From owner-acedb@hgmp.mrc.ac.uk Fri Dec 1 09:22:57 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 728F017B4F; Fri, 1 Dec 2000 09:22:56 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 1AF4917B4A; Fri, 1 Dec 2000 09:22:54 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id B530E17AF1; Thu, 30 Nov 2000 16:58:09 +0000 (GMT) Received: from moderated.news.pipex.net (moderated.news.pipex.net [158.43.192.79]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 0CA5E415DF for ; Thu, 30 Nov 2000 16:57:46 +0000 (GMT) Received: (qmail 5882 invoked by alias); 30 Nov 2000 16:57:46 -0000 Received: (qmail 5878 invoked from network); 30 Nov 2000 16:57:45 -0000 Received: from ncbi.nlm.nih.gov (130.14.25.1) by moderated.news.pipex.net with SMTP; 30 Nov 2000 16:57:45 -0000 Received: from ray.nlm.nih.gov (ray [130.14.25.2]) by ncbi.nlm.nih.gov (8.9.3/8.9.3) with ESMTP id LAA28168; Thu, 30 Nov 2000 11:57:22 -0500 (EST) Received: from cetus (cetus [130.14.25.107]) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) with SMTP id LAA19304; Thu, 30 Nov 2000 11:57:20 -0500 (EST) Message-Id: <200011301657.LAA19304@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: Update sequence? To: bionet-software-acedb@moderators.isc.org, JRSchwartz@lbl.gov, keith@thale.life.nottingham.ac.uk MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: w7G3jft1SQc2Ws8TmhlPQw== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Fri, 1 Dec 2000 09:22:54 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk There is a call in the acedb kernel to automatically update all coordinates in touched objects up and down the hierarchy provided they are declared withe the modifier COORD in the ace model however, this call is not included in any public interface and my self i never use it so i cannot garantee the reliability, but i beleive it works this means that to use this call you would have to write some c code if there is demand, you could trigger the interest of the cambridge group to add that public interface but just now, i could not spare the needed time for this, sorry jean >To: bionet-software-acedb@moderators.isc.org >From: Keith Bradnam >Subject: Re: Update sequence? >Mime-Version: 1.0 >X-Trace: oyez.ccc.nottingham.ac.uk 974805477 13264 128.243.116.150 (21 Nov 2000 11:17:57 GMT) >X-Complaints-To: usenet@news.nottingham.ac.uk >NNTP-Posting-Date: 21 Nov 2000 11:17:57 GMT >To: JRSchwartz@lbl.gov >X-Sender: keith@thale >Date: Tue, 21 Nov 2000 15:58:15 +0000 (GMT) > >On 20 Nov 2000 JRSchwartz@lbl.gov wrote: > >> >> >> Hi all, >> >> I am using acedb for annotation. I was wondering if there is a way to >> update the dna sequence for a clone, to add more to it, while preserving >> the existing annotations. I have done it in the past by hand, changing >> all the froms and tos, but it is a royal pain. Is there a nice way to >> do that? If I just delete the DNA sequence and add the new one, will >> the annotation be automatically updated? > >DNA sequences are usually specified as 'UNIQUE' objects in most acedb >databases, so if you try to read a new DNA sequence as part of an existing >Sequence object it should just replace the existing DNA sequence but not >change anything else. > >E.g. if your sequence/clone object in your database is something like: > > >Sequence : "EMBL:AB006697" >DNA "EMBL:AB006697" 80970 >Version "AB006697.1" >Database_date "26-OCT-2000" >Species "Arabidopsis thaliana" >Title "Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MAH20." >Clone "MAH20" > > >Then all you should have to do is put your new DNA sequence in an ace file >with the same name as that which already exists and read this into the >database. > > >Keith > >~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and >~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer. >~ >~ Nottingham Arabidopsis Stock Centre, University Park, >~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091 > > > > From owner-acedb@hgmp.mrc.ac.uk Fri Dec 1 09:23:01 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4C1B317B4D; Fri, 1 Dec 2000 09:23:00 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id CD0B017B47; Fri, 1 Dec 2000 09:22:54 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9D94917AC7; Thu, 30 Nov 2000 20:29:24 +0000 (GMT) Received: from ncbi.nlm.nih.gov (ncbi.nlm.nih.gov [130.14.25.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id EB763415DE for ; Thu, 30 Nov 2000 20:29:17 +0000 (GMT) Received: from ray.nlm.nih.gov (ray [130.14.25.2]) by ncbi.nlm.nih.gov (8.9.3/8.9.3) with ESMTP id PAA00928; Thu, 30 Nov 2000 15:29:14 -0500 (EST) Received: from jove (jove [130.14.25.149]) by ray.nlm.nih.gov (8.9.3+Sun/8.9.3) with SMTP id PAA29898; Thu, 30 Nov 2000 15:29:11 -0500 (EST) Message-Id: <200011302029.PAA29898@ray.nlm.nih.gov> From: Jean Thierry-Mieg Reply-To: Jean Thierry-Mieg Subject: Re: non-native byte order To: jayoung@fhcrc.org MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: wSjGPiWdaDOTMaceMmnhCA== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.3.5 SunOS 5.7 sun4u sparc Newsgroups: bionet.software.acedb Date: Fri, 1 Dec 2000 09:22:54 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk if you dump and reload, the system will be marginally faster but on the other hand this will probably decrease the disk usage. as you can see, acedb is platform independent! jean >To: bionet-software-acedb@net.bio.net >From: jayoung@fhcrc.org (Janet Young) >Subject: non-native byte order >Mime-version: 1.0 >Content-transfer-encoding: 7bit >X-Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C996917B5E; Wed, 22 Nov 2000 23:30:17 +0000 (GMT) >X-Received: from fhcrc.org (uluc01.fhcrc.org [140.107.52.11]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4531E415EB for ; Wed, 22 Nov 2000 23:30:11 +0000 (GMT) >X-Received: from snap.fhcrc.org (snap [140.107.52.19]) by fhcrc.org (8.10.2/8.10.2) with ESMTP id eAMNU9v28099 for ; Wed, 22 Nov 2000 15:30:09 -0800 (PST) >X-Received: from [140.107.30.186] ([140.107.30.186]) by snap.fhcrc.org (8.10.2/8.10.2) with ESMTP id eAMNU8m17760 for ; Wed, 22 Nov 2000 15:30:08 -0800 (PST) >X-User-Agent: Microsoft-Entourage/9.0.2509 >X-To: acedb >Date: Thu, 23 Nov 2000 10:24:28 +0000 (GMT) > >Hi > >We've moved labs recently and have moved our acedb database to a new server >(from OSF1 on an alpha to SunOS 5.7). Now when I start the new database I >get >// Database has non-native byte-order: swapping >(I tried editing and saving but that's not enough to fix it) > >This doesn't seem to be a problem right now but I just wondered if it leaves >us more open to crashes or if it will make queries slow? How could I swap >the byte order? > >thanks > >Janet > >------------------------------------------------------------------- > Dr. Janet Young >Fred Hutchinson Cancer Research Center >1100 Fairview Avenue N. tel: (206) 667 1471 >C3-168 fax: (206) 667 6524 >P.O. Box 19024 email: jayoung@fhcrc.org >Seattle, WA 98109-1024, USA. > > > >--- > > Danielle Thierry-Mieg NCBI. NLM. NIH Bldg 38A 8600 Rockville Pike Bethesda, MD 20894, USA email mieg@ncbi.nlm.nih.gov Tel 1 (301) 594 70 92 Fax 1 (301) 480 92 41 From owner-acedb@hgmp.mrc.ac.uk Fri Dec 1 13:20:34 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 507B017B55; Fri, 1 Dec 2000 13:20:31 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 9138717A82; Fri, 1 Dec 2000 13:20:19 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 08B0C17AB0; Fri, 1 Dec 2000 12:09:00 +0000 (GMT) Received: from mailsrv1.sanger.ac.uk (mailsrv1.sanger.ac.uk [193.62.207.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6BF01415DD; Fri, 1 Dec 2000 12:08:41 +0000 (GMT) Received: from griffin.sanger.ac.uk (root@griffin-e7 [193.62.207.76]) by mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id eB1C7GD08199; Fri, 1 Dec 2000 12:07:16 GMT Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id MAA01965; Fri, 1 Dec 2000 12:07:15 GMT From: Ed Griffiths To: Acedb Newsletter , acedb newsgroup on bionet , aratnasiri@ucdavis.edu, boberkfe@watson.wustl.edu, carson@mbt.washington.edu, dbaillie@gene.mbb.sfu.ca, dgrant@iastate.edu, G.REYES@CGIAR.ORG, jayne.vallance@bbsrc.ac.uk, jayoung@fhcrc.org, jmh.neefs@pandora.be, jspieth@watson.wustl.edu, jurg@sanger.ac.uk, keith@thale.life.nottingham.ac.uk, Lincoln Stein , lnothake@watson.wustl.edu, lvandela@bccancer.bc.ca, matthews@greengenes.cit.cornell.edu, mieg@sanger.ac.uk, mummi@decode.is, mwilkinson@gene.pbi.nrc.ca, r.bruskiewich@CGIAR.ORG, sjones@bcgsc.bc.ca, sness@bcgsc.bc.ca, T.van_Wezel@lumc.nl Subject: September newsletter Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Fri, 1 Dec 2000 13:20:19 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Please find the below the long delayed September newsletter. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ACEDB User Group Newsletter - September 2000 ############################################ If you want to have this newsletter mailed to you _or_ you want to make comments/suggestions about the format/content then send an email to acedb@sanger.ac.uk. Apologies +++++++++ There have been no newsletters for too long, sorry, sorry, sorry. We have had a number of problems with the build/test system for acedb which have precluded the usual monthly releases of development code. This has ended up with me delaying sending out the newsletters because there seemed little point when they refer to new features/bug fixes in code that is not yet available. General News ************ _Xref bug believed fixed..._ a long standing bug in xref which resulted in "object locked" errors when trying to update databases with objects containing particular types of xrefs has now been fixed (see bugs section). Most news this month is about bug fixes as we get ready for the next significant release which will be called Acedb 4_9. New Features ************ tace command sets +++++++++++++++++ If you issue the "?" command from within tace you get to see a list of the commands that you can issue. Previously in tace (and aceclient) this list was misleading because it included commands that the user would not be able to run because they did not have write access to the database. This has now been fixed so that if a user does not have write access they will not see commands that require write access. Bugs Fixed ********** tace bug ++++++++ When tace is run via a pipe (e.g. from a perl or shell script) it saves the database on quitting by default. This behaviour was broken in 4_8 and has now been restored. This is particularly important because running tace via scripts is one of the main mechanisms used at Sanger for doing large scale updates to databases. Expanding database ++++++++++++++++++ There was a problem in 4_8 with databases growing enormously when a large number of separate updates were made to the database. This has been fixed and was caused by old sessions (a session is a record of the state of the database after a set up updates has been made) not being deleted correctly from the database. To see the benefit from this fix you will need to rebuild the database. CDS start/end positions +++++++++++++++++++++++ Perhaps not a bug, more a confusion in meaning. For a sequence object that is a CDS you can specify the start/end positions of the CDS within the accompanying Source_exons and here in lies the problem. The start/end positions must be specified in spliced DNA coordinates, _not_ in Source_exon coordinates. This means you have to do some mental arithmetic if you are inserting the CDS positions by hand: you will need to add up the length of the Source_exon sections to get the size of the spliced DNA and work out where the CDS starts and ends within the single continuous section of exon DNA. acedb will now output an error message if a CDS is displayed where the start/end positions lie outside of the spliced DNA and will display the CDS as if it occupied the entire length of the spliced DNA. CDS start/end positions not working for reverse genes +++++++++++++++++++++++++++++++++++++++++++++++++++++ There was an annoying bug whereby, for reverese genes only, acedb would ignore a CDS start position unless an end position was specified as well. This has been fixed so that a CDS for a reverse gene now behaves the same way as for forward genes. Obscure socket server bug +++++++++++++++++++++++++ When started by inetd, the socket server crashed inetd on some linux systems because it wrongly _"shutdown"_ the listening socket when exitting. This has been fixed. XREF problem ++++++++++++ There has been a bug in the XREF code when making updates to a database for a long time. In 4_8 this has manifested itself in the form of updates failing where they involve XREFs with UNIQUE tags. This seems now to be fixed at long last, if this is not so then please send reports to acedb@sanger.ac.uk. This is an important bug to fix because it has been the principal reason for not releasing updates to large databases as "diffs". Currently databases such as the Worm database have to be released as complete new copies every time there is an update. Now the Xref bug is fixed it should be possible to release an update file which consists only of those parts of the database are different since the previous relase. No monthly build available. *************************** Unfortunately, due to system problems at the Sanger Centre a monthly build has not been possible for September. Next User Group Meeting - D213, 2.30pm, Thursday, 14th September **************************************************************** ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Ed Griffiths Last modified: Thu Nov 30 15:30:54 GMT 2000 From owner-acedb@hgmp.mrc.ac.uk Fri Dec 1 13:20:42 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 2201717A82; Fri, 1 Dec 2000 13:20:32 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id CD7BB17A83; Fri, 1 Dec 2000 13:20:22 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id C05A017B57; Fri, 1 Dec 2000 12:11:36 +0000 (GMT) Received: from mailsrv1.sanger.ac.uk (mailsrv1.sanger.ac.uk [193.62.207.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2F68B415DD; Fri, 1 Dec 2000 12:11:26 +0000 (GMT) Received: from griffin.sanger.ac.uk (root@griffin-e7 [193.62.207.76]) by mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id eB1C92D08617; Fri, 1 Dec 2000 12:09:02 GMT Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id MAA00849; Fri, 1 Dec 2000 12:09:00 GMT From: Ed Griffiths To: Acedb Newsletter , acedb newsgroup on bionet , aratnasiri@ucdavis.edu, boberkfe@watson.wustl.edu, carson@mbt.washington.edu, dbaillie@gene.mbb.sfu.ca, dgrant@iastate.edu, G.REYES@CGIAR.ORG, jayne.vallance@bbsrc.ac.uk, jayoung@fhcrc.org, jmh.neefs@pandora.be, jspieth@watson.wustl.edu, jurg@sanger.ac.uk, keith@thale.life.nottingham.ac.uk, Lincoln Stein , lnothake@watson.wustl.edu, lvandela@bccancer.bc.ca, matthews@greengenes.cit.cornell.edu, mieg@sanger.ac.uk, mummi@decode.is, mwilkinson@gene.pbi.nrc.ca, r.bruskiewich@CGIAR.ORG, sjones@bcgsc.bc.ca, sness@bcgsc.bc.ca, T.van_Wezel@lumc.nl Subject: November newsletter Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Fri, 1 Dec 2000 13:20:22 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk and the November newsletter.... the next one should be out around mid-December.... ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ACEDB User Group Newsletter - November 2000 ########################################### If you want to have this newsletter mailed to you _or_ you want to make comments/suggestions about the format/content then send an email to acedb@sanger.ac.uk. A new acedb developer joins the team, a number of new features for users and a number of bug fixes. General News ************ New acedb developer +++++++++++++++++++ After a hiatus of some months following the departure of Fred Wobus from our team (now pursuing his hobby of scuba diving in Thailand !), we have been joined by John Sturdy (jcgs@sanger.ac.uk). John is a Computer Science Ph.D. and has worked for various software companies locally for some years. Initially he will be working on improving the acedb web site so you should see quite a few improvements there over the next few weeks. New Features ************ "Tree/Text" view and "update" mode ++++++++++++++++++++++++++++++++++ An irritating feature of using "update" mode in the "Tree" window has been that the window is repositioned at the top when the mode is selected, thus losing the users place each time an update is performed. This has now been fixed: select a tag by clicking on it, then select "update" from the right button menu and the tag will stay visible in the window. "Tree/Text" view and "Tag search" menu item +++++++++++++++++++++++++++++++++++++++++++ Searching for a particular tag in a large object in the tree window can be tedious, especially when this involves opening collapsed nodes to find the tag. The right button menu now has an additional "Find tag" item that allows you to search for a tag (it will find the tag whether the tag is within a collapsed node or not). Fmap Horizontal Scrolling +++++++++++++++++++++++++ A horizontal scroll bar has been added to the fmap display so its no longer necessary to turn columns off to see whats displayed over to the right of the display. Headings/Titles/Column buttons are not redrawn as you scroll because this slows scrolling down too much. Support for 2-button mouse users ++++++++++++++++++++++++++++++++ Most MS-Windows users have 2-button mice which means they have not been able to use functions that were linked to the middle button on Xwindows/Unix machines. This has now been fixed by making shift-leftmousebutton do the same job as the middle button for 2-button users. Change to help in tace ++++++++++++++++++++++ The _"?"_ command to get help in tace has changed in the way it works. If there is only one command matching the string following "?" then the syntax for that one command will be printed, if there is more than one, then syntax for all matching commands will be printed, e.g. "?" gives a list of all available commands "? d" will give a list of all command beginning with "d" "? du" will list the "dump" command because it's the only command that matches "du" New "spick" addtion to keyset manipulating commands in tace. If you use the spush, spop etc. commands for manipulating keysets in tace then you should note a useful addition to these of spick (courtesy of Lincoln Stein). spick allows you to choose one of the stacked keysets and make it the active keyset without having to spop the stack to get to the one you want. Bugs Fixed ********** Two Acedb MS-Windows bug fixes ++++++++++++++++++++++++++++++ Printing acedb windows now works from Windows 95 in the same way as for acedb on Unix machines. You can now use the up and down arrows to scroll through the items in the keyset window. xace/tace hang when trying to get write access ++++++++++++++++++++++++++++++++++++++++++++++ Oh dear, while I'd love to say this bug was fixed, its not and can't be for the foreseeable future. The cause of the bug is based in NFS/lockmanager problems which arise from time to time on the Sanger network. Acedb uses lock files to make sure that only one user can have write access to a database at a time, this works well most of the time. There can be problems in two situations however: when the network is heavily loaded so that NFS starts to time out meaning that requests to create/write lockfiles stall and when lock managers on machines remote from yours on the network begin to hang (usually because of the NFS problems) meaning that acedb will be unable to lock its lock files. In either case xace or tace will simply hang, i.e. not respond to mouse clicks etc.. When this happens, all you can do is kill the program using the Unix "kill" command, you will need to use "ps" to find out the process id of the hung program and then type "kill -9 xxxxx" where xxxxx is the process id. The acedb code cannot detect that this problem has occurred because it cannot run while waiting to create/lock the lockfile. Sadly there is nothing we can do to solve this problem. gene finder bug +++++++++++++++ There is a bug in the November code which may cause the "Gene finder" button in fmap to crash the xace program. The problem happens when the definition of the ?Method class in the models.wrm file in the users database does not match the definition in the models.wrm file distributed with the code. Previous versions of acedb did not detect this mismatch and continued to run, probably with some errors in display of some fmap information. Detection of this sort of parse error was tightened up recently to support new function in AcePerl, hence the reason for the code failing now. Database administrators should check that the definition of the ?Method class in their models.wrm files matches that distributed with the code level they are using. We hope to make the code more tolerant of this problem in the future by altering the code to check the model of the database against its method own object and decide if it can continue if there is a difference. This will probably not happen until the New Year. Tab key: There was a bug whereby if the user pressed the Tab key while inputting text, the window would then no longer accept input. This has now been fixed and tabs can be used as input to text boxes. November monthly build now available. ************************************* You can pick up the monthly builds from: _Sanger users_ ~acedb/RELEASE.DEVELOPMENT _External users_ ftp://ftp.sanger.ac.uk/pub/acedb/Sanger-release.2000_11_21.tar.gz Next User Group Meeting - D213, 2.30pm, Thursday, 9th November ************************************************************** ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Ed Griffiths Last modified: Thu Nov 30 15:53:27 GMT 2000 From owner-acedb@hgmp.mrc.ac.uk Fri Dec 1 13:20:48 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 0748617B88; Fri, 1 Dec 2000 13:20:42 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id CCFE617AB0; Fri, 1 Dec 2000 13:20:30 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 600DA17A82; Fri, 1 Dec 2000 11:34:28 +0000 (GMT) Received: from mailsrv1.sanger.ac.uk (mailsrv1.sanger.ac.uk [193.62.207.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3D8EC415DC; Fri, 1 Dec 2000 11:34:11 +0000 (GMT) Received: from griffin.sanger.ac.uk (root@griffin-e7 [193.62.207.76]) by mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id eB1BTSD31919; Fri, 1 Dec 2000 11:29:28 GMT Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id LAA01393; Fri, 1 Dec 2000 11:29:27 GMT From: Ed Griffiths To: Acedb Newsletter , acedb newsgroup on bionet , aratnasiri@ucdavis.edu, boberkfe@watson.wustl.edu, Carson_Thoreen@brown.edu, dbaillie@gene.mbb.sfu.ca, dgrant@iastate.edu, G.REYES@CGIAR.ORG, janety@u.washington.edu, jayne.vallance@bbsrc.ac.uk, jmh.neefs@pandora.be, jspieth@watson.wustl.edu, jurg@sanger.ac.uk, keith@thale.life.nottingham.ac.uk, Lincoln Stein , lnothake@watson.wustl.edu, lvandela@bccancer.bc.ca, matthews@greengenes.cit.cornell.edu, mieg@sanger.ac.uk, mummi@decode.is, mwilkinson@gene.pbi.nrc.ca, r.bruskiewich@CGIAR.ORG, sjones@bcgsc.bc.ca, sness@bcgsc.bc.ca, T.van_Wezel@lumc.nl Subject: acedb newsletters.... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Fri, 1 Dec 2000 13:20:30 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Dear all, There have been no newsletters for some time but now the silence is to be broken. Sanger centre systems have been in some turmoil since the summer for a number of reasons (flooding, new DEC clusters installed etc. etc.), this has meant that we have not been able to reliably build/test acedb so I have been reluctant to send out monthly releases. This in turn has meant that I have not sent out the newsletters as there seemed little point in describing code changes that were simply not available. I have done three retrospective newsletters for Sept-Nov and these will be sent out to you later today. As usual the newsletters can also be seen on the web site (they will be there from tomorrow) at: http://www.acedb.org/winfo/Newsletters/ cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Fri Dec 1 13:21:01 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 94D8317A82; Fri, 1 Dec 2000 13:20:59 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 743E317AB0; Fri, 1 Dec 2000 13:20:45 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 27AD417B55; Fri, 1 Dec 2000 12:10:21 +0000 (GMT) Received: from mailsrv1.sanger.ac.uk (mailsrv1.sanger.ac.uk [193.62.207.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 13E1A415E2; Fri, 1 Dec 2000 12:09:42 +0000 (GMT) Received: from griffin.sanger.ac.uk (root@griffin [193.60.84.177]) by mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id eB1C7vD08452; Fri, 1 Dec 2000 12:07:57 GMT Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id MAA31654; Fri, 1 Dec 2000 12:07:55 GMT From: Ed Griffiths To: Acedb Newsletter , acedb newsgroup on bionet , aratnasiri@ucdavis.edu, boberkfe@watson.wustl.edu, carson@mbt.washington.edu, dbaillie@gene.mbb.sfu.ca, dgrant@iastate.edu, G.REYES@CGIAR.ORG, jayne.vallance@bbsrc.ac.uk, jayoung@fhcrc.org, jmh.neefs@pandora.be, jspieth@watson.wustl.edu, jurg@sanger.ac.uk, keith@thale.life.nottingham.ac.uk, Lincoln Stein , lnothake@watson.wustl.edu, lvandela@bccancer.bc.ca, matthews@greengenes.cit.cornell.edu, mieg@sanger.ac.uk, mummi@decode.is, mwilkinson@gene.pbi.nrc.ca, r.bruskiewich@CGIAR.ORG, sjones@bcgsc.bc.ca, sness@bcgsc.bc.ca, T.van_Wezel@lumc.nl Subject: October newsletter Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Fri, 1 Dec 2000 13:20:45 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk and the October newsletter.... ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ACEDB User Group Newsletter - October 2000 ########################################## If you want to have this newsletter mailed to you _or_ you want to make comments/suggestions about the format/content then send an email to acedb@sanger.ac.uk. Like last month, this month has been a month of bug fixes in preparation for the release of Acedb 4_9. New Features ************ Acedb MS-Windows CD packaging improvements ++++++++++++++++++++++++++++++++++++++++++ The following improvements have been made to the Install process: * - there's a new database wizard in the for the installation, it will install the acedb binaries and set up a new/empty default database. * - the file extension ".wrm" is automatically registered with MS-Windows to be opened with MS-Windows Notepad as this is a suitable editor for altering them. * - The latest Worm WS releases are now regularly packaged with the Acedb MS-Windows CD. _Coming soon -_ at the Acedb web site, a document on how to make windows packages, databases, cds, for acedb. URLs on Acedb MS-Windows ++++++++++++++++++++++++ URLs in objects now work correctly in the MS-Windows version of acedb, the URL will be displayed by whichever program is registered with MS-Windows to deal with URLs (this might be Internet Explorer or maybe Netscape). ".wrm" files on Acedb MS-Windows ++++++++++++++++++++++++++++++++ A problem with Unix vs. MS-Windows is that they signal the end of a line of text in a different way. This matters if you edit one of acedbs text files (e.g. models.wrm) on Windows and then try to edit again on a Unix machine. Acedb expects ".wrm" text files to use the Unix way of representing an end-of-line, but the MS-Windows version will also cope with the MS-Windows way of doing this. This means that Acedb will continue to work if you have editted your models.wrm file on an MS-Windows machine. Bugs Fixed ********** "%" Dumping bug +++++++++++++++ acedb 4_8 had a bug whereby "%" signs within data in the database e.g. "GC content 48%" would not be dumped correctly because the "%" was read as a formatting instruction. This is now fixed. Incorrect ordering of output to screen under tace +++++++++++++++++++++++++++++++++++++++++++++++++ Error messages in tace could get tangled with the "acedb>" prompt which was confusing. This has now been fixed. Loss of window focus ++++++++++++++++++++ Sometimes when acedb popped up messages (warnings, information etc.), this could lead to the acedb losing the keyboard focus, i.e. any typing by the user would be lost. This is now fixed. No monthly build available. *************************** Unfortunately, due to system problems at the Sanger Centre a monthly build has not been possible for September. Next User Group Meeting - D213, 2.30pm, Thursday, 12th October ************************************************************** ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Ed Griffiths Last modified: Thu Nov 30 15:41:36 GMT 2000 From owner-acedb@hgmp.mrc.ac.uk Mon Dec 4 07:57:53 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7A70D17B15; Mon, 4 Dec 2000 07:57:52 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 11C8317B13; Mon, 4 Dec 2000 07:57:49 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 296A517A59; Sat, 2 Dec 2000 11:17:26 +0000 (GMT) Received: from mailsrv1.sanger.ac.uk (mailsrv1.sanger.ac.uk [193.62.207.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id BA001415DC; Sat, 2 Dec 2000 11:17:19 +0000 (GMT) Received: from griffin.sanger.ac.uk (rd@griffin [193.60.84.177]) by mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id eB2BGoD23013; Sat, 2 Dec 2000 11:16:50 GMT From: Richard Durbin Received: (from rd@localhost) by griffin.sanger.ac.uk (8.8.7/8.8.7) id LAA27322; Sat, 2 Dec 2000 11:16:48 GMT Message-Id: <200012021116.LAA27322@griffin.sanger.ac.uk> To: T.van_Wezel@lumc.nl, acedbg@sanger.ac.uk, bionet-software-acedb@net.bio.net, edgrif@sanger.ac.uk, lnothake@watson.wustl.edu, lstein@cshl.org, lvandela@bccancer.bc.ca, matthews@greengenes.cit.cornell.edu, mieg@sanger.ac.uk, mummi@decode.is, mwilkinson@gene.pbi.nrc.ca, r.bruskiewich@CGIAR.ORG, sjones@bcgsc.bc.ca, sness@bcgsc.bc.ca Subject: Re: November newsletter Newsgroups: bionet.software.acedb Date: Mon, 4 Dec 2000 07:57:49 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Thanks Ed for all your newsletters and updates. I have one comment about the outstanding issue on xace/tace hang when trying to get write access ++++++++++++++++++++++++++++++++++++++++++++++ which I think is primarily a Sanger Centre problem. As Ed says, this is due to NFS problems. The correct way to avoid this problem is to ALWAYS run acedb from the machine that directly mounts the disk with the database on. This not only deals with NFS problems, but will also improve performance substantially. I'm going to copy copy Kate Rice here who oversees all the humgen informatics operations, because this may require changing some LSF behaviour for the humgen cluster. We have talked about this before.... Richard From owner-acedb@hgmp.mrc.ac.uk Mon Dec 4 15:56:30 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C590117ABB; Mon, 4 Dec 2000 15:56:29 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 4BDC717A5D; Mon, 4 Dec 2000 15:56:27 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 264DF17B18; Mon, 4 Dec 2000 14:49:15 +0000 (GMT) Received: from postfix1.free.fr (postfix1.free.fr [212.27.32.21]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 858F6415DD for ; Mon, 4 Dec 2000 14:49:09 +0000 (GMT) Received: from nnrp5.proxad.net (nnrp5.proxad.net [212.27.32.77]) by postfix1.free.fr (Postfix) with ESMTP id 677C928096 for ; Mon, 4 Dec 2000 15:48:50 +0100 (MET) Received: from localhost (localhost [[UNIX: localhost]]) by nnrp5.proxad.net (8.9.3/8.9.3/Debian 8.9.3-21) id PAA12609; Mon, 4 Dec 2000 15:48:50 +0100 To: bionet-software-acedb@net.bio.net Message-ID: <3A2BB010.3CEE5BC4@marseille.inserm.fr> From: "F. Coulier" Organization: INSERM X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.11 i686) X-Accept-Language: fr-FR, en MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Still have prblems settings up things right Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Complaints-To: abuse@proxad.net X-Trace: nnrp5.proxad.net 975941329 195.220.67.155 (Mon, 04 Dec 2000 15:48:49 CET) NNTP-Posting-Date: Mon, 04 Dec 2000 15:48:49 CET Date: Mon, 4 Dec 2000 15:56:27 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hello to all, I have been trying for quite some time to move Acedb (plus other databases that run with acedb) from one computer (linux mandrake 6.1) to another (linux mandrake 7.1), but I have lots of difficulties setting up web access. I can run acedb on the new machine OK, as well as 2 others small databases we are (trying to) develop in the lab. On the "new" computer, I can manually start gifaceserver to run any of these 3 databases (i.e. fc]$ gifaceserver /database/acedb 20114 1200:1200:100) and then run aceclient (i.e. fc]$ aceclient xxx.xxx.xxx.xxx -port 20114) from the PC where the gifaceserver is running, or from another one. Now, where I failed, is when I try to start the gifaceserver on the new computer by launching the aceclient (this works Ok on the "old" PC). I suspect a file permission problem, but cannot find where this problem could be. gifaceserver is executable by user acedb and group U119 fc (me, the username underwhich I tried to run aceclient) is a member of group U119. In inetd.conf I have: acedb/1 stream rpc/tcp wait acedb.U119 /usr/local/bin/rpc.gifaceserver rpc.gifaceserver /database/acedb 20114 1200:1200:0 rpc.gifaceserver is a symbolic link to gifaceserver /database/acedb and /database/acedb/database are rwx for acedb.U119 Any help or clues would be greatly appreciated! François -- François Coulier, mél: coulier@marseille.inserm.fr INSERM Unité 119, 27 bd Leï Roure, 13009 Marseille, France Tel: 33 (0) 4 91 26 04 26 (temporaire) Fax: 33 (0) 4 91 26 03 64 Site ouaibe: http://olan.marseille.inserm.fr/ From owner-acedb@hgmp.mrc.ac.uk Mon Dec 4 16:26:53 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 68EB217B1E; Mon, 4 Dec 2000 16:26:52 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C437117B18; Mon, 4 Dec 2000 16:26:50 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 9B09917B18; Mon, 4 Dec 2000 16:26:24 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3FCF5415DA for ; Mon, 4 Dec 2000 16:26:19 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id QAA15174 for bionet-software-acedb@net.bio.net; Mon, 4 Dec 2000 16:26:18 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: Still have prblems settings up things right Organization: Sanger Centre Message-ID: <3A2BC5AA.5A0933A4@sanger.ac.uk> References: <3A2BB010.3CEE5BC4@marseille.inserm.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 975947178 15172 193.60.84.177 (4 Dec 2000 16:26:18 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 4 Dec 2000 16:26:18 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Mon, 4 Dec 2000 16:26:50 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Francois, First a couple of questions: 1) What level of acedb are you using ? If you are using 4_8, you should try the socket server rather than the RPC server. The programs are called saceserver and saceclient and details for set up are in wdoc. 2) What are your entries in /etc/services /etc/rpc /etc/inetd ?? Some suggestions Have you looked in the server log or acedb log in the database to see if the server program even starts up ? If not, then its likely to be a problem either with the /etc files or with permissions. Are you trying to get write access or have you altered the server.wrm file to allow universal reading (this is a good idea just to get things started). Don't know if any of this helps.... cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Mon Dec 4 19:03:34 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 33E8917B45; Mon, 4 Dec 2000 19:03:34 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 00D9617B43; Mon, 4 Dec 2000 19:03:32 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 6CBB217B2E; Mon, 4 Dec 2000 17:12:49 +0000 (GMT) Received: from jerry.har.mrc.ac.uk.har.mrc.ac.uk (jerry.har.mrc.ac.uk [193.63.70.145]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 13025415D5 for ; Mon, 4 Dec 2000 17:12:36 +0000 (GMT) Received: from har.mrc.ac.uk (modo [193.63.70.72]) by jerry.har.mrc.ac.uk.har.mrc.ac.uk (8.9.3/8.9.1) with ESMTP id RAA20805 for ; Mon, 4 Dec 2000 17:12:33 GMT Message-ID: <3A2BD4D8.9957B4D3@har.mrc.ac.uk> From: Vitali Proutski Reply-To: V.Proutski@har.mrc.ac.uk X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: bionet-software-acedb@net.bio.net Subject: Graphics in AceBrowser Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Newsgroups: bionet.software.acedb Date: Mon, 4 Dec 2000 19:03:32 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Hey there, I'm having a problem with displaying graphics in AceBrowser. The asGig() method from Ace::Object.pm seems to quit earlier than it is supposed to. If I woiuld love to hear from anybody how had similar type of problem and solved it. Vitali. From owner-acedb@hgmp.mrc.ac.uk Tue Dec 5 16:06:19 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id CEBB117B08; Tue, 5 Dec 2000 16:06:18 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id E5F8617AC8; Tue, 5 Dec 2000 16:06:16 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id E2B7C17B6C; Tue, 5 Dec 2000 11:29:52 +0000 (GMT) Received: from postfix1.free.fr (postfix1.free.fr [212.27.32.21]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id E86E9415E1 for ; Tue, 5 Dec 2000 11:29:36 +0000 (GMT) Received: from nnrp6.proxad.net (nnrp6.proxad.net [212.27.32.78]) by postfix1.free.fr (Postfix) with ESMTP id A2C04281C9 for ; Tue, 5 Dec 2000 09:54:45 +0100 (MET) Received: from localhost (localhost [[UNIX: localhost]]) by nnrp6.proxad.net (8.9.3/8.9.3/Debian 8.9.3-21) id JAA09883; Tue, 5 Dec 2000 09:54:45 +0100 To: bionet-software-acedb@net.bio.net Message-ID: <3A2CAE36.AB28A70B@marseille.inserm.fr> From: F Coulier X-Mailer: Mozilla 4.73 [fr] (X11; I; Linux 2.2.15-4mdksecure i686) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.software.acedb Subject: Re: Still have prblems settings up things right References: <3A2BB010.3CEE5BC4@marseille.inserm.fr> <3A2BC5AA.5A0933A4@sanger.ac.uk> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Complaints-To: abuse@proxad.net X-Trace: nnrp6.proxad.net 976006485 195.220.67.166 (Tue, 05 Dec 2000 09:54:45 CET) NNTP-Posting-Date: Tue, 05 Dec 2000 09:54:45 CET Organization: Guest of ProXad - France Date: Tue, 5 Dec 2000 16:06:16 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Ed Griffiths a écrit : > Francois, > > First a couple of questions: > > 1) What level of acedb are you using ? If you are using 4_8, you should try > the socket server rather than the RPC server. The programs are called > saceserver and saceclient and details for set up are in wdoc. > I use 4_7. Do you think I should update to 4_8, or wait for 4_9 ? > > 2) What are your entries in /etc/services /etc/rpc /etc/inetd ?? > /etc/services: acedb 20114/tcp nbdb 20117/tcp madb 20118/tcp /etc/rpc: acedb 20114 rpc.gifaceserver nbdb 20117 rpc.gifaceserver madb 20118 rpc.gifaceserver /etc/inetd.conf: acedb/1 stream rpc/tcp wait acedb.U119 /usr/local/bin/rpc.gifaceserver rpc.gifaceserver /database/acedb 20114 1200:1200:0 nbdb/1 stream rpc/tcp wait acedb.U119 /usr/local/bin/rpc.gifaceserver rpc.gifaceserver /database/Nbdb 20117 1200:1200:0 madb/1 stream rpc/tcp wait acedb.U119 /usr/local/bin/rpc.gifaceserver rpc.gifaceserver /database/madb 20118 1200:1200:0 > > Some suggestions > > Have you looked in the server log or acedb log in the database to see if the > server program even starts up ? If not, then its likely to be a problem either > with the /etc files or with permissions. > There is no traces in server.log. My guess is that the server does not start at all. I actually get the following message when trying to launch :aceclient [fc@grun fc]$ aceclient xxx.xxx.xxx.xxx -port 20114 //! cannot establish connection //! usage: aceclient host [-port number] [-time_out secs] [-access_info] [-ace_out] [-ace_in] [-f reportfile parameters] > > Are you trying to get write access or have you altered the server.wrm file to > allow universal reading (this is a good idea just to get things started). I have WRITE_ACCESS_DIRECTORY /database/Write_access With the proper permission set up for this directory (tried rwx for all) I have also READ_ACCESS_DIRECTORY PUBLIC Thanks for your help! François From owner-acedb@hgmp.mrc.ac.uk Wed Dec 13 14:32:12 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id B86AA17AC2; Wed, 13 Dec 2000 14:32:11 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 3F4A117A62; Wed, 13 Dec 2000 14:32:10 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 6758917A62; Wed, 13 Dec 2000 14:31:49 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 97FE8415CF for ; Wed, 13 Dec 2000 14:31:36 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA08676 for bionet-software-acedb@net.bio.net; Wed, 13 Dec 2000 14:31:36 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Install script for Acedb Organization: Sanger Centre Message-ID: <3A378847.2970ADA9@sanger.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 976717895 8674 193.60.84.177 (13 Dec 2000 14:31:35 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 13 Dec 2000 14:31:35 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Wed, 13 Dec 2000 14:32:10 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Calling all acedb installers... I am making some changes to the acedb INSTALL script in preparation for the next release of acedb. The old script used to: install source in ./w*, binaries in ./bin, docs in ./w*, install a version of the worm database and mess about with various files in the worm database. The script also created a couple of small scripts that would invoke xace/tace on the worm database. Its no longer practical to distribute the worm database with acedb source code, its just too big. If you want the worm database, please can you now go to one of the below for this: http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/ ftp://ftp.sanger.ac.uk/pub/wormbase I propose that the INSTALL script should now be a more simple affair that unpacks source, binary and/or docs archives into the current directory and makes any links required for building the code and makes sure that files have the correct permissions. Is this acceptable ? Are there any other functions that the script should perform that are vital to users ? cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Mon Dec 18 10:48:45 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 8A1AF17AF6; Mon, 18 Dec 2000 10:48:44 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id DAA0417AEF; Mon, 18 Dec 2000 10:48:39 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 93F8F17AE7; Fri, 15 Dec 2000 15:14:52 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 10B4D415DD for ; Fri, 15 Dec 2000 15:14:46 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id PAA01988 for bionet-software-acedb@net.bio.net; Fri, 15 Dec 2000 15:14:45 GMT To: bionet-software-acedb@net.bio.net From: John Sturdy Newsgroups: bionet.software.acedb Subject: AceDB Showcase Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: X-Trace: niobium.hgmp.mrc.ac.uk 976893285 1846 193.62.207.28 (15 Dec 2000 15:14:45 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 15 Dec 2000 15:14:45 GMT X-Newsreader: Gnus v5.5/Emacs 20.3 Date: Mon, 18 Dec 2000 10:48:39 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk I'm preparing the new version of www.acedb.org, and we'd like to include an examples / showcase section, linking to various projects that use AceDb. If any of you are prepared to have your project included in this, please mail me the URL of a page describing it, and I'll include it. __John -- Dr John Sturdy jcgs@sanger.ac.uk Informatics Division Sanger Centre From owner-acedb@hgmp.mrc.ac.uk Mon Dec 18 12:21:18 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 7180317B27; Mon, 18 Dec 2000 12:21:17 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id A9DBF17B20; Mon, 18 Dec 2000 12:21:14 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 04CEE17B1F; Mon, 18 Dec 2000 12:20:16 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B5EC7415DA for ; Mon, 18 Dec 2000 12:20:09 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id MAA17755 for bionet-software-acedb@net.bio.net; Mon, 18 Dec 2000 12:20:08 GMT To: bionet-software-acedb@net.bio.net From: Ed Griffiths Newsgroups: bionet.software.acedb Subject: Re: AceDB Showcase Organization: Sanger Centre Message-ID: <3A3E00F8.285EAD89@sanger.ac.uk> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: niobium.hgmp.mrc.ac.uk 977142008 17753 193.60.84.177 (18 Dec 2000 12:20:08 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 18 Dec 2000 12:20:08 GMT X-Mailer: Mozilla 4.7 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en Date: Mon, 18 Dec 2000 12:21:14 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk Although I mentioned John in the November newsletter, for those of you that missed that item: John is a new acedb developer and he's starting off by sorting out our website and downloads sections. I noted a number of suggestions from the Acedb Vancouver meeting earlier this year (which John is implementing), if you have any comments about the acedb web or download sites then do please either post them here or send them to John direct. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk URL: http://www.sanger.ac.uk/Users/edgrif | | Tel: +44-1223-494780 Fax: +44 1223 494919 | ------------------------------------------------------------------------ From owner-acedb@hgmp.mrc.ac.uk Fri Dec 22 13:22:35 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id C094B17B4D; Fri, 22 Dec 2000 13:22:34 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id 245FF17B4B; Fri, 22 Dec 2000 13:22:32 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id AD38917AAA; Fri, 22 Dec 2000 11:32:13 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 8C7B3415F0 for ; Fri, 22 Dec 2000 11:32:09 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id LAA02183 for bionet-software-acedb@net.bio.net; Fri, 22 Dec 2000 11:32:09 GMT To: bionet-software-acedb@net.bio.net From: John Sturdy Newsgroups: bionet.software.acedb Subject: AceDB and emacs Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: X-Trace: niobium.hgmp.mrc.ac.uk 977484728 2181 193.62.207.28 (22 Dec 2000 11:32:08 GMT) X-Complaints-To: news@net.bio.net NNTP-Posting-Date: 22 Dec 2000 11:32:08 GMT X-Newsreader: Gnus v5.5/Emacs 20.3 Date: Fri, 22 Dec 2000 13:22:32 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk As I'm nearing the end (I think) of the first batch of my work on the website, I'm beginning to think ahead to making use of emacs to help with working with AceDB -- I do nearly all my work through emacs, and often write bits of elisp to help out. If any of you have any requests for what you'd like included in an emacs package for working with AceDB, or have any pieces of existing code you'd like to contribute, let me know in the next few weeks and I'll try to include them. What I have in mind includes: editing modes for model files and ace files specialized comint (shell interaction) for driving tace, with emacs menu entries, and possibly with syntax colouring of results The editing mode for model files will parse the model file to know what tags are defined, etc, and the mode for ace files will be able to make use of this data (if told which model to use), providing completion on tag names, checks for valid tags on saving the file, etc. Comments? Discussion? I'll put the resulting code on the acedb.org website. (If anyone's interested, I can also put the elisp I've used to re-work the website on-line, probably in my webspace on sanger.ac.uk) -- Dr John Sturdy jcgs@sanger.ac.uk Informatics Division Sanger Centre From owner-acedb@hgmp.mrc.ac.uk Fri Dec 22 13:22:36 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 12DF217B49; Fri, 22 Dec 2000 13:22:34 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id DF1FE17B49; Fri, 22 Dec 2000 13:22:32 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id DA16117B1C; Fri, 22 Dec 2000 13:07:43 +0000 (GMT) Received: from rutgers.rutgers.edu (rutgers.edu [165.230.4.76]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 55BC5415F4 for ; Fri, 22 Dec 2000 13:07:37 +0000 (GMT) Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by rutgers.rutgers.edu (8.8.8/8.8.8) with ESMTP id IAA16223 for ; Fri, 22 Dec 2000 08:07:30 -0500 (EST) Received: from oyez.ccc.nottingham.ac.uk ([128.243.241.164] helo=news.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.20 #2) id 149Rto-0006dP-00 for bionet-software-acedb@moderators.isc.org; Fri, 22 Dec 2000 13:06:16 +0000 Received: from news by news.nottingham.ac.uk with local (Exim 1.92 #1) for bionet-software-acedb@moderators.isc.org id 149Rux-0002P1-00; Fri, 22 Dec 2000 13:07:27 +0000 To: bionet-software-acedb@moderators.isc.org From: Keith Bradnam Newsgroups: bionet.software.acedb Subject: WormBase scripts Organization: ACS, The University of Nottingham Message-ID: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Trace: oyez.ccc.nottingham.ac.uk 977490447 9237 128.243.116.150 (22 Dec 2000 13:07:27 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 22 Dec 2000 13:07:27 GMT X-Sender: keith@thale Date: Fri, 22 Dec 2000 13:22:32 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk A while ago I asked if anyone knew if the AceBrowser scripts used on the wormbase site were publically available. I spoke to Lincoln Stein a couple of weeks ago and he informed me that the scripts are available from the wormbase ftp site at: ftp.wormbase.org need to look in the /pub/wormbase directory and grab the wormbase-site.tar.gz file which contains everything. Keith ~ Keith Bradnam - UK CropNet (http://ukcrop.net) webmaster and ~ Arabidopsis Genome Resource (http://ukcrop.net/agr) developer. ~ ~ Nottingham Arabidopsis Stock Centre, University Park, ~ University of Nottingham, NG7 2RD, UK. Tel: (0115) 951 3091 From owner-acedb@hgmp.mrc.ac.uk Fri Dec 22 18:15:55 2000 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 4919F17AF0; Fri, 22 Dec 2000 18:15:55 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6019) id C3D3617AC2; Fri, 22 Dec 2000 18:15:53 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id D6C5417AC2; Fri, 22 Dec 2000 17:47:29 +0000 (GMT) Received: from mailsrv1.sanger.ac.uk (mailsrv1.sanger.ac.uk [193.62.207.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 30551415DA; Fri, 22 Dec 2000 17:47:22 +0000 (GMT) Received: from griffin.sanger.ac.uk IDENT: root@griffin-e7 [193.62.207.76] (root@griffin-e7 [193.62.207.76]) œby mailsrv1.sanger.ac.uk (8.11.1/8.11.1) with ESMTP id eBMHj7K31814; Fri, 22 Dec 2000 17:45:11 GMT Received: from localhost (edgrif@localhost [127.0.0.1]) by griffin.sanger.ac.uk (8.8.7/8.8.7) with ESMTP id RAA02130; Fri, 22 Dec 2000 17:44:57 GMT From: Ed Griffiths To: Acedb Newsletter , acedb newsgroup on bionet , aratnasiri@ucdavis.edu, boberkfe@watson.wustl.edu, carson@mbt.washington.edu, colin.dolphin@kcl.ac.uk, dbaillie@gene.mbb.sfu.ca, Dennis.Knudson@colostate.edu, dgrant@iastate.edu, G.REYES@CGIAR.ORG, jayne.vallance@bbsrc.ac.uk, jayoung@fhcrc.org, jmh.neefs@pandora.be, jspieth@watson.wustl.edu, jurg@sanger.ac.uk, keith@thale.life.nottingham.ac.uk, Lincoln Stein , lnothake@watson.wustl.edu, lvandela@bccancer.bc.ca, Martien.Groenen@Alg.VF.WAU.NL, matthews@greengenes.cit.cornell.edu, mieg@sanger.ac.uk, mummi@decode.is, mwilkinson@gene.pbi.nrc.ca, r.bruskiewich@CGIAR.ORG, sjones@bcgsc.bc.ca, sness@bcgsc.bc.ca, T.van_Wezel@lumc.nl Subject: December newsletter Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Newsgroups: bionet.software.acedb Date: Fri, 22 Dec 2000 18:15:53 +0000 (GMT) Sender: owner-acedb@hgmp.mrc.ac.uk Precedence: bulk As promised, the December newsletter. Please note that the December monthly build will not be available until the first week in January, sorry, there just isn't time to test it before Christmas. cheers Ed ------------------------------------------------------------------------ | Ed Griffiths, Acedb development, Informatics Group, | | The Sanger Centre, Wellcome Trust Genome Campus, | | Hinxton, Cambridge CB10 1SA, UK | | | | email: edgrif@sanger.ac.uk Tel: +44-1223-494780 Fax: +44-1223-494919 | ------------------------------------------------------------------------ ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- ACEDB User Group Newsletter - December 2000 ########################################### If you want to have this newsletter mailed to you _or_ you want to make comments/suggestions about the format/content then send an email to acedb@sanger.ac.uk. This month sees: the announcement of ChickAce, a reminder for Unix users about environment limits and "out of memory" errors from Acedb, major reworking of the Acedb website, quite a number of bug fixes, and a proposal for some new variations of the Rename function. General News ************ ChickAce ++++++++ Martien Groenen emailed to say that he has been setting up an acedb database for the chicken: From: Martien.Groenen@Alg.VF.WAU.NL During the last 6 months I have set up ChickAce which now contains almost all the mapping information that is available for chicken including the linked data such as references (abstracts), sequences, Comparative mapping information (human and mouse), primers, SNP's etc. Currently the database is running satisfactory under Windows in our lab, and someone within my group is using the available CGI script to make the database available on our website (hopefully running in the beginning of next year). In one of the latest newsletters I also saw that URL's are now recognized correctly from within AceDb. Can I use that to link data directly to other databases that are available through the WWW (e.g. for all genes in ChickAce I have also added an extra entry for the Locuslink ID for human and mouse. Can I make a direct link with Locuslink?). Could you add me to the mailing list for the AceDb newsletter (you could also mention that an AceDb database for chicken has been set up in wageningen). Best regards, Martien Articles ******** User Environment Limits and Acedb on Unix +++++++++++++++++++++++++++++++++++++++++ This is a brief reminder about user limits which can cause acedb to crash if they are set too low ( applies to unix not MS-Windows users). All users who log on to a unix box (whether directly or via a network terminal) have a set of user limits which control the amount of memory/files etc. that they are allowed to use. You can look at these limits using the C shell command "limit": > limit cputime unlimited filesize unlimited datasize 262144 kbytes stacksize 2048 kbytes coredumpsize 0 kbytes memoryuse 505664 kbytes descriptors 4096 "datasize" and "stacksize" particularly affect Acedb and can cause it to crash by running out of memory. In the above example "stacksize" is about 2MB which is too low, whereas "datasize" is fine for most uses at about 260MB. If Acedb crashes unexpectedly with either of these warnings: "Memory allocation failure when acedb requested NNNNNN bytes, acedb has already allocated NNNNNN bytes...." or "ABORT : Fatal program fault, signal NN...." then you should try increasing your limits using the "unlimit" C shell command: > unlimit stacksize > unlimit datasize If this does not fix the problem then report it either using the ddts bug reporting system: * http://www.sanger.ac.uk/cgi-bin/webddts/WebDDTS.pl?Project=Acedb or by sending a description of the problem to the acedb developers at: * acedb@sanger.ac.uk Acedb Web Pages re-organisation +++++++++++++++++++++++++++++++ John Sturdy has been undertaking a major reorganisation of the acedb web pages and download site. If you visit the Acedb website you will see that the front page has changed and will continue to change quite radically until about mid-January. Of special interest are: * Separate "User", "Administrator/Curator" and "Developer" sections. * A Search box which allows you to make keyword searches of acedb documents both on the Acedb website and the Acedb document library in the States. Please do try this and if you find notable omissions then either send mail to the Acedb newsgroup or to acedb@sanger.ac.uk. * There is a new "downloads" set of pages under construction to give better access to the ftp site (available in January). * There is a new "Site map" link which gives a quick overview of the document structure of the Acedb site as a whole. John will be adding a lot of new material to the website over the next couple of weeks and our intention is to make it a lot more usable. Comments or suggestions are welcome, please send them to the Acedb newsgroup or acedb@sanger.ac.uk. New Features ************ New position readout in fmap ++++++++++++++++++++++++++++ A small change courtesy of Jean Thierry-Mieg, fmap has a friendlier readout for the position on the sequence which will now be in kilo (kb) and Mega (Mb) bases, making it a little easier to read than 1238749217498123794 as used to be displayed for long sequences. Better diagnotics from Rename/Alias failures ++++++++++++++++++++++++++++++++++++++++++++ Previously Acedb has not reported the reason for these failures, only that they happened, now parsing will report in detail the reason for any Rename or Alias failures so that fixing them should be easier. Bugs Fixed ********** Colours bug with gifs +++++++++++++++++++++ GIF images produced by Acedb 4_8c were sometimes in garish/hard to read colours, this is now fixed in the December monthly build. Dumping objects with very large tag values ++++++++++++++++++++++++++++++++++++++++++ Some tag values can be very large (e.g. DNA) and this has caused acedb to overrun one of its internal buffers, this is now fixed with dynamically growing buffers. File Chooser irritations ++++++++++++++++++++++++ Several irritating features of the File Chooser window have been fixed: * If you want to go directly to a directory, you can do this by typing the directory name in the bottom "selection" window and pressing the key. This will point the file chooser to this directory so you can then choose files from there. The key also does filename completion like the C shell. * The File Chooser window now shows a "busy" cursor when it cannot respond to user input e.g. because its waiting to list an NFS mounted directory. * The default size of the window has been increased to make it easier to see long filenames. Cut/Paste bug fixed +++++++++++++++++++ Cut and Paste of larger texts (e.g. DNA) was broken, this was a bug in the underlying Window System software (GTK) and is being fixed by installing updated versions of the software which include the bug fix. Main Window reset after "Clean Up" ++++++++++++++++++++++++++++++++++ "Clean up" behaviour has been returned to how it was in 4_7, the local/global search is left as it was before the "Clean up". Socket Server Admin users permissions bug +++++++++++++++++++++++++++++++++++++++++ If you noticed problems with Admin users not having access to some commands for the socket server, this is now fixed. Admin users should have access to all possible commands as they have the highest permission levels. Education ********* HGMP are hosting an Acedb course in the week of 22nd-26th January 2001. The next Sanger Centre course is likely to be in June 2001. If you are interested in either please mail Sylvia Martinelli (sylvia@sanger.ac.uk) Future Plans ************ If you wish to make suggestions about any of the below, please mail them to acedb@sanger.ac.uk Revised INSTALL script for Acedb ++++++++++++++++++++++++++++++++ The current INSTALL script for acedb is being revised, the section for installing the worm database will be moved into a separate script (available from the worm web site in the January). The download site will include for each acedb release the following archives: compilable source code, binaries for selected platforms, help pages, docs and a test database. Enhancements to "Rename" ++++++++++++++++++++++++ Discussions with a number of users have suggested that the "Rename" operation doesn't always so what they would like or expect. Currently it works like this: Let's say we wish to rename Sequence object "A" to "B": If the database does _not_ contain a Sequence object with the name "B", the operation is straight forward: object "A" is simply given the new name of "B" and the name "A" ceases to exist. If the database _does_ contains a Sequence object with the name "B", things are more complicated, the two objects are combined to form a new "B" object following these rules: value used for tag type tag in "A" ? tag in "B" ? tag in new "B" -------- ------------ ------------ -------------- UNIQ Y N "A"s value N Y "B"s value Y Y "A"s value non-UNIQ Y N "A"s values N Y "B"s values Y Y (all of "A"s values + all of "B"s values) In this case the original "A" and "B" objects will be replaced with the single new "B" object. The new proposal is: Given that we want to rename object "A" to "B" and that "B" already points to an object: 1. The existing rename operation will combine "A" and "B" as before. 2. New variants of rename will be provided: o safe-rename: will fail because "B" points to an existing object o replace-rename: will delete "B" and then rename "A" to "B" o overwrite-rename: will combine "A" and "B", where tags exist in both "A" will take preference. o augment-rename: as for overwrite-rename, but where tags exist in both "B" will take preference. When implemented, the third and fourth operations will probably be called "Merge-nnn". This would allow users to do renames and choose how this should work. They could for instance do a "safe-rename" which would avoid any loss of data, or conversely do a "replace-rename" which would avoid any combining of objects. A question remains about whether these operations should be inclusive or exclusive for non-UNIQ tags, i.e. should they be combined as before, or should one set of tags overwrite another. If you are regularly parsing in data to an Acedb database and have thoughts about how you would like Rename to work, then please mail acedb@sanger.ac.uk. December monthly build available in first week of January 2001 ************************************************************** Sorry, not time to do this before Christmas, build has been done and will be distributed first week in January. You can pick up the monthly builds from: _Sanger users_ ~acedb/RELEASE.DEVELOPMENT _External users_ ftp://ftp.sanger.ac.uk/pub/acedb/Sanger-release.2000_12_22.tar.gz Next User Group Meeting - D319, 2.30pm, Thursday 18th January 2001 ****************************************************************** ---------------------------------------------------------------------------- ---------------------------------------------------------------------------- Ed Griffiths Last modified: Fri Dec 22 17:38:09 GMT 2000