2H: History

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.

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").

• 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).

• 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.