From davidshepherd at rocketmail.com Tue Mar 4 19:00:16 2008 From: davidshepherd at rocketmail.com (david shepherd) Date: Tue, 4 Mar 2008 16:00:16 -0800 (PST) Subject: [MOBY-l] trouble connecting to moby central? Message-ID: <337517.58315.qm@web51412.mail.re2.yahoo.com> I am having trouble connecting to moby central to get a list of all available services using JMoby (Java). Here's my code snippet: ---------------------------------------------------- Central worker = new CentralImpl (); worker.setDebug(true); System.out.println ("KNOWN SERVICE TYPES\n"); Map types = worker.getServiceTypes(); for (Iterator it = types.entrySet().iterator(); it.hasNext();) { Map.Entry entry = (Map.Entry)it.next(); System.out.println (entry.getKey()); System.out.println ("\t" + entry.getValue()); } ---------------------------------------------------- Here's the output and error message I get: ---------------------------------------------------- KNOWN SERVICE TYPES METHOD CALL: retrieveServiceTypes ------------ ------------ ===ERROR=== org.biomoby.shared.MobyException: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.plnull =========== ---------------------------------------------------- Any ideas? Is the moby central address wrong? If so, what is a correct one? Thanks for your help!! -DS From usadel at mpimp-golm.mpg.de Wed Mar 5 03:06:49 2008 From: usadel at mpimp-golm.mpg.de (=?ISO-8859-1?Q?Bj=F6rn_Usadel?=) Date: Wed, 5 Mar 2008 09:06:49 +0100 Subject: [MOBY-l] trouble connecting to moby central? In-Reply-To: <337517.58315.qm@web51412.mail.re2.yahoo.com> References: <337517.58315.qm@web51412.mail.re2.yahoo.com> Message-ID: <47CE5499.4010001@mpimp-golm.mpg.de> Hi David, maybe try setting the central to http://moby.ucalgary.ca/moby/MOBY-Central.pl and the URI to http://whatever.you.want/MOBY/Central Probably, this might get also get fixed if you udpate your Java Biomoby, but I am not sure, as I only use the perl libs. Maybe Mark or somebody with access to the biomoby website could also change the old Central under general Docs? Best Wishes, Bj?rn > I am having trouble connecting to moby central to get a list of all available services using JMoby (Java). > Here's my code snippet: > ---------------------------------------------------- > Central worker = new CentralImpl (); > worker.setDebug(true); > System.out.println ("KNOWN SERVICE TYPES\n"); > Map types = worker.getServiceTypes(); > for (Iterator it = types.entrySet().iterator(); it.hasNext();) { > Map.Entry entry = (Map.Entry)it.next(); > System.out.println (entry.getKey()); > System.out.println ("\t" + entry.getValue()); > } > ---------------------------------------------------- > Here's the output and error message I get: > ---------------------------------------------------- > KNOWN SERVICE TYPES > > METHOD CALL: retrieveServiceTypes > ------------ > ------------ > > ===ERROR=== > org.biomoby.shared.MobyException: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.plnull > =========== > ---------------------------------------------------- > > > Any ideas? Is the moby central address wrong? If so, what is a correct one? > > Thanks for your help!! > -DS > > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > . > From martin.senger at gmail.com Wed Mar 5 09:53:26 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 5 Mar 2008 22:53:26 +0800 Subject: [MOBY-l] trouble connecting to moby central? In-Reply-To: <47CE5499.4010001@mpimp-golm.mpg.de> References: <337517.58315.qm@web51412.mail.re2.yahoo.com> <47CE5499.4010001@mpimp-golm.mpg.de> Message-ID: <4d93f07c0803050653x4f6ea733g83d6088aa8a312b0@mail.gmail.com> > maybe try setting the central to It should not be needed to set any URL and URI - the jMoby knows which one to use. But, as Bjorn correctly pointed out, you need to (cvs) update your jMoby. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Wed Mar 5 11:19:05 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 Mar 2008 08:19:05 -0800 Subject: [MOBY-l] Fwd: snippets In-Reply-To: <791014.92893.qm@web51401.mail.re2.yahoo.com> References: <791014.92893.qm@web51401.mail.re2.yahoo.com> Message-ID: ------- Forwarded message ------- From: "david shepherd" To: "Mark Wilkinson" Cc: Subject: snippets Date: Mon, 03 Mar 2008 14:36:34 -0800 I was just wondering if you have any code snippets I could provide to my students to help them access the BioMoby services in Java. Thanks, DS -- -- Mark Wilkinson iCAPTURE Centre From markw at illuminae.com Wed Mar 5 11:11:32 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 Mar 2008 08:11:32 -0800 Subject: [MOBY-l] trouble connecting to moby central? In-Reply-To: <47CE5499.4010001@mpimp-golm.mpg.de> References: <337517.58315.qm@web51412.mail.re2.yahoo.com> <47CE5499.4010001@mpimp-golm.mpg.de> Message-ID: On Wed, 05 Mar 2008 00:06:49 -0800, Bj?rn Usadel wrote: > Maybe Mark or somebody with access to the biomoby website > could also change the old Central under general Docs? Can you send the URL to teh incorrect docs? M From martin.senger at gmail.com Wed Mar 5 19:10:33 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 6 Mar 2008 08:10:33 +0800 Subject: [MOBY-l] Fwd: snippets In-Reply-To: References: <791014.92893.qm@web51401.mail.re2.yahoo.com> Message-ID: <4d93f07c0803051610o6405d3d5x6ae1baf0b97e274e@mail.gmail.com> > I was just wondering if you have any code snippets I could provide to my > students to help them access the BioMoby services in Java. E.g. here for writing clients: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-clients.html and here for writing services: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses.html Regards, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From phillip.lord at newcastle.ac.uk Fri Mar 7 06:26:03 2008 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Fri, 07 Mar 2008 11:26:03 +0000 Subject: [MOBY-l] CFP: Bio-Ontologies 2008: Knowledge in Biology Message-ID: <87fxv23hdg.fsf@dinley.ncl.ac.uk> ** Call for Papers Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2008. *** Key Dates - Submission due: **Friday 2nd May** - Notifications: **Friday 23rd May** - Final Version Due: **Friday 30th May** - Workshop: **Sunday 20th July** *** Introduction Bio-Ontologies has existed as a SIG at ISMB (http://www.iscb.org/ismb2008) for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year's reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology. So, for example: - Semantic and/or Scientific wikis. - Multimedia blogs - Folksonomies - Tag Clouds - Collaborative Curation Platforms - Collaborative Ontology Authoring and Peer-Review Mechanisms are topics which will be of relevance to the SIG, in addition to the more traditional areas for bio-ontologies. - Biological Applications of Ontologies - Reports on Newly Developed or Existing Bio-Ontologies - Tools for Developing Ontologies - Use of Ontologies in Data Communication Standards - Use of Semantic Web technologies in Bioinformatics - Implications of Bio-Ontologies or the Semantic Web for drug discovery - Current Research In Ontology Languages and its implication for Bio-Ontologies Please note, that this year ISCB have made an innovative schedule, holding some of the SIGs **DURING** ISMB. Bio-Ontologies is on the Sunday parallel to the main conference. *** Submissions Submissions are now open and can be submitted through easychair (http://www.easychair.org/conferences/?conf=bioontologies2008). *** Instructions to Authors We are inviting two types of submissions. - Short papers, up to 4 pages. - Poster abstracts, up to 1/2 page. Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccesful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic. *** Organisers Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Matt Cockerill, BioMedCentral *** Programme Committee The programme committee, organised alphabetically is: Mike Bada, University of Colorado Judith Blake, Jackson Laboratory Frank Gibson, Newcastle University Cliff Joslyn, Pacific National Laboratory Wacek Kusnierczyk, Norwegian University of Science and Technology Robin MacEntire, GSK Helen Parkinson, EBI Daniel Rubin, Stanford University Alan Ruttenberg, Science Commons Robert Stevens, University of Manchester and the conference organisers. *** Templates Submission templates are available from the website (http://bio-ontologies.org.uk). From schoof at mpiz-koeln.mpg.de Mon Mar 10 07:51:54 2008 From: schoof at mpiz-koeln.mpg.de (Heiko Schoof) Date: Mon, 10 Mar 2008 12:51:54 +0100 Subject: [MOBY-l] open-bio.org down Message-ID: Hi friends, I can't reach open-bio.org and thus biomoby.org right now. Does anyone know if this is a temporary problem, or if it's just us? Thanks, Heiko ______________________ Max Planck Institute for Plant Breeding Research Plant Computational Biology Dr. Heiko Schoof Carl-von-Linne Weg 10 50829 Koeln Germany +49-(0)221 / 5062 - 445 Fax +49 221 5062 413 http://bioinfo.mpiz-koeln.mpg.de schoof at mpiz-koeln.mpg.de From haase_dirk at web.de Mon Mar 10 08:45:05 2008 From: haase_dirk at web.de (Dirk Haase) Date: Mon, 10 Mar 2008 13:45:05 +0100 Subject: [MOBY-l] open-bio.org down Message-ID: <980651209@web.de> > Hi friends, > I can't reach open-bio.org and thus biomoby.org right now. Does > anyone know if this is a temporary problem, or if it's just us? I have no problem to access it. Cheers, dirk From maliha.aziz at yahoo.com Fri Mar 14 16:37:02 2008 From: maliha.aziz at yahoo.com (maliha aziz) Date: Fri, 14 Mar 2008 13:37:02 -0700 (PDT) Subject: [MOBY-l] new installation Message-ID: <781263.64923.qm@web57405.mail.re1.yahoo.com> hi I am trying to install biomoby on a machine ... I am gettin the following error.... any suggestions as to wot am i doing wrong here Buildfile: C:\Documents and Settings\Maliha\workspace\jmoby\build.xml [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\testout pre-compile: [welcome] ------------------------------------------ [welcome] | Welcome to the jMoby world. | [welcome] | Project documentation is available at: | [welcome] | http://biomoby.org/ | [welcome] ------------------------------------------ [version] Apache Ant version 1.6.5 compiled on June 2 2005 [version] Java: 1.5.0_10 [version] Windows XP 5.1 check-ant-version: bootstrap: [get] Getting: http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar [get] To: C:\Documents and Settings\Maliha\workspace\jmoby\lib\maven-ant-tasks-2.0.8.jar [get] .......................................... [get] last modified = Sat Dec 15 16:49:48 MST 2007 libcheck: [touch] Creating C:\Documents and Settings\Maliha\workspace\jmoby\build.properties [Give Cache Name] Local cache: C:/Documents and Settings/Maliha/workspace/jmoby/myCache [build] The jMoby is going to build itself. It will need to [build] fetch a lot of libraries from the Internet (using the [build] Maven technology for resolving project dependencies). [build] Just be patient, please... cleanapi: clean: [delete] Deleting directory C:\Documents and Settings\Maliha\workspace\jmoby\build checkmaven: initmaven: init: [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\classes [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\lib [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\Clients [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\registry_servlets [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\run [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\others [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\test [copy] Copying 1 file to C:\Documents and Settings\Maliha\workspace\jmoby [copy] Copying 1 file to C:\Documents and Settings\Maliha\workspace\jmoby\lib [copy] Copying 1 file to C:\Documents and Settings\Maliha\workspace\jmoby\src\Perl [copy] Copying 1 file to C:\Documents and Settings\Maliha\workspace\jmoby\generated [copy] Copying 1 file to C:\Documents and Settings\Maliha\workspace\jmoby\docs [copy] Copying 1 file to C:\Documents and Settings\Maliha\workspace\jmoby\docs\API [copy] Copying 1 file to C:\Documents and Settings\Maliha\workspace\jmoby\docs\panels [copy] Copying 1 file to C:\Documents and Settings\Maliha\workspace\jmoby\docs\dist config: [copy] Copying 1 file to C:\Documents and Settings\Maliha\workspace\jmoby\build\classes [copy] Copying 25 files to C:\Documents and Settings\Maliha\workspace\jmoby\build\run [copy] Copying 9 files to C:\Documents and Settings\Maliha\workspace\jmoby\build\Clients\help [copy] Copying 20 files to C:\Documents and Settings\Maliha\workspace\jmoby\build\classes\templates [copy] Copying 154 files to C:\Documents and Settings\Maliha\workspace\jmoby\build\classes compile: [javac] Compiling 344 source files to C:\Documents and Settings\Maliha\workspace\jmoby\build\classes [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] Compiling 25 source files to C:\Documents and Settings\Maliha\workspace\jmoby\build\Clients post-compile: checkmaven: initmaven: init: moses-init: [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\generated\datatypes [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\generated\skeletons [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\others\datatypes [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\others\skeletons samples-init: [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\others\samples [mkdir] Created dir: C:\Documents and Settings\Maliha\workspace\jmoby\build\others\samples\resources dashboard-init: dashboard-config: [jar] Building jar: C:\Documents and Settings\Maliha\workspace\jmoby\build\lib\dashboard-config.jar [Local cache] The jMoby is now creating a local cache. Depending [Local cache] on the network speed, it may take several minutes [Local cache] (usually it should be done within about a minute). [Local cache] [Local cache] [You can check the progress in the jMoby.log file.] [Local cache] Retrieving namespaces... 0:00:04.703 [Local cache] ===ERROR=== [Local cache] org/apache/xerces/util/XMLChar [Local cache] =========== Retrieving data types... BUILD FAILED C:\Documents and Settings\Maliha\workspace\jmoby\xmls\install.xml:99: Java returned: 1 thnx maliha _________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. [1]Try it now. References 1. http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From martin.senger at gmail.com Fri Mar 14 19:35:58 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 14 Mar 2008 19:35:58 -0400 Subject: [MOBY-l] Problem with xercexImpl fixed (for jMoby users) Message-ID: <4d93f07c0803141635p2183436fn5db83c5f45628c68@mail.gmail.com> Hi all, After an emergency (thanks very much to those you reported the problem), I have put back (into our dependency file xmls/project.pom) the xercesImpl.jar- but now its newer version ( 2.7.1.). This fixes the reported problem (a class not found). Please cvs update and type 'ant clean compile' (that should bring the new library to your machine). After I create more junit tests (in order to spot a similar emergency in time, next time) I will upload the newer version of jMoby to the Maven repository (it will be vesion 1.0.1). But, of course, I do not know if the newer xercesImpl version is suitable for those users you complained about xerces in the first place (that was a reason why I removed the xerces dependency). Please try your code and if you have again problems we can discuss the options. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com m.senger at cgiar.org skype: martinsenger From darin.london at duke.edu Tue Mar 18 14:17:00 2008 From: darin.london at duke.edu (darin.london at duke.edu) Date: Tue, 18 Mar 2008 13:17:00 -0500 Subject: [MOBY-l] BOSC 2008 Announcement and Call For Submissions Message-ID: <200803181817.m2IIH0F3007308@tenero.duhs.duke.edu> BOSC 2008 Call for Abstracts The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008). The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. Many Open Source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation and dissemination of new computational methods as well as informatics infrastructure. Since the work of the Open Source Bioinformatics Community represents some of the most cutting edge of Bioinformatics in general, the overall theme for the conference this year is "Tackling Hard Problems with Emerging Technologies". Topics under this umbrella include cyberinfrastructure, grid computing and workflow management and discovery, and visualization. We will also have a series of update talks about the main Open Source Bioinformatics Software suites. One of the hallmarks of BOSC is the coming together of the open source developer community in one location. A face-to-face meeting of this community creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done. This year, BOSC is accepting abstract submissions on the conference theme "Tackling Hard Problems with Emerging Technologies". The conference theme reflects that there are new technologies emerging on both the scientific front (new sequencing technologies, etc.) and the IT front (workflows, mashup/web 2.0, improvements in all of the major programming languages, etc.), which may allow the open source community to solve problems that were previously intractable. Abstracts may be submitted for the following topics. 1. Cyberinfrastructure - We are interested in presentations on topics dealing with the development of infrastructure on the web to facilitate software and data re-use (mashups, or traditional), interoperability and inter-process communication, system/service discovery, and data movement and modeling in distributed systems. This may include peer-to-peer systems of data transfer, Web Services, various flavors of data representation (SOAP, JSON, XML, others), and technologies commonly referred to under the Web 2.0 paradigm (e.g. folksonomies/tagging, user-based content generation, content feeds, and Social Networking). 2. Grid Computing and Workflow Management and Discovery - We particularly invite talks that report progress in making workflow systems easier to use and on how to do distributed-collaborative research , e.g. workflows that encompass the coordination of systems running in different parts of the world. 3. Visualization - Visualization is a maturing area of open source software development. We particularly invite talks that demonstrate innovative visualization systems in the context of workflows. 4. Open Source Software - Speakers will present talks on the use, development, or philosophy of open source software in bioinformatics. 5. Bio* Open Source Project Updates - We invite abstracts from the representatives of the open source projects sponsored by or affiliated to the O|B|F (see Projects). Please consult the official BOSC 2008 website at http://www.open-bio.org/wiki/Upcoming_BOSC_conference for all updates and extra information. Submission Process: All abstracts must be submitted through our Open Conference Systems site (http://events.open-bio.org/BOSC2008/openconf.php). The form will ask for a small Abstract Text to be pasted into it, and a full paper. The small Abstract text should be a summary, while the longer abstract (should provide more details, including the open-source license requirement details) Full-length abstracts are limited to one page with one inch (2.5 cm) margins on the top, sides, and bottom. The full-length abstract should include the title, authors, and affiliations. We prefer your abstract to be in PDF format, although plain t Important Dates: May 11: Abstract submission deadline. June 2: Notification of accepted talks. June 4: Early registration discount cut-off. July 18-19: BOSC 2008! We hope to see you at BOSC 2008! Kam Dahlquist and Darin London BOSC 2008 Co-organizers From ola.spjuth at farmbio.uu.se Thu Mar 27 11:02:30 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Thu, 27 Mar 2008 16:02:30 +0100 Subject: [MOBY-l] Problems starting dashboard in trunk Message-ID: Hi, After following the docs for jMoby in eclipse (I had to add Home/ to line line 108 in build.xml to look like ), and generating datatypes, I tried to start dashboard and got the following exception: dashboard: [Dashboard] Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/collections/map/ LinkedMap [Dashboard] at org.apache.commons.configuration.BaseConfiguration. (BaseConfiguration.java:54) [Dashboard] at org.apache.commons.configuration.CompositeConfiguration.clear (CompositeConfiguration.java:159) [Dashboard] at org.apache.commons.configuration.CompositeConfiguration. (CompositeConfiguration.java:56) [Dashboard] at org.biomoby.service.dashboard.DashboardConfig.get (DashboardConfig.java:117) [Dashboard] at org.biomoby.service.dashboard.DashboardConfig.getString (DashboardConfig.java:243) [Dashboard] at org.biomoby.service.dashboard.Dashboard.getProperty (Dashboard.java:208) [Dashboard] at org.biomoby.service.dashboard.Dashboard.getComponent (Dashboard.java:485) [Dashboard] at org.biomoby.service.dashboard.Dashboard. (Dashboard.java:176) [Dashboard] at org.biomoby.service.dashboard.Dashboard.main (Dashboard.java:988) I am new to maven and don't really now how I should fix this dependency. Any suggestions for a solution? Cheers, /Ola From groscurt at mpiz-koeln.mpg.de Thu Mar 27 11:28:37 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 27 Mar 2008 16:28:37 +0100 Subject: [MOBY-l] Problems starting dashboard in trunk Message-ID: <47EBBD25.4080508@mpiz-koeln.mpg.de> Hi Ola, the current docs (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/EclipseAndJMoby.html) do not suggest to edit any build files... and the 'Home' makes me wondering - what Java installation is that ? never seen a Java installation that has a 'Home' directory inside ?! which Java version do you work with - is your JAVA_HOME set correctly and does Eclipse uses the correct JDK (and not some JRE) ? Best andreas Ola Spjuth wrote: > Hi, > > After following the docs for jMoby in eclipse (I had to add Home/ to > line line 108 in build.xml to look like dir="${java.home}/../Home/lib">), and generating datatypes, I tried to > start dashboard and got the following exception: > > dashboard: > [Dashboard] Exception in thread "main" java.lang.NoClassDefFoundError: > org/apache/commons/collections/map/LinkedMap > [Dashboard] at > org.apache.commons.configuration.BaseConfiguration.(BaseConfiguration.java:54) > > [Dashboard] at > org.apache.commons.configuration.CompositeConfiguration.clear(CompositeConfiguration.java:159) > > [Dashboard] at > org.apache.commons.configuration.CompositeConfiguration.(CompositeConfiguration.java:56) > > [Dashboard] at > org.biomoby.service.dashboard.DashboardConfig.get(DashboardConfig.java:117) > > [Dashboard] at > org.biomoby.service.dashboard.DashboardConfig.getString(DashboardConfig.java:243) > > [Dashboard] at > org.biomoby.service.dashboard.Dashboard.getProperty(Dashboard.java:208) > [Dashboard] at > org.biomoby.service.dashboard.Dashboard.getComponent(Dashboard.java:485) > [Dashboard] at > org.biomoby.service.dashboard.Dashboard.(Dashboard.java:176) > [Dashboard] at > org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:988) > > I am new to maven and don't really now how I should fix this dependency. > Any suggestions for a solution? > > Cheers, > > /Ola > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From groscurt at mpiz-koeln.mpg.de Fri Mar 28 05:17:46 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 28 Mar 2008 10:17:46 +0100 Subject: [MOBY-l] Problems starting dashboard in trunk In-Reply-To: References: <47EBBD25.4080508@mpiz-koeln.mpg.de> Message-ID: <47ECB7BA.4030207@mpiz-koeln.mpg.de> Hi Ola, I hope a apple person can jump in here because I have no idea about apples and its JVM.... is it a JRE or a JDK ? andreas Ola Spjuth wrote: > Hi Andreas, > > Sorry, I should have clarified this: > > I have apples JVM1.5.0 installed at > /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0 with the > following structure: > > Classes > Commands > Headers > Home > bin > lib > Libraries > Resources > > The JRE container in Eclipse points to > /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home, and > setting is to not use deprecated JRE_LIB. I have set the JAVA_HOME in > Eclipse and in bash to this as well, so that should not be a problem > (don't know why that wasn't picked up by ant). Anyway, I can build > jmoby, moses datatypes, run sample clients, but not dashboard. I do > see commons-collections-2.1.jar under Maven dependencies in Eclipse. > > Cheers, > > /Ola > > On Mar 27, 2008, at 16:28 , Andreas Groscurth wrote: > >> Hi Ola, >> >> the current docs >> (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/EclipseAndJMoby.html) >> do not suggest to edit any build files... and the 'Home' makes me >> wondering - what Java installation is that ? never seen a Java >> installation that has a 'Home' directory inside ?! >> >> which Java version do you work with - is your JAVA_HOME set correctly >> and does Eclipse uses the correct JDK (and not some JRE) ? >> >> Best >> andreas >> >> Ola Spjuth wrote: >>> Hi, >>> >>> After following the docs for jMoby in eclipse (I had to add Home/ to >>> line line 108 in build.xml to look like >> dir="${java.home}/../Home/lib">), and generating datatypes, I tried >>> to start dashboard and got the following exception: >>> >>> dashboard: >>> [Dashboard] Exception in thread "main" >>> java.lang.NoClassDefFoundError: >>> org/apache/commons/collections/map/LinkedMap >>> [Dashboard] at >>> org.apache.commons.configuration.BaseConfiguration.(BaseConfiguration.java:54) >>> >>> [Dashboard] at >>> org.apache.commons.configuration.CompositeConfiguration.clear(CompositeConfiguration.java:159) >>> >>> [Dashboard] at >>> org.apache.commons.configuration.CompositeConfiguration.(CompositeConfiguration.java:56) >>> >>> [Dashboard] at >>> org.biomoby.service.dashboard.DashboardConfig.get(DashboardConfig.java:117) >>> >>> [Dashboard] at >>> org.biomoby.service.dashboard.DashboardConfig.getString(DashboardConfig.java:243) >>> >>> [Dashboard] at >>> org.biomoby.service.dashboard.Dashboard.getProperty(Dashboard.java:208) >>> [Dashboard] at >>> org.biomoby.service.dashboard.Dashboard.getComponent(Dashboard.java:485) >>> >>> [Dashboard] at >>> org.biomoby.service.dashboard.Dashboard.(Dashboard.java:176) >>> [Dashboard] at >>> org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:988) >>> >>> I am new to maven and don't really now how I should fix this >>> dependency. >>> Any suggestions for a solution? >>> >>> Cheers, >>> >>> /Ola >>> _______________________________________________ >>> moby-l mailing list >>> moby-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-l >> >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l > From ola.spjuth at farmbio.uu.se Fri Mar 28 05:10:19 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Fri, 28 Mar 2008 10:10:19 +0100 Subject: [MOBY-l] Problems starting dashboard in trunk In-Reply-To: <47EBBD25.4080508@mpiz-koeln.mpg.de> References: <47EBBD25.4080508@mpiz-koeln.mpg.de> Message-ID: Hi Andreas, Sorry, I should have clarified this: I have apples JVM1.5.0 installed at /System/Library/Frameworks/ JavaVM.framework/Versions/1.5.0 with the following structure: Classes Commands Headers Home bin lib Libraries Resources The JRE container in Eclipse points to /System/Library/Frameworks/ JavaVM.framework/Versions/1.5.0/Home, and setting is to not use deprecated JRE_LIB. I have set the JAVA_HOME in Eclipse and in bash to this as well, so that should not be a problem (don't know why that wasn't picked up by ant). Anyway, I can build jmoby, moses datatypes, run sample clients, but not dashboard. I do see commons- collections-2.1.jar under Maven dependencies in Eclipse. Cheers, /Ola On Mar 27, 2008, at 16:28 , Andreas Groscurth wrote: > Hi Ola, > > the current docs (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/ > Java/docs/EclipseAndJMoby.html) do not suggest to edit any build > files... and the 'Home' makes me wondering - what Java installation > is that ? never seen a Java installation that has a 'Home' > directory inside ?! > > which Java version do you work with - is your JAVA_HOME set > correctly and does Eclipse uses the correct JDK (and not some JRE) ? > > Best > andreas > > Ola Spjuth wrote: >> Hi, >> >> After following the docs for jMoby in eclipse (I had to add Home/ >> to line line 108 in build.xml to look like ), and generating datatypes, I tried to >> start dashboard and got the following exception: >> >> dashboard: >> [Dashboard] Exception in thread "main" >> java.lang.NoClassDefFoundError: org/apache/commons/collections/map/ >> LinkedMap >> [Dashboard] at >> org.apache.commons.configuration.BaseConfiguration. >> (BaseConfiguration.java:54) >> [Dashboard] at >> org.apache.commons.configuration.CompositeConfiguration.clear >> (CompositeConfiguration.java:159) >> [Dashboard] at >> org.apache.commons.configuration.CompositeConfiguration. >> (CompositeConfiguration.java:56) >> [Dashboard] at >> org.biomoby.service.dashboard.DashboardConfig.get >> (DashboardConfig.java:117) >> [Dashboard] at >> org.biomoby.service.dashboard.DashboardConfig.getString >> (DashboardConfig.java:243) >> [Dashboard] at >> org.biomoby.service.dashboard.Dashboard.getProperty(Dashboard.java: >> 208) >> [Dashboard] at >> org.biomoby.service.dashboard.Dashboard.getComponent >> (Dashboard.java:485) >> [Dashboard] at org.biomoby.service.dashboard.Dashboard. >> (Dashboard.java:176) >> [Dashboard] at org.biomoby.service.dashboard.Dashboard.main >> (Dashboard.java:988) >> >> I am new to maven and don't really now how I should fix this >> dependency. >> Any suggestions for a solution? >> >> Cheers, >> >> /Ola >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From martin.senger at gmail.com Fri Mar 28 05:43:04 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 28 Mar 2008 17:43:04 +0800 Subject: [MOBY-l] Problems starting dashboard in trunk In-Reply-To: References: Message-ID: <4d93f07c0803280243y7d5d1389kc0d21f622825aeec@mail.gmail.com> Hi, You do not need to add tools.jar to your classpath (so it does not matter how it is coded in build.xml) because Apple has this jar file included together with all normal Java files. So, your problem: java.lang.NoClassDefFoundError: org/apache/commons/collections/map/ > LinkedMap must be a different one. Try to start dashboard without ant. Try 'build/run/run-dashboard'. The same error? Can you run other Ant's task (e.g. run install)? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From usadel at mpimp-golm.mpg.de Fri Mar 28 06:21:10 2008 From: usadel at mpimp-golm.mpg.de (=?windows-1252?Q?Bj=F6rn_Usadel?=) Date: Fri, 28 Mar 2008 11:21:10 +0100 Subject: [MOBY-l] Problems starting dashboard in trunk In-Reply-To: <47ECB7BA.4030207@mpiz-koeln.mpg.de> References: <47EBBD25.4080508@mpiz-koeln.mpg.de> <47ECB7BA.4030207@mpiz-koeln.mpg.de> Message-ID: <47ECC696.60702@mpimp-golm.mpg.de> Hi, looks very similar to what Marc experienced on his Mac. I attached his solution below. We don't know if this is the appropriate solution, as we are really more into Perl Biomoby than Java Biomoby. But this did the trick for Marc. Maybe one of the Java guys can chip in here? Cheers, Bj?rn --------------- Hi Bj?rn, yes i can comment on this: When looking at the stack trace of the exception thrown you see that it is again the java.lang.NoClassDefFoundError: org/apache/commons/collections/map/LinkedMap error. So you?ll need to get version 3.2 of the commons-collections (commons-collections-3.2.jar) and put it in the right place. I did this manually on the command line since i do know nothing about ?maven dependencies? - but i guess that if you change ?commons-collections-2.1.jar? to ?commons-collections-3.2.jar? in the dependency list you?ll be fine after rebuilding the dashboard (and i suggest you do ?ant clean? or whatever is the equivalent to this in eclipse before rebuilding). I hope this solves your problem, bests, Marc P.S.: I do not think this is a JVM-related problem as i am using the same version of apple?s JVM. Andreas Groscurth wrote: > Hi Ola, > > I hope a apple person can jump in here because I have no idea about > apples and its JVM.... is it a JRE or a JDK ? > > andreas > > Ola Spjuth wrote: >> Hi Andreas, >> >> Sorry, I should have clarified this: >> >> I have apples JVM1.5.0 installed at >> /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0 with the >> following structure: >> >> Classes >> Commands >> Headers >> Home >> bin >> lib >> Libraries >> Resources >> >> The JRE container in Eclipse points to >> /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home, and >> setting is to not use deprecated JRE_LIB. I have set the JAVA_HOME in >> Eclipse and in bash to this as well, so that should not be a problem >> (don't know why that wasn't picked up by ant). Anyway, I can build >> jmoby, moses datatypes, run sample clients, but not dashboard. I do >> see commons-collections-2.1.jar under Maven dependencies in Eclipse. >> >> Cheers, >> >> /Ola >> >> On Mar 27, 2008, at 16:28 , Andreas Groscurth wrote: >> >>> Hi Ola, >>> >>> the current docs >>> (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/EclipseAndJMoby.html) >>> do not suggest to edit any build files... and the 'Home' makes me >>> wondering - what Java installation is that ? never seen a Java >>> installation that has a 'Home' directory inside ?! >>> >>> which Java version do you work with - is your JAVA_HOME set correctly >>> and does Eclipse uses the correct JDK (and not some JRE) ? >>> >>> Best >>> andreas >>> >>> Ola Spjuth wrote: >>>> Hi, >>>> >>>> After following the docs for jMoby in eclipse (I had to add Home/ to >>>> line line 108 in build.xml to look like >>> dir="${java.home}/../Home/lib">), and generating datatypes, I tried >>>> to start dashboard and got the following exception: >>>> >>>> dashboard: >>>> [Dashboard] Exception in thread "main" >>>> java.lang.NoClassDefFoundError: >>>> org/apache/commons/collections/map/LinkedMap >>>> [Dashboard] at >>>> org.apache.commons.configuration.BaseConfiguration.(BaseConfiguration.java:54) >>>> >>>> [Dashboard] at >>>> org.apache.commons.configuration.CompositeConfiguration.clear(CompositeConfiguration.java:159) >>>> >>>> [Dashboard] at >>>> org.apache.commons.configuration.CompositeConfiguration.(CompositeConfiguration.java:56) >>>> >>>> [Dashboard] at >>>> org.biomoby.service.dashboard.DashboardConfig.get(DashboardConfig.java:117) >>>> >>>> [Dashboard] at >>>> org.biomoby.service.dashboard.DashboardConfig.getString(DashboardConfig.java:243) >>>> >>>> [Dashboard] at >>>> org.biomoby.service.dashboard.Dashboard.getProperty(Dashboard.java:208) >>>> [Dashboard] at >>>> org.biomoby.service.dashboard.Dashboard.getComponent(Dashboard.java:485) >>>> >>>> [Dashboard] at >>>> org.biomoby.service.dashboard.Dashboard.(Dashboard.java:176) >>>> [Dashboard] at >>>> org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:988) >>>> >>>> I am new to maven and don't really now how I should fix this >>>> dependency. >>>> Any suggestions for a solution? >>>> >>>> Cheers, >>>> >>>> /Ola >>>> _______________________________________________ >>>> moby-l mailing list >>>> moby-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-l >>> _______________________________________________ >>> moby-l mailing list >>> moby-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-l > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > > This email was Anti Virus checked by the MPIMP-Golm Astaro Security Gateway. > > . > This email was Anti Virus checked by the MPIMP-Golm Astaro Security Gateway. From martin.senger at gmail.com Fri Mar 28 06:50:14 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 28 Mar 2008 18:50:14 +0800 Subject: [MOBY-l] Problems starting dashboard in trunk In-Reply-To: <47ECC696.60702@mpimp-golm.mpg.de> References: <47EBBD25.4080508@mpiz-koeln.mpg.de> <47ECB7BA.4030207@mpiz-koeln.mpg.de> <47ECC696.60702@mpimp-golm.mpg.de> Message-ID: <4d93f07c0803280350k2eb73f75t710bc36aa4c0c3fa@mail.gmail.com> > java.lang.NoClassDefFoundError: > org/apache/commons/collections/map/LinkedMap > > error. So you'll need to get version 3.2 of the commons-collections > (commons-collections-3.2.jar) > and put it in the right place. I did this manually ...but you should get it from maven. The best to see what you are getting from maven is to look into run scripts, eg. run-any-client, in build/run directory (the scripts are create there once you run 'ant config' (which is called from other tasks, as well). Are you starting the dashboard from eclipse or from the command-line? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Fri Mar 28 07:20:25 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 28 Mar 2008 19:20:25 +0800 Subject: [MOBY-l] Problems starting dashboard in trunk In-Reply-To: References: <4d93f07c0803280350k2eb73f75t710bc36aa4c0c3fa@mail.gmail.com> Message-ID: <4d93f07c0803280420u2a51278cl33c8be11b83e0d62@mail.gmail.com> > that the maven > dependency list contained commons-collections-2.1.jar which does not > declare the LinkedMap class > - it is included in commons-collections-3.2.jar, though Sorry, I have not paid enough attention to the question. I had a better look now: the problem - as Marc correctly described - is that some other dependency downloads commons-collections-2.1 and the correct one (2.3.) is made not-accessible. And it can happen randomly (depending on the order how the dependencies are being resolved?) - because on my machine it does download the correct version. The solution is to use 'exclusion' in the xmls/project.pom. The our culprit is the commons-dbcp. I have updated xmls/project.pom and committed but I would like more people to try - if it helped (there may be more "culprits"). Just make 'cvs update -dP' and then 'ant clean compile'. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From ola.spjuth at farmbio.uu.se Fri Mar 28 07:12:55 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Fri, 28 Mar 2008 12:12:55 +0100 Subject: [MOBY-l] Problems starting dashboard in trunk In-Reply-To: <47ECC696.60702@mpimp-golm.mpg.de> References: <47EBBD25.4080508@mpiz-koeln.mpg.de> <47ECB7BA.4030207@mpiz-koeln.mpg.de> <47ECC696.60702@mpimp-golm.mpg.de> Message-ID: <0D7C7592-E658-4C8C-90A1-D2BFAD3F1F1B@farmbio.uu.se> Hi, This looks exactly like my problem. Let me first say again that I am new to maven. I could not find commons-collections in moby-live/Java/ pom.xml. I added it there like: commons-collections commons-collections 3.2 and maven collected it for me and 3.2 now shows up in maven dependencies of Eclipse instead of the previous 2.1, and I confirm that map/LinkedMap is there. However, I still cannot start dashboard (I get the same exception). Cleanall didn't help. Is there something else I should do for the dep to be picked up by ant and build.xml? Martin: I tried firstly from Eclipse but 'build/run/run-dashboard' from command line gives the same exception. Thanks, /Ola On Mar 28, 2008, at 11:21 , Bj?rn Usadel wrote: > Hi, > > looks very similar to what Marc experienced on his Mac. > > I attached his solution below. We don't know if this is the > appropriate solution, as we are really more into Perl Biomoby than > Java Biomoby. But this did the trick for Marc. Maybe one of the > Java guys can chip in here? > > Cheers, > Bj?rn > --------------- > Hi Bj?rn, > > yes i can comment on this: > > When looking at the stack trace of the exception thrown you see > that it is again the > > java.lang.NoClassDefFoundError: org/apache/commons/collections/map/ > LinkedMap > > error. So you?ll need to get version 3.2 of the commons- > collections (commons-collections-3.2.jar) > and put it in the right place. I did this manually on the command > line since i do know nothing about > ?maven dependencies? - but i guess that if you change ?commons- > collections-2.1.jar? to > ?commons-collections-3.2.jar? in the dependency list you?ll be fine > after rebuilding the dashboard > (and i suggest you do ?ant clean? or whatever is the equivalent to > this in eclipse before rebuilding). > > I hope this solves your problem, > > bests, > Marc > > P.S.: I do not think this is a JVM-related problem as i am using > the same version of > apple?s JVM. > > Andreas Groscurth wrote: >> Hi Ola, >> I hope a apple person can jump in here because I have no idea about >> apples and its JVM.... is it a JRE or a JDK ? >> andreas >> Ola Spjuth wrote: >>> Hi Andreas, >>> >>> Sorry, I should have clarified this: >>> >>> I have apples JVM1.5.0 installed at >>> /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0 with the >>> following structure: >>> >>> Classes >>> Commands >>> Headers >>> Home >>> bin >>> lib >>> Libraries >>> Resources >>> >>> The JRE container in Eclipse points to >>> /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home, and >>> setting is to not use deprecated JRE_LIB. I have set the >>> JAVA_HOME in >>> Eclipse and in bash to this as well, so that should not be a problem >>> (don't know why that wasn't picked up by ant). Anyway, I can build >>> jmoby, moses datatypes, run sample clients, but not dashboard. I do >>> see commons-collections-2.1.jar under Maven dependencies in Eclipse. >>> >>> Cheers, >>> >>> /Ola >>> >>> On Mar 27, 2008, at 16:28 , Andreas Groscurth wrote: >>> >>>> Hi Ola, >>>> >>>> the current docs >>>> (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ >>>> EclipseAndJMoby.html) >>>> do not suggest to edit any build files... and the 'Home' makes me >>>> wondering - what Java installation is that ? never seen a Java >>>> installation that has a 'Home' directory inside ?! >>>> >>>> which Java version do you work with - is your JAVA_HOME set >>>> correctly >>>> and does Eclipse uses the correct JDK (and not some JRE) ? >>>> >>>> Best >>>> andreas >>>> >>>> Ola Spjuth wrote: >>>>> Hi, >>>>> >>>>> After following the docs for jMoby in eclipse (I had to add >>>>> Home/ to >>>>> line line 108 in build.xml to look like >>>> dir="${java.home}/../Home/lib">), and generating datatypes, I >>>>> tried >>>>> to start dashboard and got the following exception: >>>>> >>>>> dashboard: >>>>> [Dashboard] Exception in thread "main" >>>>> java.lang.NoClassDefFoundError: >>>>> org/apache/commons/collections/map/LinkedMap >>>>> [Dashboard] at >>>>> org.apache.commons.configuration.BaseConfiguration. >>>>> (BaseConfiguration.java:54) >>>>> >>>>> [Dashboard] at >>>>> org.apache.commons.configuration.CompositeConfiguration.clear >>>>> (CompositeConfiguration.java:159) >>>>> >>>>> [Dashboard] at >>>>> org.apache.commons.configuration.CompositeConfiguration. >>>>> (CompositeConfiguration.java:56) >>>>> >>>>> [Dashboard] at >>>>> org.biomoby.service.dashboard.DashboardConfig.get >>>>> (DashboardConfig.java:117) >>>>> >>>>> [Dashboard] at >>>>> org.biomoby.service.dashboard.DashboardConfig.getString >>>>> (DashboardConfig.java:243) >>>>> >>>>> [Dashboard] at >>>>> org.biomoby.service.dashboard.Dashboard.getProperty >>>>> (Dashboard.java:208) >>>>> [Dashboard] at >>>>> org.biomoby.service.dashboard.Dashboard.getComponent >>>>> (Dashboard.java:485) >>>>> >>>>> [Dashboard] at >>>>> org.biomoby.service.dashboard.Dashboard.(Dashboard.java:176) >>>>> [Dashboard] at >>>>> org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:988) >>>>> >>>>> I am new to maven and don't really now how I should fix this >>>>> dependency. >>>>> Any suggestions for a solution? >>>>> >>>>> Cheers, >>>>> >>>>> /Ola >>>>> _______________________________________________ >>>>> moby-l mailing list >>>>> moby-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/moby-l >>>> _______________________________________________ >>>> moby-l mailing list >>>> moby-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-l >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l >> This email was Anti Virus checked by the MPIMP-Golm Astaro >> Security Gateway. >> . > > > This email was Anti Virus checked by the MPIMP-Golm Astaro Security > Gateway. > > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From martin.senger at gmail.com Fri Mar 28 07:44:24 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 28 Mar 2008 19:44:24 +0800 Subject: [MOBY-l] Problems starting dashboard in trunk In-Reply-To: <0D7C7592-E658-4C8C-90A1-D2BFAD3F1F1B@farmbio.uu.se> References: <47EBBD25.4080508@mpiz-koeln.mpg.de> <47ECB7BA.4030207@mpiz-koeln.mpg.de> <47ECC696.60702@mpimp-golm.mpg.de> <0D7C7592-E658-4C8C-90A1-D2BFAD3F1F1B@farmbio.uu.se> Message-ID: <4d93f07c0803280444y1aa218e3w7c981f1c7b6e3297@mail.gmail.com> > pom.xml First of all, never edit pom.xml, but only xmls/project.pom. The pom.xml is used only by Eclipse and it is generated from the xmls/project.pom (so if something looks bad in eclipse, just remove pom.xml (there is also one in src/main directory) and run 'ant config' - the pom.xml will be re-created. > I added it there like: > > > commons-collections > commons-collections > 3.2 > > No need to add it because it will be added automatically by commons-configuration. But you need to exclude it from commons-dbcp. This is what I commited (half an hour ago), hoping that it fixes the problem: commons-dbcp commons-dbcp 1.1 ... commons-collections commons-collections Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From ola.spjuth at farmbio.uu.se Fri Mar 28 08:11:11 2008 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Fri, 28 Mar 2008 13:11:11 +0100 Subject: [MOBY-l] Problems starting dashboard in trunk In-Reply-To: <4d93f07c0803280444y1aa218e3w7c981f1c7b6e3297@mail.gmail.com> References: <47EBBD25.4080508@mpiz-koeln.mpg.de> <47ECB7BA.4030207@mpiz-koeln.mpg.de> <47ECC696.60702@mpimp-golm.mpg.de> <0D7C7592-E658-4C8C-90A1-D2BFAD3F1F1B@farmbio.uu.se> <4d93f07c0803280444y1aa218e3w7c981f1c7b6e3297@mail.gmail.com> Message-ID: <6CA7913B-637B-49F6-8C06-5459C86D86E2@farmbio.uu.se> Thanks Martin, this solves my problem. /Ola On Mar 28, 2008, at 12:44 , Martin Senger wrote: > > pom.xml > > First of all, never edit pom.xml, but only xmls/project.pom. The > pom.xml is used only by Eclipse and it is generated from the xmls/ > project.pom (so if something looks bad in eclipse, just remove > pom.xml (there is also one in src/main directory) and run 'ant > config' - the pom.xml will be re-created. > > I added it there like: > > > commons-collections > commons-collections > 3.2 > > > No need to add it because it will be added automatically by commons- > configuration. But you need to exclude it from commons-dbcp. This > is what I commited (half an hour ago), hoping that it fixes the > problem: > > > commons-dbcp > commons-dbcp > 1.1 > > ... > > commons-collections > commons-collections > > > > > Martin > > > -- > Martin Senger > email: martin.senger at gmail.com,m.senger at cgiar.org > skype: martinsenger From maliha.aziz at yahoo.com Mon Mar 31 19:01:50 2008 From: maliha.aziz at yahoo.com (maliha aziz) Date: Mon, 31 Mar 2008 16:01:50 -0700 (PDT) Subject: [MOBY-l] a general question about biomoby Message-ID: <32247.60269.qm@web57413.mail.re1.yahoo.com> hi I was wondering if someone could direct me to some papers about the questions that I have ( I could not find much on this topic) BioMoby is a plug in in Taverna. This means that myGrid's Feta Semantic publishing component( not the discovery one) does not take biomoby services and go through the whole manual annotation process using the myGrid ontology... thus Taverna is not able to perform keyword etc search using it FETA search option on biomoby... but I have read somewhere (cudnt fine any papers discussing this) that myGrid and BioMoby are working towards allowing Feta search engine to work on BioMoby registry and i also read some where that "BioMoby is migrating to using the myGrid service ontology and registry"(myGrid website) the two seem conflicting statments to me but what i really want to know is what exactly is it that biomoby and myGrid are working towards??? making moby registry/ services myGrid ontology compliant or just enabling FETA search on biomoby and letting biomoby be independant with its various ontologies. Regards Maliha _________________________________________________________________ Special deal for Yahoo! users & friends - [1]No Cost. Get a month of Blockbuster Total Access now References 1. http://us.rd.yahoo.com/evt=47521/*http://tc.deals.yahoo.com/tc/blockbuster/text3.com