-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Mummi.
We've done our best over the last few days to iron out as many MartEditor bugs as possible for 0.6, including the one you report below (or at least, we have managed to stop it from doing what we think it is doing on your side - it's hard to pin down the cause without seeing exactly what you're doing step-by-step, as I'm sure you can understand). Please give the 0.6 release a go when it comes out to see if it fixes your problem. cheers, Richard Guðmundur Árni Þórisson wrote: > Thanks for the heads-up, Richard. I knew from before that there were > plans to revamp the config system completely, but thought those plans > had been postponed or whatever when MEditor stayed the largely the same > (!). > > I'll try the MEditor 0.5 release for stability. I don't think I'm > doing anything fancy that requires 0.6. Unless MartBuilder 0.6 (from > CVS) is incompatible with 0.5 MEditor which would cause me trouble > elsewhere. > > > Mummi > > On 5 Jun 2007, at 16:33, Richard Holland wrote: > > I appreciate the problems you're having, but we are no longer developing > MartEditor after the 0.6 release (except for fixing show-stopping bugs). > > Instead we are concentrating on writing an entirely new config tool from > scratch for the 0.7 release of BioMart. The 0.6 release is imminent and > the current intention is to release 0.7 in around 6 months time. > > This new config tool will accompany a rethink of our entire > configuration system which is beginning to have scaling problems > associated with the ever-increasing range of species available in > Ensembl marts. It will also address the problems associated with the > parallel maintenance of the template- and dataset-config XMLs, one of > which you appear to have encountered already if I read your email > correctly. > > So all I can really say is hold in there... I promise it will get a lot > better after 0.7! > > cheers, > Richard > > > > Guðmundur Árni Þórisson wrote: >>>> Damian, I'm running into the same problems as Trevor with MartEditor: >>>> after several iterations of successful editing & exporting to db of a >>>> given dataset, MEditor starts importing configuration for the template >>>> ($datasetname_template). It subsequently insists on saving this back to >>>> the database, with no effect on the actual dataset I was trying to edit. >>>> >>>> I'll try to use the workaround Trevor mentioned to salvage my config, >>>> but annoying nonetheless. I am using martj from CVS, is this a lesser >>>> problem in the official 0.5 release perhaps? I am reluctant to invest >>>> much work in configuring datasets if this keeps happening. >>>> >>>> >>>> >>>> BTW In case it gives a clue in resolving this bug: when I do 'Save >>>> all' to save config XML to disk, I get one file named $dataset.xml and >>>> another named $dataset_template.template.xml for each dataset in my >>>> mart. Here's a sample diff of the first few elements in one of those >>>> pairs. Besides the extra filter in the second XML (the one I'm trying to >>>> add but can't!!), there's differences in the DatasetConfig element,I >>>> reckon that's where Trevor did his editing before loading back to the >>>> db. Dunno if that's normal for template vs non-template XML? >>>> >>>> >>>> >>>> [EMAIL PROTECTED] /tmp/allelefrequency.xml >>>> /tmp/allelefrequency_template.template.xml >>>> 3c3,4 >>>> < <DatasetConfig dataset="AlleleFrequency" datasetID="3" >>>> displayName="AlleleFrequency" hideDisplay="false" interfaces="default" >>>> internalName="default" martUsers="default" modified="2007-06-05 >>>> 14:52:41" softwareVersion="0.6" template="AlleleFrequency" >>>> type="TableSet" visible="1"> >>>> --- >>>>> <DatasetConfig dataset="AlleleFrequency_template" >>>> displayName="AlleleFrequency" hideDisplay="false" interfaces="default" >>>> internalName="template" martUsers="default" modified="2007-06-05 >>>> 11:44:23.589" softwareVersion="0.6" template="AlleleFrequency" >>>> type="TableSet" visible="1"> >>>>> <DynamicDataset hideDisplay="false" internalName="AlleleFrequency" /> >>>> 10a12,16 >>>>> <FilterDescription displayName="Frequencyasproportion" >>>> displayType="text" field="frequencyasproportion" hidden="false" >>>> hideDisplay="false" internalName="frequencyasproportion" >>>> key="AlleleFrequencyID_key" legal_qualifiers="=" qualifier="=" >>>> tableConstraint="main" type="text"> >>>>> <Option displayName="0.1" hidden="false" hideDisplay="false" >>>> internalName="0.1" isSelectable="1" value="0.1" /> >>>>> <Option displayName="0.3" hidden="false" hideDisplay="false" >>>> internalName="0.3" isSelectable="1" value="0.3" /> >>>>> <Option displayName="0.3" hidden="false" hideDisplay="false" >>>> internalName="0.3" isSelectable="1" value="0.3" /> >>>>> </FilterDescription> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Mummi >>>>> Damian Smedley >>>>> Tue, 13 Mar 2007 08:55:48 -0800 >>>>> >>>>> sounds like the template file which is what you are really editing when >>>>> using MartEditor has lost its mapping to the actual datasetConfig XML. >>>>> This template code in MartEditor is not particularly robust yet so the >>>>> XML >>>>> has probably got into a mess - do you want to send it to us and we can >>>>> try >>>>> and spot what the problem is >>>>> >>>>> cheers >>>>> Damian >>>>> >>>>> >>>>> On Tue, 13 Mar 2007, trevor paterson (RI) wrote: >>>>> >>>>>> I am getting into difficulties trying to redit dataset configuration >>>>>> files using MartEditor... >>>>>> >>>>>> changes that i make don't seem to get 'Export'-ed back to the >>>>> database - >>>>>> (though they do hang around in the Marteditor memory) >>>>>> >>>>>> >>>>>> eg >>>>>> >>>>>> if i have a dataset called maps... >>>>>> >>>>>> if i connect to the dataset witwith MartEditor and edit the config of >>>>>> filters on maps.. >>>>>> >>>>>> 'Export' does not write changes back to the database config tables >>>>>> >>>>>> if I 'SaveAll' the edits do get saved to a file e.g >>>>> maps.template.xml... >>>>>> >>>>>> I can then copy and rename this to maps.xml (changing a couple of >>>>>> attributes in the file) >>>>>> >>>>>> and then overwrite the changes to the database using 'Upload All' - >>>>> this >>>>>> then works >>>>>> >>>>>> >>>>>> however this is very laborious and error prone - are their known >>>>>> issues >>>>>> with this process, or any work arounds ? - >>>>>> >>>>>> the logic of the two files maps.xml and maps.template.xml is opaque to >>>>>> me >>>>>> >>>>>> cheers >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Trevor Paterson >>>> -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFGbWFc4C5LeMEKA/QRAgFkAJ4iJ11tpXvPlkJ7GGBiHhHwvzH0xACffpFo s9dIHCuF2a4mdeZPYx8yRHk= =0Who -----END PGP SIGNATURE-----
