[base] New Release of Tab2mageImport and Export Plugins
We are happy to announce the release of a new version of the Tab2Mage import and Tab2Mage export plugins available for download from the base2plugin website: Import: http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageImporter Export: http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageExporter Extra feature and some of the fixed bugs can be viewed in the change logs. ChangeLogs: importer:http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/ChangeLog.txt exporter:http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageExporter/ChangeLog.txt Additional documentation are also available on the download page. If you have an existing Annotation Type and Cv Importer plugin and Affymetrix Array Design Batch Importer plugin, please note that the ebi-plugins-util.jar file has changed and should be updated. Change Logs: Annotation Type and Cv Importer: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/AnnotationTypeCvImporter/ChangeLog.txt Affymetrix Array Design Batch Importer: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/ChangeLog.txt Please report all issues either to this list or to our contact email addresses available on the download page. Regards, Dominic - SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Tab2Mage Importer has problemsfinding AnnotationTypeCvImporter
vegard nygaard wrote: Dominic wrote: Quick question, are using the AnnotationTypeCvImporter plugin contained in the Tab2MageImporter.jar file? No. I installed and tested the AnnotationTypeCvImporter with its own jar file and assumed it was the same. I now changed to use the Tab2MageImporter.jar and the plug-in finished without errors reported to the plug-in window in BASE. Though there were a bunch of error messages in the tomcat log. This is just the start: Executing job: Importing data to raw bioassay: H_PropylParabenC1T1.gpr 13:19:29,197 ERROR jobqueue:435 - Exception while executing job: Job[id=78; name=Importing data to raw bioassay: N_PropylParabenC1T2.gpr] net.sf.basedb.core.BaseException: Permission denied: The item RawBioAssay[id=102] was modified by another transaction. at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:429) at java.lang.Thread.run(Thread.java:595) Caused by: net.sf.basedb.core.ItemModifiedException: Permission denied: The item RawBioAssay[id=102] was modified by another transaction. at net.sf.basedb.core.HibernateUtil.commit(HibernateUtil.java:914) at net.sf.basedb.core.DbControl.commit(DbControl.java:393) at net.sf.basedb.plugins.RawDataFlatFileImporter.end(RawDataFlatFileImporter.ja va:521) This is not a problem that hampers the Tab2mage importer, as you have observed. The tomcat messages had been identified and handled (or fixed) and will not appear with the new release of the importer. When I briefly inspected what was created in BASE it looked OK despite the error messages in the log. The overview tab for the experiment crashed though, but it has done that for me a lot and may not be caused by the tab2mage importer. Anyways here is the error message Further to the information by Nicklas. With the example zip file you are running, the importer creates new protocol types e.g. (grow ) identified in the tab2mage file. You can manually identify the protocol whose protocoltype is NOT a base-known protocoltype and change to a base known protocoltype and the experiment overview should work. And of course, you could upgrade to base 2.4.4. ¬Dominic - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space
Jari Häkkinen wrote: Just for your information: Dominic Oyeniran wrote: This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section. We prefer to use links to the more generic http://baseplugins.thep.lu.se since lev is merely the current host of the baseplugins (and base) and it may changes in the future. That is the above link should be a more archive safe http://baseplugins.thep.lu.se/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt Noted Jari. Thanks. However, I actually got the link from the base website. (At that time I could not remember the website link) This is the flow of what I did: 1. From here: http://base.thep.lu.se/, I clicked on Base plugins website at the Plug-ins section, which takes me to: http://lev.thep.lu.se/trac/baseplugins. 2. Clicking on 'download page' on the plugins site (want to be a downloader?) section takes me to: http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload etc .. Hope this is useful a information. Thanks. ¬Dominic - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Tab2Mage Importer has problems finding AnnotationTypeCvImporter
vegard nygaard wrote: Hi. This is for Dominic I guess. The last error I reported yesterday was from my own shortcutting and is fixed. (I had not yet made a design). Today I got an error when the plug-in tried to use the AnnotationTypeCvImporter. BASE error message: IMPORT FAILS: The tab2mage file supplied is not compliant with the tab2mage specification This was the error message from tomcat: . . auto-detecting PluginConfiguration net.sf.basedb.core.InvalidDataException: Plugin does not implement uk.ac.ebi.nugo.plugins.AnnotationTypeCvImporter: Plugin definition[id=28; name=Annotation Type and CV Loader] at Quick question, are using the AnnotationTypeCvImporter plugin contained in the Tab2MageImporter.jar file? I had installed the AnnotationTypeCvImporter with the annotationtypecvimporter.xml config. I found the annotation file made by the importer (anntype.txt) on BASE2's file system and successfully imported it using only AnnotationTypeCvImporter. I did all this as the same user with admin role. Somehow the importer plug-in was not able to find the AnnotationTypeCvImporter I could manually find and use. When I tried to debug in eclipse I found that the top java ref was not in my source code; uk.ac.ebi.nugo.plugins.util.PluginConfigDetector.getConfigs. It was at uk\ac\ebi\nugo\plugins\util\tab2mage\PluginConfigDetector.java in the source code I downloaded from http://lev.thep.lu.se/trac/baseplugins/browser/trunk. So I think the jar file is out of sync with the source code. This problem might have been fixed but not included in the jar file. I hope this is the case. Sorry, I have made some improvement to the code to fix bugs, enhancements e.g. pooling support and also working on an enhanced validation routine. A sub branch to hold previous version would suffice but Jari is the expert on this. May I also refer you to Jari's email on links. Please use this link for the source. http://baseplugins.thep.lu.se/browser/trunk/uk/ ¬Dominic - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] tab2mage exporter question
Hi Micha, Micha Bayer wrote: Hi Dominic, We are trying to export our first experiment for real so we can submit it to ArrayExpress, and initially it looked like everything had worked okay. But now we have found an error with the annotation that I wanted to ask you about. Our experiment is a two-colour one, and we have a factor which can take the value of mutant or wildtype. Both mutant and wildtype sample is applied to the hybridization (one per channel) and we then want the RawBioAssay item to inherit its annotations. The only way we could find to do that was to inherit from both the samples, but then only one of them is exported into the tab2mage file, which presumably is not good enough for ArrayExpress. This is becuase BASE chooses the first of the inherited annotations values that it finds for sample, assigns and displays this as the factor value for the experiment. And the tab2mage exporter exports this assigned value during export. I will post this response on the mailing list so that Nicklas and others can pick it up. I reckon we should list the inherited values for two channel raw bioassay on the experiment page (at the raw bio assay section. And then we can find a mechanism to export that. I think array express will accept the exported file as it is. Although there will be a loss of information. I.e. instead of having mutant and wildtype as factor value on each Hyb channel row of the tab2mage file, you will only have either one that Base has assigned as factor value. ¬Dominic - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] tab2mage exporter question
Nicklas Nordborg wrote: Dominic Oyeniran wrote: Hi Micha, Micha Bayer wrote: Hi Dominic, We are trying to export our first experiment for real so we can submit it to ArrayExpress, and initially it looked like everything had worked okay. But now we have found an error with the annotation that I wanted to ask you about. Our experiment is a two-colour one, and we have a factor which can take the value of mutant or wildtype. Both mutant and wildtype sample is applied to the hybridization (one per channel) and we then want the RawBioAssay item to inherit its annotations. The only way we could find to do that was to inherit from both the samples, but then only one of them is exported into the tab2mage file, which presumably is not good enough for ArrayExpress. This is becuase BASE chooses the first of the inherited annotations values that it finds for sample, assigns and displays this as the factor value for the experiment. BASE doesn't choose one of them. All inherited annotation values are always displayed. BASE actually chooses one of them, at least as shown on the GUI here. It's not the exprimental factors section of the GUI parse that's relevant here, based on my understanding, but the Raw Bio assays section listing each raw bio assay included in the experiment. Since experimental factor values/annotation values has to be propagated through the Raw Bio assays. For each Raw Bio assay in an experiment, you can only see or get one of the inherited values having inherited annotations from two different Sample items each from a line in the two channel hyb. However, the inherited values are displayed as separate annotations for the raw bio assays on the 'Inherited annotations and protocol parameters section' of the view page. If this is not the case then I must have a wrong understanding of how factor values annotation are obtained or handled in BASE. ¬Dominic - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space
I had this problem too, but had not yet got round to figuring out the solution. It is very helpful to read the README.TXT file on the BasePlugins download page before using the tab2mage importer plugin to avoid any issues /problems. The direct link to the file as stated in the last email is : http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Just an information for other interested users too. Thanks, ¬Dominic Bob MacCallum wrote: Dominic Oyeniran writes: vegard nygaard wrote: I am trying out the Tab2Mage importer. When starting it from the import button in an experiment it quickly returns with an error. I am running it as root on base2.4.3 having added tab2mage importer and Annotation Type and CV Loader as plug-ins. Input file is the genepix example file found at http://www.ebi.ac.uk/~oyeniran/pages/download.html. This is output from the plugin window: Name Run plugin: Tab2Mage Importer Description Priority 4 (1 = highest, 10 = lowest) Status Error: IMPORT FAILS: The directory containing the unzipped files could not be found. You may NOT have sufficient Disk Space Percent complete 100% This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section. Simply, we recommend not running the importer as the root user. I believe it's advisable to run BASE as an administrator and not the root user as well. In the next release of the importer, a root user will be able to run the importer as well. In my efforts to solve the problem I wanted to inspect the code but was unable to find the java files referred in the stack trace. Where can I find them? In the jar file I found only class files. I downloaded the whole Nutribase-2.0.2-src.zip, but was unable to unpack the file properly. Are the source files for the importer inside and if so how do I unpack the zip file? The source file for the importer is available at: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space
And it is also linked from http://lev.thep.lu.se/trac/baseplugins/wiki/uk.ac.ebi.Tab2MageImporter But the readme file is not very precise about this problem, it advices me not to use root. I disregarded that advice :(. If it will only run as a non-root user with a limited quota, that should be stated as an imperative. Changed and checked in. Anyways, I got past that problem now but ran into another one. Error: IMPORT FAILS: The tab2mage file supplied is not compliant with the tab2mage specification I use the genepix example zip file. If this is another known issue please let me know, if not I will look more into it in detail tomorrow and let you know if I am stuck. Please check the exceptions on the server and send it to me to have a look at. ¬Dominic - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Null pointer exception on deleting affymetrix raw data
Nicklas Nordborg wrote: Dominic Oyeniran wrote: I am experiencing the problem with deletion of items. See the exception below. Description: When you start deleting from the trash can either with delete permanently or empty trash, the process dialog comes up but never finishes and throws the exception below The db control is also not closed once an excpetion occurs I have noticed that it only occurs with raw bio assay. Any clue on how to solve this. It stops me from re-using a file for example since I could delete an already linked file, ad same with other items. I think this problem only happens for Affymetrix data. I am not able to reproduce it for any other raw data types. I think the source of the problem is that when deleting a raw bioassay, BASE also tries to delete the raw data associated with it. Since Affymetrix data isn't stored in the database this will of course fail. After that I really don't know what is happening. The NullPointerException is coming from the cleanup code that is cleaning up after the first error, thus the DbControl fails to be closed and the Found unclosed DbControl is warning is logged. I will have to investigate more before I know why the error in the cleanup code happens. In any case, there is an easy workaround. Edit the raw bioassay and select 'none' as the CEL file. Save the changes and then retry deleting it from the trashcan again. /Nicklas The workaround works. But thats after I removed each raw bioassay and its associated experiment first and thereafter remove all the other items by emptying the trash. Note I have multiple experiments loaded :affy, genepix and agilent from Biosource to Experiment items. I will try deleting all at one go again and let you know Cheers, ¬Dominic - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] BatchDataImporter broken w/ 2.4?
Hi all, Sorry everyone for my late response or contribution, I have been away. I hope this short email will address some of the issues raised on the tab2mage importer Owing to the fact that the importer supports only affymetrix, genepix and agilent platforms, I reckon interested users can stick to the batch importer for the non- supported platforms. However, the tab2mage importer can be extended to other platforms but will require a little bit of coding. Incidentally does anyone know of a SOFT to Tab2Mage converter for people wanting to import GEO data? I do not know much about SOFT, hence do not know if a converter exists or not. Regards, ¬Dominic - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Unable to view BioMaterials items after upgrade to 2.3.2
Hi James, Option 2 on that ticket (http://base.thep.lu.se/ticket/682) works quite well for me. Especially if your application/installation is not particularly gaining any substantial features of mysql 5.0.27. So migrating to a lower Mysql version should be ok. Do remember to backup your data though. However, if your machine has a massive memory capability then go for option 3. ¬Dominic Collett, James R wrote: Hello All, I've attempted an upgrade of my base-2.2.2 installation with base-2.3.2 multiple times, but each time I am unable to view items listed in the BioMaterials table using the Samples, Extracts, or Label Extracts web pages. Almost all the icons for managing items on these pages are missing as well, such the ones that say New, Delete, Restore, Share, etc., as well as the preset filter, number of records to see, etc. The Samples page has one little stub of an icon for New. If I click this I can bring up the New Sample dialog box and create a sample that is written to the MySQL BioMaterials table, but the new item fails to show up on the Samples page. My installation is pretty standard (Red Hat 3.4.6-8, apache-tomcat-5.5.20, MySQL-server-standard-5.0.27-0, jdk 1.6.0). I have been following the documentation instructions to the letter, using updatedb.sh and updateindexes.sh, and I edited base.config to match my system. Prior to the upgrade, I had modified the extended-properties.xml and raw-data-types.xml files, but they worked fine with 2.2.2. Any ideas on what could be going wrong? Thanks, Jim Collett James R. Collett, Ph.D. Systems Biology Fellow Battelle Memorial Institute Pacific Northwest National Laboratory - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] tab2mage/annotation questions
Hi Bob http://base.thep.lu.se/chrome/site/doc/html/userdoc/analysis/experiments_analysis.experiments.html#experiments_analysis.magexport Dumb question: An Annotation Type such as Age(hours) or body mass(kg) when applied to a biosource will be exported as a BioMaterialCharacteristic, right? We don't have to mark/tag the Annotation Type as a 'BioMaterialCharacteristic' in some way? I guess it would be good to put all of these in an Annotation Type Category (called BioMaterialCharacteristic, for example), but that's just for convenience? You would not need a new category for BioMaterialCharacteristic, I reckon biosource annotations should simply be exported as a BioMaterialCharacteristic. And a related question: we (base admins) should create Annotation Types just for the 'leaves' in the MGED ontology, is that correct? Is there a convention for capitalisation, spaces etc? e.g. 1. DevelopmentalStage 2. Developmental Stage 3. developmental stage It's not consistent in the manual (see link above) e.g. Age(week) - capitalised body mass(kg) - lower case body temperature (degree_C) - an extra space before the units Has anyone made any progress importing MGED or other ontologies as a whole? I haven't made any effort at importing MGED ontologies and I do not know of any convention for capitalisation in Base2. While we're at it, a more advanced question: say we have a Biosource Annotation Type called OrganismPart, which is free text (or a text enum). How could you enter values from a separate anatomy ontology, so that it goes into tab2mage correctly (or perhaps MAGE-TAB at a later date)? I don't understand this fully. Do you mean into base2 first and then exported in tab2mage? Also, we have a tab2mage export available on the base2 plugin source code (svn) page. Its not been packaged as a separate plugin distribution yet. However, we are hoping to do this soon. It need some extra enhancements. -- ¬Dominic - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] batch importer plugin is available for testing now
Hi Micha,
Nice work.
I tested the batch import today, on an affy experiment and I got the ff
exception:
=
===NEW BATCH IMPORT =
=
zn =HG-U133A.cdf
experiment: Experiment[id=5; name=Batch Importer Test]
file selected: affyMicher.zip
java.lang.NullPointerException
at sbrn.base.BatchDataImport.unpackZipFile(BatchDataImport.java:135)
at sbrn.base.BatchDataImport.importData(BatchDataImport.java:197)
at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:137)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
st.java:88)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
va:420)
at java.lang.Thread.run(Thread.java:595)
-
Is this happeneing because of the file format you mentioned in your read
me note? The zippped file is in affy format and containes 4 cel file and
a cdf file. (5 files in total)
Also
--
7:59:52,287 WARN DbControl:1046 - Found unclosed DbControl during
finalize; is
LoggedIn = true; clientId = 0; userId = 1
java.lang.Throwable: Please check the code to make sure that
DbControl.close() i
s always called. Stacktrace of code that created this DbControl:
at net.sf.basedb.core.DbControl.init(DbControl.java:140)
at
net.sf.basedb.core.SessionControl.newDbControl(SessionControl.java:26
0)
at sbrn.base.BatchDataImport.init(BatchDataImport.java:109)
at sbrn.base.BatchDataImporter.run(BatchDataImporter.java:136)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReque
st.java:88)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.ja
va:420)
at java.lang.Thread.run(Thread.java:595)
---
About the above warning, I suggest you close the dbcontrol object in
your code:
i.e. finally
{
if (dc != null)
dc.close();
}
Regards,
Dominic
-
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Re: [base] Offline files
Hi,
public class ZipFileImporter extends AbstractPlugin implements
InteractivePlugin, AutoDetectingImporter {
private static final SetGuiContext guiContexts =
Collections.singleton(new GuiContext(Item.EXPERIMENT,
GuiContext.Type.ITEM));
then I'll get an import tab created in the Experiment list view which
will let me import the zip file using my plugin?
That code is correct but to see an import tab you will have to specify that
the plugin is an import plugin .For instance:
public MainType getMainType()
{
return Plugin.MainType.IMPORT;
}
Please, see the plugin examples in base2 source code for more information on
this.
We're planning to make the Excel plugin available for everyone too BTW,
once it's finished.
Cool, this will be good for the community.
Dominic
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Micha Bayer
Sent: 30 November 2006 09:52
To: BASE ML
Subject: Re: [base] Offline files
That sounds like a hell of a lot more work than what I have done so far
:-)
My first shot at this has been quite basic and it only creates new
RawBioAssays and a single Experiment that these belong to. It could of
course be extended to do more stuff, but my time allowance for this is
limited and I don't think I'll be able to spend a lot more time on this than
I already have.
I think the upshot of all this discussion has been:
1. people need a batch importer (desperately, in fact), and 2. a plugin is
much better and will (hopefully) be possible
With that in mind, I'll go away and look into turning my stuff into a plugin
now, and when I have got the basic version of that working (i.e. file
upload, RawBioAssay and Experiment creation only, as above) I'll make the
code available to the community somehow and someone else can pick it up from
there if they want to make it fancier. I hope that's okay -- even with no
extra effort from someone else it'll still mean that a hell of a lot of
effort can be saved.
Perhaps the dev team can point me in the right direction initially. My
colleague Iain here is just working on a file importer plugin that handles
Excel files and his code starts off like this:
public class ExcelFileImporter extends AbstractPlugin implements
InteractivePlugin, AutoDetectingImporter {
private static final SetGuiContext guiContexts =
Collections.singleton(new GuiContext(Item.RAWBIOASSAY,
GuiContext.Type.ITEM));
So am I right in thinking that if I change this to the following...
public class ZipFileImporter extends AbstractPlugin implements
InteractivePlugin, AutoDetectingImporter {
private static final SetGuiContext guiContexts =
Collections.singleton(new GuiContext(Item.EXPERIMENT,
GuiContext.Type.ITEM));
then I'll get an import tab created in the Experiment list view which
will let me import the zip file using my plugin?
We're planning to make the Excel plugin available for everyone too BTW, once
it's finished.
Cheers
Micha
==
Dr Micha M Bayer
Bioinformatics Specialist
Genetics Programme
The Scottish Crop Research Institute
Invergowrie
Dundee
DD2 5DA
Scotland, UK
Telephone +44(0)1382 562731 ext. 2309
Fax +44(0)1382 562426
http://www.scri.sari.ac.uk/MichaBayer.htm
=
-Original Message-
From: [EMAIL PROTECTED] [mailto:basedb-users-
[EMAIL PROTECTED] On Behalf Of Bob MacCallum
Sent: 29 November 2006 18:36
To: BASE ML
Subject: Re: [base] Offline files
It looks like I let the cat out of the bag on this one...
Some discussion among the community would be good to establish what we
want from a bulk loader. For example, I would like all objects
created and linked, from samples (with annotations) right up to raw
bioassays (grouped into an experiment as Micha does, ideally).
Obviously to do this you need to specify the relationships between all
the samples, annotations, dyes, hybs, data files, but that could
easily end up being as much work as manually loading the data ;-)
Therefore you have to make compromises; the main one being that you
treat every sample/extract/etc in exactly the same way (same
protocols, same amounts, same labels, same array design). This would
probably work for most people - but let's discuss it anyway...
One issue with the bulk loader I wrote for BASE 1 is that if your
experiment involves a dye swap for one biological replicate, the bulk
loader will label each extract with both dyes for *all* replicates
(leaving you with unused labelled extracts after linking to the hybs).
One quite low cost way to define your experiment for a bulk loader is
Tab2MAGE (soon to be MAGE-TAB, see
http://www.biomedcentral.com/1471-2105/7/489/abstract ) - although it
feels strange to say this because I have been *exporting* Tab2MAGE
from BASE 1.2 rather than importing it. The input files for our bulk
Re: [base] Offline files
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Micha Bayer Hi Micha, I have just finished writing one. The user uploads a zip file, a new directory is created in the user's raw data directory (with the same name as the zip file) and the files are then unzipped in there. They are then imported one by one as new RawBioAssay objects and at the end a new Experiment is created that has all these hanging off it. At the moment it only works for non-Affy data though. To do this I had to hack the BASE source (plugin wasn't possible as far as I can tell), and I am always reluctant to do that sort of thing because of versioning/upgrade issues (i.e. having to repeat this every time a new version is out). I have modified the JSP page that controls the menus and inserted a new item there, and added a couple of JSP pages myself that provide the UI for all this. I did some more detailed testing yesterday and things worked fine but it's all still pretty raw and probably full of bugs. I am happy to share the code with others though, or even make it a full contribution to BASE if people are happy with it (perhaps after it has been gone over by some of the BASE team). I also think the exception handling needs more work probably. Base 2 has plans to have tab2mage import (importing experiments and associated files) see Ticket #338 on base2 trac http://base.thep.lu.se/ticket/338 system, and your zip file loader would certaily help to in importing experiments from repositories and doing other interesting stuff. We have this on our do list and would certainly appreciate if you can share the code with us to help in this process. Also, do you have plans to extend the functionality to non-affy data too? Thanks and hope to read from you. Dominic - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Changing CDF/CEL association
Hi, Since you are running the demo installation, your privileges may have been limited. I can unlink affy array design/ raw files association on my installation. Note: I have admin rights. Regards, Dominic -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Steve Taylor Sent: 29 September 2006 11:25 To: BASEDBUSERS Subject: [base] Changing CDF/CEL association Hi, Using BASE2 on (on the demo site) I accidentally associated the wrong CDF file with the CEL file. It looks like you should be able to change 'Array design' in 'Raw bioassay' but if you 'Edit' there doesn't appear to be an option to change it. Is there a work around or do I have to delete the raw bioassay and start again? Or is this a feature that could be added to the list please? Thanks for any help, Steve -- Medical Sciences Division Weatherall Institute of Molecular Medicine/Sir William Dunn School Oxford University - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
