Re: [mart-dev] Trying to find hooks in the java api

2006-05-22 Thread Richard Holland
libraries. Martj as a whole is pretty out-of-date and needs a serious rewrite. It's on the to-do list! cheers, Richard -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416

Re: [mart-dev] Use of OR and NOT in MQL query.

2006-10-06 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 OR and NOT are not implemented anywhere in the BioMart API. The API only understands AND. Therefore, MartShell can only use AND as it depends on the API to run the queries for it. cheers, Richard [EMAIL PROTECTED] wrote: Hello, Can any one please

Re: [mart-dev] re: push action

2006-10-13 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Just as a first thought, there are spaces in the internalName for the Anopheles option. Internal names should not have whitespace or Javascript-sensitive symbols in as this can cause weird problems elsewhere in the software. Try removing the space

[mart-dev] Re: [ensembl-dev] Ensembl 41 biomart

2006-10-20 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Marie. BioMart-related questions should be directed to mart-dev instead of ensembl-dev. I've copied this email to that list so hopefully one of the team (maybe even me!) will answer it later. cheers, Richard Marie Vivian Wong NONLILLY wrote:

Re: [mart-dev] Request to make BioMart Java 1.5 compatible

2006-11-02 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi. Thanks for noticing this - I've now renamed all instances of variables called enum in the CVS code for 0.5. In general, we don't officially support Java 1.5, simply because we haven't tested against that platform. We develop against Java 1.4

Re: [mart-dev] Dataset and configuration modified dates

2007-01-17 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The dates don't necessarily follow each other. The dataset modified date is the last time that someone ran an 'update all', or the date when the dataset was first created if no updates have been made yet. The dataset configuration modified date was

Re: [mart-dev] Configuration bombs

2007-01-22 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 This was solved by installing DBD::mysql. The configure.pl script was correctly parsing the registry XML, but on attempting to connect via DBI was failing because it could not load the appropriate database driver, due to it not being installed. Note

Re: [mart-dev] martview problems

2007-01-24 Thread Richard Holland
/MartRegistry Jennifer Richard Holland wrote: Hello again. That's not registry XML. That's the XML that MartBuilder uses to store dataset definitions when you use the File-Save menu option, so that you can continue working with them later if you need to. If this is the file that you gave

Re: [mart-dev] martview configuration settings.

2007-01-24 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The first concerns regular expressions. I have an attribute that is a peptide sequence and would like to be able to search for a regular expression, so for example give me all the results where the peptide contains the sequence EIL. In

Re: [mart-dev] martview configuration settings.

2007-01-24 Thread Richard Holland
actually still work. Damian can probably help you get it configured, or you can connect to dictybase with MartEditor and copy what you find there. Next time I should test things first! :) cheers, Richard Arek Kasprzyk wrote: On 24 Jan 2007, at 16:52, Richard Holland wrote: We don't support LIKE

Re: [mart-dev] Fwd/Back arrows for results?

2007-01-26 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Interesting idea, but unfortunately it wouldn't work, as hash codes are not unique. There is a chance that two rows of a dataset could produce the same hash even though they were different rows, and hence some distinct results would be treated as

Re: [mart-dev] Results table does not appear on martview

2007-02-13 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 This line of the log indicates the problem: Can't open a reference at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 1850. This is a Perl version incompatibility. It is trying to open a filehandle over a string then write the results

Re: [mart-dev] Results table does not appear on martview [SYED]

2007-02-14 Thread Richard Holland
cheers, Richard Etai Jacob wrote: Yes we have, the last version:( On 2/13/07, Richard Holland [EMAIL PROTECTED] wrote: Hmm. Well it must be a CPAN module then... not sure exactly as I've not seen this problem before. The line I quoted is definitely the line that is causing your

Re: [mart-dev] Webservice querying problem

2007-02-21 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Not sure if this is your email client formatting it wrong, but it seems that you have spaces around the equals signs in your XML query. This is not valid XML syntax so is likely to be one potential cause of the problem. Your Query XML should read like

Re: [mart-dev] Webservice querying problem

2007-02-21 Thread Richard Holland
Bioinformatics Roslin Institute -Original Message- From: Richard Holland [mailto:[EMAIL PROTECTED] Sent: 21 February 2007 13:17 To: trevor paterson (RI) Cc: mart-dev@ebi.ac.uk; andy law (RI) Subject: Re: [mart-dev] Webservice querying problem Not sure if this is your email

Re: [mart-dev] BioMart output

2007-02-27 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Will Spooner wrote: On Tue, 27 Feb 2007, Arek Kasprzyk wrote: For the dimension named 'foo', the main table has the following attributes; foo_count - the number of corresponding records in foo__dm foo_dmlist - the list of names of the

Re: [mart-dev] martshell.sh: reduce startup time?

2007-02-27 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 When starting up, MartShell reads the local registry file and downloads all the dataset configs from the various marts described in the registry. It does this every time, whether or not the registry is the default one (which redirects to a full config

Re: [mart-dev] is exturl working?

2007-03-15 Thread Richard Holland
Institute (Edinburgh) (the Institute) unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK

Re: [mart-dev] re: marteditor hanging

2007-03-21 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Preferences in MartEditor are stored using the Java Preferences API. The location is OS-dependent but on my Ubuntu Linux machine it is: ~/.java/.userPrefs/org/ensembl/mart/editor/ The safest way to clear it out is to remove the entire

Re: [mart-dev] re: marteditor hanging

2007-03-21 Thread Richard Holland
or change the connection details? Do you mean the window just doesn't open? There is no code at all in MartEditor that blocks users from viewing or changing the information in the connection dialog. cheers, Richard Richard Holland wrote: Preferences in MartEditor are stored using the Java Preferences

Re: [mart-dev] Feeding martservice query results into a martview

2007-04-02 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I believe that the only way to do this at present is to construct a GET request URL string, exactly like the mart links on the left panel of Ensembl's ComparaView. This supports only a limited range of functions, e.g. only a single dataset can be

Re: [mart-dev] Marteditor dropdown list

2007-04-03 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The dropdown options are preserved during export regardless of table content. cheers, Richard Robert Hamon wrote: Does this also mean that whatever options I remove from a Make Dropdown they will still popup in biomart because the template is

[mart-dev] PIpes and newlines

2007-04-04 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Robert. We are considering putting this function back in for 0.6. In the meantime you can work around it by modifying the HTML formatter code in your local copy. Line 131 of biomart-perl/lib/Formatter/HTML.pm looks like this: push

[mart-dev] Re: Changes to Ensembl marts for release 44

2007-04-10 Thread Richard Holland
. The existing 'Exon (Gene)' option remains and is unaltered in the forthcoming 44 release, but in the 45 release it will be renamed to just 'Exon' to reflect the fact that it is independent of the Gene/Transcript distinction in Ensembl. cheers, Richard Richard Holland wrote: Hi all. Ensembl 44

Re: [mart-dev] Uploading XML via MartShell

2007-04-16 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 If I'm going to be perfectly honest, the way we do it in Ensembl is to use mysqldump to dump the meta* tables from the old release and then run the scripts that mysqldump generates against the new database, effectively copying-and-pasting the XML

Re: [mart-dev] Unable to have MartEditor (Martj-5) created option list control displayed

2007-04-18 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 By list boxes do you mean boxes where you can type in multiple IDs or upload files of IDs, or do you mean drop-down menus of values from the database? If the latter, there is an automated way of doing this - right click on the filter and choose 'make

Re: [mart-dev] OS X installation

2007-05-02 Thread Richard Holland
--clean when reconfiguring. Thanks On 5/1/07 3:20 AM, Richard Holland [EMAIL PROTECTED] wrote: Could you send us the httpd.conf file that was generated so that we can see if we can spot any patterns. Also, what was the command you typed to start Apache, and what is the current

Re: [mart-dev] Martview results don't appear

2007-05-16 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Out of curiosity, when you say that for some main table entries there are no corresponding dimension entries, do you mean that corresponding rows simply do not exist? It's a mart requirement that dimension rows must always exist for every main row

Re: [mart-dev] MartBuilder question

2007-05-24 Thread Richard Holland
as description_biodatabase,b.name as name_biodatabase from public.bioentry as a left join bioseqdbmart-# public.biodatabase as b on a.biodatabase_id=b.biodatabase_id; ERROR: relation public.bioentry does not exist bioseqdbmart=# Brian O. On 5/24/07 10:36 AM, Richard Holland [EMAIL PROTECTED

Re: [mart-dev] MartBuilder question

2007-05-25 Thread Richard Holland
a schema, not just a database (it's based on Mysql). BIO On 5/24/07 10:36 AM, Richard Holland [EMAIL PROTECTED] wrote: Yes, I know BioSQL well! :) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

Re: [mart-dev] MartBuilder question

2007-05-25 Thread Richard Holland
to dump out the data to textfiles, to support heterogenous db-engine setups. The tables could then be created in the target database and textfiles subsequently loaded. Mummi On 24 May 2007, at 16:59, Richard Holland wrote: Hello. The quick answer is 'no'. The slightly

Re: [mart-dev] MartBuilder for multi-table joins, how deep?

2007-06-03 Thread Richard Holland
--- -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK

Re: [mart-dev] Filter, regexp buttonURL

2007-06-15 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 buttonURL is for a type of filter that allows an external panel to be opened for purposes of value selection (e.g. the Expression filters in the Ensembl Gene datasets). It's very specific to this set of filters and not really intended for use

Re: [mart-dev] upstream_flank

2007-06-27 Thread Richard Holland
the API, irrespective of the web-service querying method. 2007/6/27, Richard Holland [EMAIL PROTECTED]: This is deliberate. 'upstream_flank' is something called an AttributeFilter - it is an attribute because it appears in the attribute pages, but it is also a filter because it has a user

Re: [mart-dev] Re: a question

2007-07-05 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 So the question is: if I ask for 5'UTR+upstream-800, shouldn't I always be getting at least 800 bp of upstream sequence, irrespective of the absence/presence of the 5'UTR? The upstream/downstream generator adds extra bases relative to the

Re: [mart-dev] Gramene datasets, error 502

2007-07-23 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 HTTP 502 = Bad Gateway usually means a proxying problem. Matteo Floris wrote: Dear developers, I get this error when I try to download 3 gramene datasets (I can download only Rice Polymorphism): Debug:

Re: [mart-dev] Dataset name conflict for gaculeatus_gene_ensembl

2007-07-24 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello. This happens when multiple marts contain dataset with the same names. You need to do what the error message says and regroup marts with conflicting datasets into separate virtual schema tags. Then, you need to insert the appropriate virtual

Re: [mart-dev] Question on Filter Values

2007-07-25 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Andrew needs 0.4 so if you could send him a few lines that need to be modified, it should be ok, I think Andrew: you need to open up DatabaseDatabaseConfigUtils.java in the martj/src/java/org/ensembl/mart/lib/config and find the following lines

Re: [mart-dev] Biomart over Chado

2007-07-31 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The error is being generated by Postgres and means exactly what it says - - your disks are full. As Postgres is well-designed and generally well-behaved software, it will be deleting all temporary files before exiting and reporting the error message.

Re: [mart-dev] datasets species and types

2007-08-07 Thread Richard Holland
single entry. So, for A.Gam and X.Tro with Orthologues, there is only one entry in the CSV file - compara_agam_xtro_ortholog. This is the entry that will get selected regardless of the order in which the user selects the two species involved. cheers, Richard Gianfranco Frau wrote: Richard Holland

Re: [mart-dev] Making Mart go on 64 bit machines

2007-08-20 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 This is going to sound obvious but it's worth checking to see if the machine actually has a 64-bit version of expat installed? If that doesn't fix it, then the question may be better directed at the relevant Apache forums as it relates specifically

Re: [mart-dev] Cannot install biomart on ubuntu 7.04

2007-08-23 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 You need to change the settings.conf file so that the line referring to /usr/sbin/httpd refers to the actual location of your Apache httpd binary. cheers, Richard Joel Hedlund wrote: Hi! I can't install standalone biomart on ubuntu 7.04. Could

Re: [mart-dev] Cannot install biomart on ubuntu 7.04

2007-08-28 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I was on annual leave on Friday, then it was a public holiday here in the UK on Monday. Back at work now though! Could you post the entire stacktrace of the exception message that you get? That will pinpoint the specific line of code that is causing

Re: [mart-dev] Cannot install biomart on ubuntu 7.04

2007-08-28 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Funnily enough Syed had this exact same bug on his machine the other day, which was the first time I'd ever seen it. It affects only machines where the Java GTK look-and-feel is used. It is due to a naming clash between methods in the Swing API and

Re: [mart-dev] Cannot install biomart on ubuntu 7.04

2007-08-28 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Apologies. Step 1 should have read: cd ~/.biomart cheers, Richard Joel Hedlund wrote: 1. cd ~/.biomart/martbuilder OK. 2. Edit the 'properties' file. No such file. Created it. 3. If there is a line that starts

Re: [mart-dev] Cannot install biomart on ubuntu 7.04

2007-08-28 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 An even smaller note: Martbuilder does not protest if the original table has no primary key. SQL is generated with no problem. But then marteditor chokes when following the steps in 3.2 Configuration using MartEditor, right when I press Naive.

Re: [mart-dev] 'no such link' error

2007-10-29 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi David. We're aware of this and are working on a solution. It'll be around 7-10 days until it is fixed. cheers, Richard David Withers wrote: When I submit the query: ?xml version=1.0 encoding=UTF-8? !DOCTYPE Query Query

Re: [mart-dev] Sorting results

2007-11-07 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Currently there is no such feature. But Arek may have something planned for the future...? cheers, Richard Allan Kamau wrote: Hi, Is there a provision to order the resultset in 0.6? Allan. -BEGIN PGP SIGNATURE- Version: GnuPG

Re: [mart-dev] intersection style queries in BioMart

2007-11-14 Thread Richard Holland
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 BioMart cannot currently use the results from one query or subquery as a filter to apply to another query, which is what I think you're asking? (You would want to obtain genomic coordinates for the ESTs as your subquery then use those as input to some

[mart-dev] Recent fixes on biomart.org

2007-11-18 Thread Richard Holland
are currently available on the biomart.org website and to users working directly with the marts from martdb.ensembl.org:3316. The ensembl.org website will be updated at a later date. cheers, Richard - -- Richard Holland (BioMart) EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD

Re: [mart-dev] Refreshing the Contents of a Mart

2007-12-07 Thread Richard Holland
in the next release of MartBuilder/Runner - not yet out, but Arek probably has a date in mind. cheers, Richard - -- Richard Holland (BioMart) EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK Tel. +44 (0)1223 494416 http://www.biomart.org/ http://www.biojava.org

Re: [mart-dev] archived datasets

2007-12-12 Thread Richard Holland
using the database locations described above. cheers, Richard Aristotelis Tsirigos wrote: How can we query biomart on older ensembl datasets? Say for example I want the GO annotations for human, release 42. Thanks! Aris - -- Richard Holland (BioMart) EMBL EBI, Wellcome Trust Genome Campus

Re: [mart-dev] Biomart Error on one server but not another

2007-12-13 Thread Richard Holland
\nModPerl::Registry::handler('ModPerl::Registry', 'Apache2::RequestRec=SCALAR(0x35c1410)') called at -e line 0\neval {...} at -e line 0\n - -- Richard Holland (BioMart) EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK Tel. +44 (0)1223 494416 http://www.biomart.org/ http

Re: [mart-dev] Tips on making tables from sequence/annotation data

2007-12-19 Thread Richard Holland
, - Amir Karger Research Computing Life Sciences Division Harvard University -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK

[mart-dev] Re: Bmart-dev: use BioMart for the sea urchin genome

2008-02-01 Thread Richard Holland
, but not both. I am not sure how to fix this. Have you experienced this before? Regards, Wick Gankanda California Institute of Technology Pasadena, California 626-395-5816 - -- Richard Holland (BioMart) EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK Tel. +44 (0

Re: [mart-dev] martEditor not saving

2008-02-26 Thread Richard Holland
copies of them stored in different places, which would need to be compressed and checksummed using the same algorithm MEditor uses. Quite apart from the fact that the XML syntax is not really human-readable in this instance. I hope the above helps a bit! cheers, Richard -- Richard Holland BioMart

RE: [mart-dev] martEditor not saving

2008-02-27 Thread Richard Holland
. We'll let everyone know when it's ready. cheers, Richard -- Richard Holland BioMart (http://www.biomart.org/) EMBL-EBI Hinxton, Cambridgeshire CB10 1SD, UK

Re: [mart-dev] biosql?

2008-03-10 Thread Richard Holland
of EMBL genome .embl files and run a script on them that would use Bioperl to throw them into BioSQL tables, and then MartBuilder could create a mart out of them. http://news.open-bio.org/archives/2008_03.html#94 Perhaps you already know all about this. -Amir - -- Richard Holland

Re: [mart-dev] error in CVS HEAD for martj

2008-05-09 Thread Richard Holland
The specific problem lies in the fact that the API for DataSource changed in Java 1.6, and requires implementing classes to support extra methods in the interface that weren't there in 1.4/1.5. Hence our DetailedDataSource class, which was written to comply with the 1.4/1.5 APIs do not support the

Re: [mart-dev] BioMart Installation #1

2008-05-16 Thread Richard Holland
Also - BioMart builds its own httpd.conf and does not integrate with any existing Apache installation, if that's what you mean by a broken httpd.conf? On top of that, without apxs, it wouldn't have been able to build it's own httpd.conf anyway. cheers, Richard 2008/5/16 Arek Kasprzyk [EMAIL

Re: [mart-dev] BioMart Installation #1

2008-05-18 Thread Richard Holland
by the people who design the distro's packages and stuff gets installed all over the place...). cheers, Richard 2008/5/17 Renato golin [EMAIL PROTECTED]: Richard Holland wrote: Also - BioMart builds its own httpd.conf and does not integrate with any existing Apache installation, if that's what you

Re: [mart-dev] mart builder

2008-06-05 Thread Richard Holland
Yup - it'll only merge them into a single dataset if they are all connected X-Y-Z with 1:M X-Y, 1:M Y-Z, etc. Otherwise you'll get one dataset per table. cheers, Richard 2008/6/5 Renato golin [EMAIL PROTECTED]: Richard Holland wrote: Your dataset is called CV_COMMENT_TOPICS and so is your

Re: [mart-dev] Exporting to MySQL

2008-06-10 Thread Richard Holland
Hello. Glad that the cross-schema thing got sorted. Yes, you can create marts in any schema based on any other schema in the same server (and in the case of Oracle, you can even do it cross-server if you have cross-database links configured - ask your DBA!), but you definitely cannot build a mart

Re: [mart-dev] Wrong Oracle query

2008-06-10 Thread Richard Holland
Yup, that's a bug! Not sure how that one slipped through. Could you confirm what version you are using (0.5/0.6/0.7)? Then let Arek/Syed know. Arek/Syed - once you know the version, can you find OracleDialect, and do a search-and-replace for all instances of 'add column' to 'add'? I don't have

Re: [mart-dev] Problem with list filters and data containing commas

2008-06-13 Thread Richard Holland
Yup, it's a known problem. When you do a list query, BioMart concatenates all the values together into a comma-separated list and passes it to the 'IN' clause of the database SQL query. Obviously if the values themselves contain commas, this doesn't work too well. Not sure what the progress is

Re: [mart-dev] Another Oracle glitch

2008-06-16 Thread Richard Holland
That's a bug in MBuilder that's resulted from the Oracle code being cut-and-pasted from the Postgres code. Arek/Syed - you'll have to go through OracleDialect and completely remove any lines which output 'set' to the SQL buffer. 2008/6/16 Renato Golin [EMAIL PROTECTED]: Hi, Just got

Re: [mart-dev] MartView on Windows XP?

2008-06-20 Thread Richard Holland
MartView/MartService are designed to be served from within an Apache instance, which in turn must have mod_perl enabled, and the system must have a number of Perl modules installed as prerequisites for MartView to work. As long as you can install Apache+mod_perl+the Perl modules on your XP

Re: [mart-dev] Question about MartEditor

2008-06-20 Thread Richard Holland
Yes, if you set up the second filter as a 'pointerFilter' to the first one. Take a look in the Ensembl MartEditor configs for guidance on how to set up pointer filters. (You can get the configs by pointing MartEditor at martdb.ensembl.org). 2008/6/20 Sandra Derozier [EMAIL PROTECTED]: Hi, If I

Re: [mart-dev] substring search

2008-07-01 Thread Richard Holland
you know how to fix this? (I guess some kind of extra step is needed during SQL construction that spots the like qualifier and wraps the search expression in % symbols unless it already contains one). cheers, Richard 2008/7/1 Renato Golin [EMAIL PROTECTED]: Richard Holland wrote: Can you check

Re: [mart-dev] Problem with export all

2008-07-15 Thread Richard Holland
an unpredictable subset of the query's rows. You might be asking for the tenth through twentieth rows, but tenth through twentieth in what ordering? The ordering is unknown, unless you specified ORDER BY. Thanks for your help Olivier Le 11 juil. 08 à 20:29, Richard Holland a écrit : I'm

Re: [mart-dev] Problem with export all

2008-07-15 Thread Richard Holland
! :) cheers, Richard 2008/7/15 Arek Kasprzyk [EMAIL PROTECTED]: On 15-Jul-08, at 10:15 AM, Richard Holland wrote: Olivier is right. BioMart has been built around the rather convenient but undocumented feature (or bug?) of MySQL that identical queries will always return results in the same order

[mart-dev] 'like' filters

2008-09-19 Thread Richard Holland
a filter on the page where I can just type a word and it will return me all records containing that word, not just equal to it. cheers, Richard -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: [EMAIL PROTECTED] http://www.eaglegenomics.com/

Re: [mart-dev] 'like' filters

2008-09-19 Thread Richard Holland
-09-19 at 15:47 +0100, Richard Holland wrote: Hello. When I make a 'like' filter, I have to type '%' signs into the filter value to indicate the position of the wildcards. Is there any type of filter I can use where it internally automatically adds '%' to both ends of the filter value before

[mart-dev] Patch for MEditor

2008-11-13 Thread Richard Holland
; // Don't muck with these! 130a131,134 if (key.equals(internalName)) { // Don't overwrite internal names. value = to.getAttribute(key); } cheers, Richard -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics

Re: [mart-dev] Accessing SOAP services from a local biomart installation

2009-01-08 Thread Richard Holland
Science Newcastle University Newcastle upon Tyne, NE1 7RU -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] Accessing SOAP services from a local biomart installation

2009-01-08 Thread Richard Holland
? Thanks! :) 2009/1/8 Richard Holland holl...@eaglegenomics.com mailto:holl...@eaglegenomics.com The BioMart SOAP scripts are only available on the release-0_7 branch of /cvsroot/biomart/biomart-perl at cvs.sanger.ac.uk http://cvs.sanger.ac.uk. They have not been

Re: [mart-dev] Biomart WSDL

2009-01-08 Thread Richard Holland
://www.cisban.ac.uk School of Computing Science Newcastle University Newcastle upon Tyne, NE1 7RU -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] Biomart WSDL

2009-01-08 Thread Richard Holland
-01-08 at 19:47 +, Richard Holland wrote: The only way to stop it doing this and to generate class names that match the XSD names exactly (thus avoiding the case clash) is to write a But isn't that a sure way to no ends of hacks ? Without knowing for sure I'd guess that many contemporary

Re: [mart-dev] Expected XML response from SOAP service does not start with XML

2009-01-10 Thread Richard Holland
Centre for Integrated Systems Biology for Ageing and Nutrition Newcastle University http://www.cisban.ac.uk School of Computing Science Newcastle University Newcastle upon Tyne, NE1 7RU -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holl

Re: [mart-dev] Expected XML response from SOAP service does not start with XML

2009-01-10 Thread Richard Holland
200 OK [...] [newline] Status: 200 OK [...] -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] questions about Mart building

2009-01-13 Thread Richard Holland
-- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] questions about Mart building

2009-01-13 Thread Richard Holland
? or I missed some httpd configuration? Thanks! Dong -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd M: +44 7500 438846 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] Error Stating MartView

2009-02-26 Thread Richard Holland
. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at i...@cropdesign.com. -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http

Re: [mart-dev] Building a mart, preferably fully automated

2009-03-23 Thread Richard Holland
it is trivial to set up ensembl_mart_52, I would rather rely on a set of scripts or similar to repeat the mart building process for the Ensembl version 53 database. Thanks, Joachim -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl

Re: [mart-dev] query regarding multiple Dataset

2009-03-25 Thread Richard Holland
/merging attribute ? Thanks Nikhil -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] Problem with boolean optimiser columns

2009-04-29 Thread Richard Holland
as to the problem? Dr. Jay Moore Senior Research Fellow in Bioinformatics -- Warwick Systems Biology Centre Coventry House University of Warwick Coventry CV4 7AL U.K. +44 (0)24 761 50332 http://www2.warwick.ac.uk/fac/sci/systemsbiology/ -- Richard Holland, BSc MBCS Finance Director, Eagle

Re: [mart-dev] Choice of linux distros

2009-05-06 Thread Richard Holland
distribution. Does anyone have any tips on a good linux distro to choose for BioMart (for example versions of Apache, Perl, etc) which would give me an easy install. Is Suse better? Thanks for your help. Robert -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd T: +44

Re: [mart-dev] end-user problems

2009-05-08 Thread Richard Holland
access that data until the database server comes back up or it is reconfigured to use an alternative source instead (reconfiguration requires a restart). Hopefully this helps! thanks, Richard Thanks very much, Stephen -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd T: +44 (0

Re: [mart-dev] Case sensitivity

2009-05-15 Thread Richard Holland
to be the same as ours. We are using an oracle database and they are using mysql. Could this make a difference? Thanks Rebecca -- Richard Holland, BSc MBCS Finance Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

[mart-dev] Java 6

2009-10-08 Thread Richard Holland
that for these machines Java will no longer be officially supported at all, therefore taking martj with it. Java 1.5 will also no longer be available to install from the repositories in Ubuntu Linux from version 10.04 onwards. cheers, Richard -- Richard Holland, BSc MBCS Operations and Delivery Director

Re: [mart-dev] __main table to __dm table relation

2009-11-03 Thread Richard Holland
are seeing that if attributes are selected from transcripts__main and from different dm tables, only those transcript that have rows in ALL selected dm tables are displayed onthe results page. Thanks, rochak -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44

Re: [mart-dev] Pointer attributes not displayed

2009-11-10 Thread Richard Holland
for help. Regards. Jennifer -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] Having problem with web service client access to biomart

2009-11-16 Thread Richard Holland
runs of this type. Also, if there's an obviously better way of getting this sort of data (counts of SNPs per gene), let me know...I may very well be missing something. Thanks! =-=- Jennifer Drummond // j...@io.com -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics

Re: [mart-dev] Perl API - 500 read timeout

2009-11-20 Thread Richard Holland
=/biomart/martservice port=80 serverVirtualSchema=default visible=0 / /MartRegistry -- -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] problem to start marteditor

2009-11-20 Thread Richard Holland
-- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] ensembl (biomart) vs. ucsc genome browser

2009-12-01 Thread Richard Holland
and when I should use which tools? UCSC genome browser provide mysql database access and processed datafiles. Biomart also provides queries. Could somebody also compare them so that I choose the more appropriate one for any give task that is at my hand. -- Richard Holland, BSc MBCS Operations

Re: [mart-dev] update a mart

2009-12-17 Thread Richard Holland
am trying to update an existing local Ensembl mart. Thank you in advance. -Kiran -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

Re: [mart-dev] Using Biomart + WSDL + java

2010-03-22 Thread Richard Holland
, Joachim -- B.1079 Michael Smith Building Faculty of Life Sciences The University of Manchester Oxford Road Manchester M13 9PT United Kingdom -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com

Re: [mart-dev] latest available BioMart presentations

2010-04-14 Thread Richard Holland
presentation? I've looked in http://www.ebi.ac.uk/~arek/talks/ which has talks from 2007 and earlier. thanks for any help, Leandro -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http

Re: [mart-dev] dataset not suitable for biomart?

2010-05-17 Thread Richard Holland
! Zhengyan (George) Kan Computational Biology Pfizer, La Jolla -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com http://www.eaglegenomics.com/

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