From segura.eduardo at gmail.com Mon Feb 5 04:12:17 2007 From: segura.eduardo at gmail.com (eduardo segura) Date: Mon, 5 Feb 2007 01:12:17 -0800 Subject: [MOBY-l] CFP: SPAC 07 - Software Patterns: Addressing Challenges In-Reply-To: References: Message-ID: My apologies for duplicates * The First IEEE International Workshop on **Software Patterns: Addressing Challenges **SPAC 2007 **Call for Papers* *Beijing, China, July 24-27, 2007 (in conjunction with COMPSAC 2007)* * * http://conferences.computer.org/compsac/2007/ (COMPSAC 2007 Link) http://conferences.computer.org/compsac/2007/workshops/SPAC (Workshop Link-1) http://www.engr.sjsu.edu/~fayad/workshops/COMPSAC07 (Workshop Link-2) http://www.vrlsoft.com/workshops/SPAC07 (WorkshopLink-3)* * *THEME OF THE WORKSHOP* As software increases in size and becomes more complex and costly, the need for techniques to ease software development is likewise increasing. Over the last decade, pattern community has evolved and received more interest in both academia and industry. Developing software using patterns holds the promise to reduce the cost and condensing the time of developing software systems, while simultaneously maintaining the quality of these systems. However, the potential of using patterns in developing systems is not fully realized and we need to address many challenges. For example, developing pattern repositories and catalogs, from which patterns can be retrieved and reused, still forms a challenge to software engineering, knowledge engineering and information systems communities. In addition, the need for (semi-) automated approaches for patterns mining and integration poses several open research questions to the software engineering community. Many think these challenges and others preclude the realization of the benefit of patterns as a reuse approach. This workshop aims at bringing together researchers and practitioners who are interested in resolving research challenges or who have practical experience with the different issues of patterns reuse and integration to discuss and advance the state-of-the-art and the state-of-the-practice in patterns reuse. Patterns have emerged as a promising reuse technique for both improving the quality and reducing the cost and time of software development. However, there is an immense belief that patterns have not fulfilled the expectations software developers wanted. Nevertheless, this belief does not rebuff the fact that patterns, as a concept, have the potential to play a key role in developing systems in the near future. This near future will never come unless there are serious attempts from both developers and researchers to investigate and provide creative solutions to current challenges that hinder utilizing patterns in practice. Among these challenges, this workshop focuses on investigating how to develop systems using patterns. We are sure that this topic will attract many developers and researchers in the field to participate in this workshop. *WORKSHOP CHALLENGES* The workshop will address software patterns challenges and debate several issues related to the following questions. We want researchers, framework developers, and application developers to discuss and debate the following questions related to: *I. **Pattern Creation and Development* a. Leaving experience claim on the side, can you show how to create and develop patterns? b. What are the bases of creating patterns? c. Are there guidelines, methodologies, and/or processes for pattern creations and developments? d. Would you show an example or two? *II. **Patterns Selection Process: * a. How does one select analysis and design patterns to build any system? b. What is the basis for selecting these patterns? c. If someone would like to build a system from patterns, how does she select patterns? d. What kind of patterns should one select to build a system from patterns? e. Is there a guideline for the selection process? *III. **Patterns Composition* a. How does one integrate the selected patterns to build any system? or How does one compose any system from patterns? b. What are the various claims related to patterns composition? Are they true? c. Are there guidelines or techniques for patterns composition? Would you illustrate how to use them? *IV. **System of Patterns and General Reuse* a. What do we mean when we say "systems of patterns"? b. Are the various claims related to building any system from patterns reasonable? c. How to develop pattern repositories and catalogs, from which patterns can be retrieved and reused? d. Are there automated approaches for patterns mining and integration? e. What other concepts will help build any system from patterns? . *V. **Impacts* a. What is the impact of software stability on the above issues? Check any of the following websites for all columns and accepted position papers: http://conferences.computer.org/compsac/2007/workshops/SPAC (Main Link) www.engr.sjsu.edu/~fayad//workshops/COMPSAC07 (Workshop Link 2) www.vrlsoft.com/workshops/SPAC07 (Workshop Link 3 -- Under Construction) *PAPER FORMAT AND SUBMISSIONS* Detailed instructions for electronic paper submission and review process can be found at http://www.compsac.org/. People interested in participating in the workshop are requested to submit a short position paper (*3-5 pages*) or regular workshop paper (limited to *6 pages*, double spaced, including figures) representing views and experiences relevant to the discussion topic. The title page should include a maximum 150-word abstract, five keywords, full mailing address, e-mail address, phone number, fax number, and a designated contact author. Papers will be selected depending on the originality, quality and relevance to the workshop. All submitted papers will be evaluated according to its originality, significance, correctness, presentation and relevance. Papers should be submitted electronically at: http://compsac.cs.iastate.edu/2007/SPAC/ . Please follow the instructions given by the web page. Camera Ready manuscripts must be submitted following IEEE conference proceedings style and guidelines. We encourage authors to present novel ideas, critique of existing work, and practical studies. Each accepted paper must be presented in person by the author or one of the authors. To foster lively discussions, each author is encouraged to present open questions and one or two main statements that will be discussed at the workshop. Submissions must be either MS-Word or RTF formats (please, DO NOT compress files). Depending on the number and spread of contributions, the scope may be narrowed to ensure effective communication and information sharing. Accepted position papers will be distributed to the participants before the workshop and made generally available through the WWW and FTP. Accepted papers will be published in the Workshop Proceedings of the 31st IEEE Computer Software and Applications Conference (COMPSAC 2007). At least one of the authors of each accepted paper must register as a full participant in the workshop to have the paper published in the COMPSAC 2007 Proceedings. The workshop selected best papers will be published in online Journal of International Journal Of Patterns (IJOP) ? *www.ijop.org* *WORKSHOP PARTICIPATION* Interested in participating in the workshop without submission are requested to fill out the participation form and e-mail to the co-chair Haitham Hamza , Eduardo Segura , or to the workshop chair M.E. Fayad . ------------------------------------------------- PARTICIPATION FORM: Name and Affiliation: Position: Address: E-mail: URL: Areas of interest: Why would you like to participate? ------------------------------------------------- Please note that registration is required in order to participate in the workshop. An early registration discount is available. An overhead projector and a flipchart will be available. For more information please visit any of the following websites: * * http://conferences.computer.org/compsac/2007/workshops/SPAC (Main Link) www.engr.sjsu.edu/~fayad//workshops/COMPSAC07 (Workshop Link 2) www.vrlsoft.com/workshops/SPAC07 (Workshop Link 3 -- Under Construction) You may also contact the organizers. *PROPOSED AGENDA* 1. Welcome and introduction of participants. The organizers will first give a short overview of any open issues and of the main arguments arising out of the position papers. (Estimated time: 20-30 minutes) 2. Selected authors (representing the main trends) will be given 20 minutes to explain how their position relates to other positions and what each sees as the three major issues. We expect about 5-10 position papers. (Estimated time: 120-130 minutes) 3. The organizers will propose an identification of the major issues, and the participants will then discuss and select what they think are the hottest issues to be examined. (Estimated time: 10-15 minutes) 4. The participants will work for 70-95 minutes in small groups, with a designated moderator in each group. The groups will each deal with two different hot issues identified and will produce a summary in the form of points and counterpoints, showing either how several views are irreducibly opposed or how they are complementary. The number of groups will depend on the number of participants and number of issues selected; ideally there should be 3-5 p people in each group. (Estimated time: 60-70 minutes) 5. Each group will be given 10-15 minutes to present its findings to the workshop. A closing discussion will follow. The workshop report will be written on the basis of these findings and will include an agenda for future exploration and cooperation; it will be made available through the WWW and FTP. (Estimated time: 50-60 minutes for five teams) (Total estimated time: 285-315 minutes, i.e. about five hours +/- 15 minutes; lunch and breaks are not included.) *IMPORTANT DATES* We will be updated based on acceptance process *Feb. 23, 2007*: Full paper and short paper due *Mar. 25, 2007*: Decision notification (electronic) *Apr. 30, 2007*: Camera-ready copy and author registration due *July 24-27, 2007**:* The workshop Date *ORGANIZERS* * * *Chair and Point of Contact:* *Dr.** M.E.** Fayad * Professor of Computer Engineering Computer Engineering Dept., College of Engineering San Jos? State University One Washington Square, San Jos?, CA 95192-0180 Ph: (408) 924-7364, Fax: (408) 924-4153 E-mail: m.fayad at sjsu.edu, me fayad at gmail.com http://www.engr.sjsu.edu/fayad *Co-Chairs:* Dr. H.S. Hamza (Co-Chair) Faculty of Computers and Informatics, Information Technology Department Cairo University, Orman, Giza 12613 - Egypt Ph: (02) 335-8355 (office) E-mail: hshamza at gmail.com * * Eduardo M. Segura vrlSoft, Inc. 2065 Martin Ave., Suite 103 Santa Clara, CA 95050-2707 Phone/Fax: (408) 654-8972 E-mail: esegura at vrlsoft.com, eduardo.segura at sjsu.edu http://www.vrlsoft.com *PROGRAM COMMITTEE* *Leonor Barroca **Open University, England* *Sjaak Brinkkemper Utrecht University, the Netherlands * *Chia-Chu Chiang University of Arkansas at Little Rock, USA* *Rogerio Atem de Carvalho CEFET Campos, Brazil* *Andrea D'Ambrogio University of Roma TorVergata, Italy* *Issam Wajih Damaj Dhofar University, Salalah - Sultanate of Oman * *Khalil DRIRA LAAS-CNRS, France* ** *Islam A. M. El-Maddah Ain Shams University, Egypt* *M.E. Fayad San Jose State University & vrlSoft, Inc., USA* *Joao M. Fernandes Universidade do Minho, Portugal* *IanGraham * *Trireme International Ltd, London, England* *Jiang Guo California State University Los Angeles, USA* *Wilhelm Hasselbring University of Oldenburg, Germany* *Tarek Helmy King Fahd Univ. of Petroleum and Minerals, Saudi Arabia* *H.S. Hamza Cairo University, Egypt* *Pilar Herrero Universidad Polit?cnica de Madrid , Spain.* *Hoda Hosny American University in Cairo, Egypt* *Pao-Ann Hsiung National Chung Cheng University, Chiayi, TAIWAN* *Ali Jaoua University of Qatar, Qatar* *Mohamed-Khireddine KHOLLADI University of Constantine, France* *Dae-Kyoo Kim Oakland University, MI, USA* *Seok-Won Lee The University of North Carolina at Charlotte, USA* *Jeff Lei University of Texas at Arlington, USA* *Ricardo J. Machado Universidade do Minho, Portugal* *Ahmed Mahdy Texas A&M University - Corpus Christi, USA* *Michael Oudshoorn ** Montana State University**, MT, USA* *Srini Ramaswamy University of Arkansas at Little Rock, USA* *Gustavo Rossi LIFIA, Facultad de Informatica, UNLP, Argentina* *Stuart Rubin SPAWAR, SSC-San Diego, USA* *Kannamma Sampath Coimbatore Institute of Technology, India* *Sanchez, Arturo University of North Florida, USA* *Kassem A. Saleh American University of Sharjah, UAE* *Arno Schmidmeier AspectSoft, Hersbruck, Germany * *E.M. Segura San Jose State University & vrlSoft, Inc., USA* *Manolis Tzagarakis Research Academic Technology Institute (RACTI), Greece* *Laurence** T. Yang St Francis Xavier University, Canada* *I-Ling Yen University of Texas at Dallas, USA* From karthik085 at gmail.com Sun Feb 11 17:18:25 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 17:18:25 -0500 Subject: [MOBY-l] Local BioMOBY Central - Ontology test fails Message-ID: Hi, I am setting up a local biomoby central. I am following this document: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html 1. When I do, make test - all test cases passes for all the files, except for Client-OntologyServer.t. I attached my test results for all('make test') and for Client-OntologyServer.t('perl t/Client-OntologyServer.t') along this mail. Here is just the summary: Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/Client-OntologyServer.t 13 3328 27 13 9-17 19-22 1 test skipped. Failed 1/13 test scripts. 13/381 subtests failed. Files=13, Tests=381, 79 wallclock secs ( 7.82 cusr + 0.70 csys = 8.52 CPU) Failed 1/13 test programs. 13/381 subtests failed. make: *** [test_dynamic] Error 255 2. t/Config file is being skipped for testing. It says: all skipped: Required only when you have your own local MOBY Central How do I test t/Config? Any help would be appreciated. -- Best Regards, Rajasekar Karthik karthik085 at gmail.com -------------- next part -------------- PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Central.....................ok t/Client-Central..............ok t/Client-CollectionArticle....ok t/Client-OntologyServer....... # Failed test at t/Client-OntologyServer.t line 111. # got: '0' # expected: '1' # Namespace 'Rub1' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 111. # got: '0' # expected: '1' # Namespace 'Rub2' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 120. # got: '0' # expected: '1' # Object 'Object' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 120. # got: '0' # expected: '1' # Object 'String' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 120. # got: '0' # expected: '1' # Object 'Integer' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 120. # got: '0' # expected: '1' # Object 'Float' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 120. # got: '0' # expected: '1' # Object 'DateTime' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 127. # got: '0' # expected: '1' # Service type 'Rub1' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 127. # got: '0' # expected: '1' # Service type 'Rub2' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 140. # got: '0' # expected: '1' # Relationship 'ISA' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 140. # got: '0' # expected: '1' # Relationship 'HASA' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 140. # got: '0' # expected: '1' # Relationship 'HAS' reported erroneously as non-existent. # Failed test at t/Client-OntologyServer.t line 146. # got: '0' # expected: '1' # Relationship 'ISA' reported erroneously as non-existent. # Looks like you failed 13 tests of 27. dubious Test returned status 13 (wstat 3328, 0xd00) DIED. FAILED tests 9-17, 19-22 Failed 13/27 tests, 51.85% okay t/Client-Registration.........ok t/Client-SecondaryArticle.....ok t/Client-Service..............ok t/Client-ServiceInstance......ok t/Client-SimpleArticle........ok t/CommonSubs..................ok t/Config......................skipped all skipped: Required only when you have your own local MOBY Central t/CrossReference..............ok t/Template....................ok Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/Client-OntologyServer.t 13 3328 27 13 9-17 19-22 1 test skipped. Failed 1/13 test scripts. 13/381 subtests failed. Files=13, Tests=381, 77 wallclock secs ( 7.68 cusr + 0.70 csys = 8.38 CPU) Failed 1/13 test programs. 13/381 subtests failed. make: *** [test_dynamic] Error 255 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: test_Client_Ontology_results.txt Url: http://lists.open-bio.org/pipermail/moby-l/attachments/20070211/c35a49e8/attachment-0001.txt From markw at illuminae.com Sun Feb 11 19:05:50 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 11 Feb 2007 16:05:50 -0800 Subject: [MOBY-l] Local BioMOBY Central - Ontology test fails In-Reply-To: References: Message-ID: Hi Karthik, Make sure that you have all three environment variables set: MOBY_SERVER=http://localhost/path/to/MOBY-Central.pl MOBY_URI=http://localhost/MOBY/Central MOBY_ONTOLOGYSERVER=http://localhost/path/to/OntologyServer.cgi That should solve your problems... I hope :-) M On Sun, 11 Feb 2007 14:18:25 -0800, Rajasekar Karthik wrote: > Hi, > > I am setting up a local biomoby central. I am following this document: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html > > 1. When I do, make test - all test cases passes for all the files, except > for Client-OntologyServer.t. I attached my test results for all('make > test') > and for Client-OntologyServer.t('perl t/Client-OntologyServer.t') along > this > mail. Here is just the summary: > > Failed Test Stat Wstat Total Fail List of Failed > ------------------------------------------------------------------------------- > t/Client-OntologyServer.t 13 3328 27 13 9-17 19-22 > 1 test skipped. > Failed 1/13 test scripts. 13/381 subtests failed. > Files=13, Tests=381, 79 wallclock secs ( 7.82 cusr + 0.70 csys = 8.52 > CPU) > Failed 1/13 test programs. 13/381 subtests failed. > make: *** [test_dynamic] Error 255 > > > 2. t/Config file is being skipped for testing. It says: > all skipped: Required only when you have your own local MOBY Central > How do I test t/Config? > > Any help would be appreciated. > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From karthik085 at gmail.com Sun Feb 11 19:33:10 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 19:33:10 -0500 Subject: [MOBY-l] Local BioMOBY Central - Ontology test fails In-Reply-To: References: Message-ID: Hi Mark, I do have all the environment variables as suggested. Still, the same results. :-( I tested against the default http://mobycentral.icapture.ubc.ca/cgi-bin/On tologyServer.cgi and 4 testcases fail: ok 1 - use MOBY::Client::OntologyServer; ok 2 - MOBY::Client::OntologyServer->can(...) ok 3 ok 4 ok 5 ok 6 ok 7 not ok 8 # TODO How come I cant' set proxy back to its original value? # Failed (TODO) test at t/Client-OntologyServer.t line 101. # got: 'bar' # expected: undef # Couldn't return proxy to previous value not ok 9 # Failed test at t/Client-OntologyServer.t line 111. # got: '0' # expected: '1' # Namespace 'Rub1' reported erroneously as non-existent. not ok 10 # Failed test at t/Client-OntologyServer.t line 111. # got: '0' # expected: '1' # Namespace 'Rub2' reported erroneously as non-existent. ok 11 ok 12 ok 13 ok 14 ok 15 not ok 16 # Failed test at t/Client-OntologyServer.t line 127. # got: '0' # expected: '1' # Service type 'Rub1' reported erroneously as non-existent. not ok 17 # Failed test at t/Client-OntologyServer.t line 127. # got: '0' # expected: '1' # Service type 'Rub2' reported erroneously as non-existent. ok 18 - MOBY::Client::OntologyServer->can('relationshipExists') ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 1..27 # Looks like you failed 4 tests of 27. On 2/11/07, Mark Wilkinson wrote: > > Hi Karthik, > > Make sure that you have all three environment variables set: > > MOBY_SERVER=http://localhost/path/to/MOBY-Central.pl > MOBY_URI=http://localhost/MOBY/Central > MOBY_ONTOLOGYSERVER=http://localhost/path/to/OntologyServer.cgi > > That should solve your problems... I hope :-) > > M > > > > > On Sun, 11 Feb 2007 14:18:25 -0800, Rajasekar Karthik > wrote: > > > Hi, > > > > I am setting up a local biomoby central. I am following this document: > > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html > > > > 1. When I do, make test - all test cases passes for all the files, > except > > for Client-OntologyServer.t. I attached my test results for all('make > > test') > > and for Client-OntologyServer.t('perl t/Client-OntologyServer.t') along > > this > > mail. Here is just the summary: > > > > Failed Test Stat Wstat Total Fail List of Failed > > > ------------------------------------------------------------------------------- > > t/Client-OntologyServer.t 13 3328 27 13 9-17 19-22 > > 1 test skipped. > > Failed 1/13 test scripts. 13/381 subtests failed. > > Files=13, Tests=381, 79 wallclock secs ( 7.82 cusr + 0.70 csys = 8.52 > > CPU) > > Failed 1/13 test programs. 13/381 subtests failed. > > make: *** [test_dynamic] Error 255 > > > > > > 2. t/Config file is being skipped for testing. It says: > > all skipped: Required only when you have your own local MOBY Central > > How do I test t/Config? > > > > Any help would be appreciated. > > > > > > -- > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From karthik085 at gmail.com Sun Feb 11 19:41:18 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 19:41:18 -0500 Subject: [MOBY-l] Local BioMOBY Central - Ontology test fails In-Reply-To: References: Message-ID: Also, I forgot to add: >From dashboard, I am able to retrieve/register/deregister services, namespaces, data types... from localhost. In data types, I can see Object, String, Integer, Float...so, it does exist. Testcases in Client-OntologyServer.t like 11-15 tests for that. > > I do have all the environment variables as suggested. Still, the same > results. :-( > I tested against the default http://mobycentral.icapture.ubc.ca/cgi-bin/On > > tologyServer.cgi and 4 testcases fail: > > ok 1 - use MOBY::Client::OntologyServer; > ok 2 - MOBY::Client::OntologyServer->can(...) > ok 3 > ok 4 > ok 5 > ok 6 > ok 7 > not ok 8 # TODO How come I cant' set proxy back to its original value? > # Failed (TODO) test at t/Client-OntologyServer.t line 101. > # got: 'bar' > # expected: undef > # Couldn't return proxy to previous value > not ok 9 > # Failed test at t/Client-OntologyServer.t line 111. > # got: '0' > # expected: '1' > # Namespace 'Rub1' reported erroneously as non-existent. > not ok 10 > # Failed test at t/Client-OntologyServer.t line 111. > # got: '0' > # expected: '1' > # Namespace 'Rub2' reported erroneously as non-existent. > ok 11 > ok 12 > ok 13 > ok 14 > ok 15 > not ok 16 > # Failed test at t/Client-OntologyServer.t line 127. > # got: '0' > # expected: '1' > # Service type 'Rub1' reported erroneously as non-existent. > not ok 17 > # Failed test at t/Client-OntologyServer.t line 127. > # got: '0' > # expected: '1' > # Service type 'Rub2' reported erroneously as non-existent. > ok 18 - MOBY::Client::OntologyServer->can('relationshipExists') > ok 19 > ok 20 > ok 21 > ok 22 > ok 23 > ok 24 > ok 25 > ok 26 > ok 27 > 1..27 > # Looks like you failed 4 tests of 27. > > > On 2/11/07, Mark Wilkinson wrote: > > > > Hi Karthik, > > > > Make sure that you have all three environment variables set: > > > > MOBY_SERVER=http://localhost/path/to/MOBY-Central.pl > > MOBY_URI=http://localhost/MOBY/Central > > MOBY_ONTOLOGYSERVER= http://localhost/path/to/OntologyServer.cgi > > > > That should solve your problems... I hope :-) > > > > M > > > > > > > > > > On Sun, 11 Feb 2007 14:18:25 -0800, Rajasekar Karthik > > wrote: > > > > > Hi, > > > > > > I am setting up a local biomoby central. I am following this document: > > > > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html > > > > > > 1. When I do, make test - all test cases passes for all the files, > > except > > > for Client-OntologyServer.t . I attached my test results for all('make > > > test') > > > and for Client-OntologyServer.t('perl t/Client-OntologyServer.t') > > along > > > this > > > mail. Here is just the summary: > > > > > > Failed Test Stat Wstat Total Fail List of Failed > > > > > ------------------------------------------------------------------------------- > > > t/Client-OntologyServer.t 13 3328 27 13 9-17 19-22 > > > 1 test skipped. > > > Failed 1/13 test scripts. 13/381 subtests failed. > > > Files=13, Tests=381, 79 wallclock secs ( 7.82 cusr + 0.70 csys = > > 8.52 > > > CPU) > > > Failed 1/13 test programs. 13/381 subtests failed. > > > make: *** [test_dynamic] Error 255 > > > > > > > > > 2. t/Config file is being skipped for testing. It says: > > > all skipped: Required only when you have your own local MOBY Central > > > How do I test t/Config? > > > > > > Any help would be appreciated. > > > > > > > > > > > -- > > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > > > > > > -- > Best Regards, > Rajasekar Karthik > karthik085 at gmail.com > -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From markw at illuminae.com Sun Feb 11 19:52:30 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 11 Feb 2007 16:52:30 -0800 Subject: [MOBY-l] Local BioMOBY Central - Ontology test fails In-Reply-To: References: Message-ID: Hi Karthik, I don't think you will be able to test the OntologyServer at mobycentral independently of all other calls going to mobycentral also, so if you have only changed the MOBY_ONTOLOGYSERVER environment variable, leaving the other ones at localhost, you will expect at least some of the errors you report below. M On Sun, 11 Feb 2007 16:33:10 -0800, Rajasekar Karthik wrote: > Hi Mark, > > I do have all the environment variables as suggested. Still, the same > results. :-( > I tested against the default > http://mobycentral.icapture.ubc.ca/cgi-bin/On > tologyServer.cgi and 4 testcases fail: > > ok 1 - use MOBY::Client::OntologyServer; > ok 2 - MOBY::Client::OntologyServer->can(...) > ok 3 > ok 4 > ok 5 > ok 6 > ok 7 > not ok 8 # TODO How come I cant' set proxy back to its original value? > # Failed (TODO) test at t/Client-OntologyServer.t line 101. > # got: 'bar' > # expected: undef > # Couldn't return proxy to previous value > not ok 9 > # Failed test at t/Client-OntologyServer.t line 111. > # got: '0' > # expected: '1' > # Namespace 'Rub1' reported erroneously as non-existent. > not ok 10 > # Failed test at t/Client-OntologyServer.t line 111. > # got: '0' > # expected: '1' > # Namespace 'Rub2' reported erroneously as non-existent. > ok 11 > ok 12 > ok 13 > ok 14 > ok 15 > not ok 16 > # Failed test at t/Client-OntologyServer.t line 127. > # got: '0' > # expected: '1' > # Service type 'Rub1' reported erroneously as non-existent. > not ok 17 > # Failed test at t/Client-OntologyServer.t line 127. > # got: '0' > # expected: '1' > # Service type 'Rub2' reported erroneously as non-existent. > ok 18 - MOBY::Client::OntologyServer->can('relationshipExists') > ok 19 > ok 20 > ok 21 > ok 22 > ok 23 > ok 24 > ok 25 > ok 26 > ok 27 > 1..27 > # Looks like you failed 4 tests of 27. > > > On 2/11/07, Mark Wilkinson wrote: >> >> Hi Karthik, >> >> Make sure that you have all three environment variables set: >> >> MOBY_SERVER=http://localhost/path/to/MOBY-Central.pl >> MOBY_URI=http://localhost/MOBY/Central >> MOBY_ONTOLOGYSERVER=http://localhost/path/to/OntologyServer.cgi >> >> That should solve your problems... I hope :-) >> >> M >> >> >> >> >> On Sun, 11 Feb 2007 14:18:25 -0800, Rajasekar Karthik >> wrote: >> >> > Hi, >> > >> > I am setting up a local biomoby central. I am following this document: >> > >> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html >> > >> > 1. When I do, make test - all test cases passes for all the files, >> except >> > for Client-OntologyServer.t. I attached my test results for all('make >> > test') >> > and for Client-OntologyServer.t('perl t/Client-OntologyServer.t') >> along >> > this >> > mail. Here is just the summary: >> > >> > Failed Test Stat Wstat Total Fail List of Failed >> > >> ------------------------------------------------------------------------------- >> > t/Client-OntologyServer.t 13 3328 27 13 9-17 19-22 >> > 1 test skipped. >> > Failed 1/13 test scripts. 13/381 subtests failed. >> > Files=13, Tests=381, 79 wallclock secs ( 7.82 cusr + 0.70 csys = >> 8.52 >> > CPU) >> > Failed 1/13 test programs. 13/381 subtests failed. >> > make: *** [test_dynamic] Error 255 >> > >> > >> > 2. t/Config file is being skipped for testing. It says: >> > all skipped: Required only when you have your own local MOBY Central >> > How do I test t/Config? >> > >> > Any help would be appreciated. >> > >> >> >> >> -- >> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ >> > > > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From markw at illuminae.com Sun Feb 11 19:54:27 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 11 Feb 2007 16:54:27 -0800 Subject: [MOBY-l] Local BioMOBY Central - Ontology test fails In-Reply-To: References: Message-ID: Can you confirm that your test suite runs when you have NO environment variables set? (i.e. when you are connecting to my default mobycentral in all cases)? M On Sun, 11 Feb 2007 16:41:18 -0800, Rajasekar Karthik wrote: > Also, I forgot to add: >> From dashboard, I am able to retrieve/register/deregister services, > namespaces, data types... from localhost. In data types, I can see > Object, > String, Integer, Float...so, it does exist. Testcases in > Client-OntologyServer.t like 11-15 tests for that. > >> >> I do have all the environment variables as suggested. Still, the same >> results. :-( >> I tested against the default >> http://mobycentral.icapture.ubc.ca/cgi-bin/On >> >> tologyServer.cgi and 4 testcases fail: >> >> ok 1 - use MOBY::Client::OntologyServer; >> ok 2 - MOBY::Client::OntologyServer->can(...) >> ok 3 >> ok 4 >> ok 5 >> ok 6 >> ok 7 >> not ok 8 # TODO How come I cant' set proxy back to its original value? >> # Failed (TODO) test at t/Client-OntologyServer.t line 101. >> # got: 'bar' >> # expected: undef >> # Couldn't return proxy to previous value >> not ok 9 >> # Failed test at t/Client-OntologyServer.t line 111. >> # got: '0' >> # expected: '1' >> # Namespace 'Rub1' reported erroneously as non-existent. >> not ok 10 >> # Failed test at t/Client-OntologyServer.t line 111. >> # got: '0' >> # expected: '1' >> # Namespace 'Rub2' reported erroneously as non-existent. >> ok 11 >> ok 12 >> ok 13 >> ok 14 >> ok 15 >> not ok 16 >> # Failed test at t/Client-OntologyServer.t line 127. >> # got: '0' >> # expected: '1' >> # Service type 'Rub1' reported erroneously as non-existent. >> not ok 17 >> # Failed test at t/Client-OntologyServer.t line 127. >> # got: '0' >> # expected: '1' >> # Service type 'Rub2' reported erroneously as non-existent. >> ok 18 - MOBY::Client::OntologyServer->can('relationshipExists') >> ok 19 >> ok 20 >> ok 21 >> ok 22 >> ok 23 >> ok 24 >> ok 25 >> ok 26 >> ok 27 >> 1..27 >> # Looks like you failed 4 tests of 27. >> >> >> On 2/11/07, Mark Wilkinson wrote: >> > >> > Hi Karthik, >> > >> > Make sure that you have all three environment variables set: >> > >> > MOBY_SERVER=http://localhost/path/to/MOBY-Central.pl >> > MOBY_URI=http://localhost/MOBY/Central >> > MOBY_ONTOLOGYSERVER= http://localhost/path/to/OntologyServer.cgi >> > >> > That should solve your problems... I hope :-) >> > >> > M >> > >> > >> > >> > >> > On Sun, 11 Feb 2007 14:18:25 -0800, Rajasekar Karthik >> > wrote: >> > >> > > Hi, >> > > >> > > I am setting up a local biomoby central. I am following this >> document: >> > > >> > >> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html >> > > >> > > 1. When I do, make test - all test cases passes for all the files, >> > except >> > > for Client-OntologyServer.t . I attached my test results for >> all('make >> > > test') >> > > and for Client-OntologyServer.t('perl t/Client-OntologyServer.t') >> > along >> > > this >> > > mail. Here is just the summary: >> > > >> > > Failed Test Stat Wstat Total Fail List of Failed >> > > >> > >> ------------------------------------------------------------------------------- >> > > t/Client-OntologyServer.t 13 3328 27 13 9-17 19-22 >> > > 1 test skipped. >> > > Failed 1/13 test scripts. 13/381 subtests failed. >> > > Files=13, Tests=381, 79 wallclock secs ( 7.82 cusr + 0.70 csys = >> > 8.52 >> > > CPU) >> > > Failed 1/13 test programs. 13/381 subtests failed. >> > > make: *** [test_dynamic] Error 255 >> > > >> > > >> > > 2. t/Config file is being skipped for testing. It says: >> > > all skipped: Required only when you have your own local MOBY Central >> > > How do I test t/Config? >> > > >> > > Any help would be appreciated. >> > > >> > >> > >> > >> > -- >> > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ >> > >> >> >> >> -- >> Best Regards, >> Rajasekar Karthik >> karthik085 at gmail.com >> > > > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From karthik085 at gmail.com Sun Feb 11 20:34:06 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 20:34:06 -0500 Subject: [MOBY-l] Local BioMOBY Central - Ontology test fails In-Reply-To: References: Message-ID: Mark, With no environment variables set, I was able to run the test suites and most of them passed, except for Client-OntologyServer.t(13 testcases failed). Failed Test Stat Wstat Total Fail List of Failed ------------------------------------------------------------------------------- t/Client-OntologyServer.t 13 3328 27 13 9-17 19-22 1 test skipped. Failed 1/13 test scripts. 13/381 subtests failed. Files=13, Tests=381, 35 wallclock secs ( 7.67 cusr + 0.78 csys = 8.45 CPU) Failed 1/13 test programs. 13/381 subtests failed. make: *** [test_dynamic] Error 255 When MOBY_SERVER and MOBY_URI environment variables was set to localhost. a) MOBY_ONTOLOGYSERVER: Did not set any environment variables or did not modify default value in OntologyServer.pm Client-OntologyServer.t(13 testcases failed) b) MOBY_ONTOLOGYSERVER: Set environment variable to: http://mobycentral.icapture.ubc.ca/cgi-bin/OntologyServer.cgi Client-OntologyServer.t(4 testcases failed). When MOBY_SERVER and MOBY_URI environment variables was set to default ( http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl and http://mobycentral.icapture.ubc.ca/MOBY/Central respectively), a) MOBY_ONTOLOGYSERVER: Did not set any environment variables or did not modify default value in OntologyServer.pm all testcases passed b) MOBY_ONTOLOGYSERVER: Set environment variable to: http://mobycentral.icapture.ubc.ca/cgi-bin/OntologyServer.cgi all testcases passed. On 2/11/07, Mark Wilkinson wrote: > > Can you confirm that your test suite runs when you have NO environment > variables set? (i.e. when you are connecting to my default mobycentral in > all cases)? > > > M > > > > On Sun, 11 Feb 2007 16:41:18 -0800, Rajasekar Karthik > wrote: > > > Also, I forgot to add: > >> From dashboard, I am able to retrieve/register/deregister services, > > namespaces, data types... from localhost. In data types, I can see > > Object, > > String, Integer, Float...so, it does exist. Testcases in > > Client-OntologyServer.t like 11-15 tests for that. > > > >> > >> I do have all the environment variables as suggested. Still, the same > >> results. :-( > >> I tested against the default > >> http://mobycentral.icapture.ubc.ca/cgi-bin/On > >> > >> tologyServer.cgi and 4 testcases fail: > >> > >> ok 1 - use MOBY::Client::OntologyServer; > >> ok 2 - MOBY::Client::OntologyServer->can(...) > >> ok 3 > >> ok 4 > >> ok 5 > >> ok 6 > >> ok 7 > >> not ok 8 # TODO How come I cant' set proxy back to its original value? > >> # Failed (TODO) test at t/Client-OntologyServer.t line 101. > >> # got: 'bar' > >> # expected: undef > >> # Couldn't return proxy to previous value > >> not ok 9 > >> # Failed test at t/Client-OntologyServer.t line 111. > >> # got: '0' > >> # expected: '1' > >> # Namespace 'Rub1' reported erroneously as non-existent. > >> not ok 10 > >> # Failed test at t/Client-OntologyServer.t line 111. > >> # got: '0' > >> # expected: '1' > >> # Namespace 'Rub2' reported erroneously as non-existent. > >> ok 11 > >> ok 12 > >> ok 13 > >> ok 14 > >> ok 15 > >> not ok 16 > >> # Failed test at t/Client-OntologyServer.t line 127. > >> # got: '0' > >> # expected: '1' > >> # Service type 'Rub1' reported erroneously as non-existent. > >> not ok 17 > >> # Failed test at t/Client-OntologyServer.t line 127. > >> # got: '0' > >> # expected: '1' > >> # Service type 'Rub2' reported erroneously as non-existent. > >> ok 18 - MOBY::Client::OntologyServer->can('relationshipExists') > >> ok 19 > >> ok 20 > >> ok 21 > >> ok 22 > >> ok 23 > >> ok 24 > >> ok 25 > >> ok 26 > >> ok 27 > >> 1..27 > >> # Looks like you failed 4 tests of 27. > >> > >> > >> On 2/11/07, Mark Wilkinson wrote: > >> > > >> > Hi Karthik, > >> > > >> > Make sure that you have all three environment variables set: > >> > > >> > MOBY_SERVER=http://localhost/path/to/MOBY-Central.pl > >> > MOBY_URI=http://localhost/MOBY/Central > >> > MOBY_ONTOLOGYSERVER= http://localhost/path/to/OntologyServer.cgi > >> > > >> > That should solve your problems... I hope :-) > >> > > >> > M > >> > > >> > > >> > > >> > > >> > On Sun, 11 Feb 2007 14:18:25 -0800, Rajasekar Karthik > >> > wrote: > >> > > >> > > Hi, > >> > > > >> > > I am setting up a local biomoby central. I am following this > >> document: > >> > > > >> > > >> > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html > >> > > > >> > > 1. When I do, make test - all test cases passes for all the files, > >> > except > >> > > for Client-OntologyServer.t . I attached my test results for > >> all('make > >> > > test') > >> > > and for Client-OntologyServer.t('perl t/Client-OntologyServer.t') > >> > along > >> > > this > >> > > mail. Here is just the summary: > >> > > > >> > > Failed Test Stat Wstat Total Fail List of Failed > >> > > > >> > > >> > ------------------------------------------------------------------------------- > >> > > t/Client-OntologyServer.t 13 3328 27 13 9-17 19-22 > >> > > 1 test skipped. > >> > > Failed 1/13 test scripts. 13/381 subtests failed. > >> > > Files=13, Tests=381, 79 wallclock secs ( 7.82 cusr + 0.70 csys = > >> > 8.52 > >> > > CPU) > >> > > Failed 1/13 test programs. 13/381 subtests failed. > >> > > make: *** [test_dynamic] Error 255 > >> > > > >> > > > >> > > 2. t/Config file is being skipped for testing. It says: > >> > > all skipped: Required only when you have your own local MOBY > Central > >> > > How do I test t/Config? > >> > > > >> > > Any help would be appreciated. > >> > > > >> > > >> > > >> > > >> > -- > >> > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > >> > > >> > >> > >> > >> -- > >> Best Regards, > >> Rajasekar Karthik > >> karthik085 at gmail.com > >> > > > > > > > > > > -- > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From karthik085 at gmail.com Sun Feb 11 22:20:56 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 22:20:56 -0500 Subject: [MOBY-l] Multiple Centrals on Same server Message-ID: Hi, Is it possible to setup multiple local centrals on a same server? With the databases, there can be multiple ones created. All the executables like MOBY-Central.PL, OntologyServer.cgi....can be moved into two directories of webserver cgi-bin folder. But, what about httpd.conf configuration file in apache? How do I modify that? -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From markw at illuminae.com Sun Feb 11 22:29:24 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 11 Feb 2007 19:29:24 -0800 Subject: [MOBY-l] Multiple Centrals on Same server In-Reply-To: References: Message-ID: As far as I know, nobody has ever tried this, so you are breaking new ground (and as someone new to MOBY, that might not be the easiest thing to do :-) ) But the answer to your question is that you can only run one instance of MOBY Central per instance of the Apache server. You can run multiple instances of Apache, each with their own config file, where each config file points to a different mobycentral.config file. On the client side (in Perl, I don't know about Java) you can create an instance of MOBY::Client::Central that connects to two different MOBY Centrals by name (you create the name when you assign the URL during creation of the object), and you have to specify the name of the MOBY Central you are addressing when you make your MOBY Central call using the "Registry => "somename"" parameter. Some MOBY::Client::Central calls don't allow you to address more than one registry. In particular, ones that involve registration of new objects, service types, or namespaces. That's because the ontologies are assumed to be canonical, and can only exist in one place - mobycentral.icapture.ubc.ca - if you create your own registry and chose to run your own ontologies there is NO guarantee that you will continue to be interoperable with any other services in the world. Having said that, for other calls (like findService and registerService) you should be able to run as many registries as you wish. ... caveat emptor... I don't think anyone has EVER tried to do this, so the code might not work... M On Sun, 11 Feb 2007 19:20:56 -0800, Rajasekar Karthik wrote: > Hi, > > Is it possible to setup multiple local centrals on a same server? With > the > databases, there can be multiple ones created. All the executables like > MOBY-Central.PL, OntologyServer.cgi....can be moved into two directories > of > webserver cgi-bin folder. But, what about httpd.conf configuration file > in > apache? How do I modify that? > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From karthik085 at gmail.com Sun Feb 11 22:35:51 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 22:35:51 -0500 Subject: [MOBY-l] Multiple Centrals on Same server In-Reply-To: References: Message-ID: Mark, You are right. I will just setup multiple central on different machine. After I am more comfortable with MOBY, I will try it. On 2/11/07, Mark Wilkinson wrote: > > As far as I know, nobody has ever tried this, so you are breaking new > ground (and as someone new to MOBY, that might not be the easiest thing to > do :-) ) > > But the answer to your question is that you can only run one instance of > MOBY Central per instance of the Apache server. You can run multiple > instances of Apache, each with their own config file, where each config > file points to a different mobycentral.config file. On the client side > (in Perl, I don't know about Java) you can create an instance of > MOBY::Client::Central that connects to two different MOBY Centrals by name > (you create the name when you assign the URL during creation of the > object), and you have to specify the name of the MOBY Central you are > addressing when you make your MOBY Central call using the "Registry => > "somename"" parameter. > > Some MOBY::Client::Central calls don't allow you to address more than one > registry. In particular, ones that involve registration of new objects, > service types, or namespaces. That's because the ontologies are assumed > to be canonical, and can only exist in one place - > mobycentral.icapture.ubc.ca - if you create your own registry and chose to > run your own ontologies there is NO guarantee that you will continue to be > interoperable with any other services in the world. > > Having said that, for other calls (like findService and registerService) > you should be able to run as many registries as you wish. > > ... caveat emptor... I don't think anyone has EVER tried to do this, so > the code might not work... > > M > > > > > > On Sun, 11 Feb 2007 19:20:56 -0800, Rajasekar Karthik > wrote: > > > Hi, > > > > Is it possible to setup multiple local centrals on a same server? With > > the > > databases, there can be multiple ones created. All the executables like > > MOBY-Central.PL, OntologyServer.cgi....can be moved into two directories > > of > > webserver cgi-bin folder. But, what about httpd.conf configuration file > > in > > apache? How do I modify that? > > > > > > -- > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From markw at illuminae.com Sun Feb 11 22:40:17 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 11 Feb 2007 19:40:17 -0800 Subject: [MOBY-l] Multiple Centrals on Same server In-Reply-To: References: Message-ID: Hi Karthik! Actually, I didn't express myself clearly. Running multiple MOBY Centrals on the same machine is fine - I know from personal experience that I can run up to three instances on the same server. It is the CLIENT libraries that I am not sure about. I have never tried "in the real world" to use the Perl client libraries to talk to more than one instance of MOBY at the same time. I wrote them such that they SHOULD be able to do this, but I have never thoroughly tested this functionality, so I am not certain that it will work for you. I can assure you, however, that running multiple instances of teh registry on the same machine in different instances of Apache works just fine :-) M On Sun, 11 Feb 2007 19:35:51 -0800, Rajasekar Karthik wrote: > Mark, > > You are right. I will just setup multiple central on different machine. > After I am more comfortable with MOBY, I will try it. > > On 2/11/07, Mark Wilkinson wrote: >> >> As far as I know, nobody has ever tried this, so you are breaking new >> ground (and as someone new to MOBY, that might not be the easiest thing >> to >> do :-) ) >> >> But the answer to your question is that you can only run one instance of >> MOBY Central per instance of the Apache server. You can run multiple >> instances of Apache, each with their own config file, where each config >> file points to a different mobycentral.config file. On the client side >> (in Perl, I don't know about Java) you can create an instance of >> MOBY::Client::Central that connects to two different MOBY Centrals by >> name >> (you create the name when you assign the URL during creation of the >> object), and you have to specify the name of the MOBY Central you are >> addressing when you make your MOBY Central call using the "Registry => >> "somename"" parameter. >> >> Some MOBY::Client::Central calls don't allow you to address more than >> one >> registry. In particular, ones that involve registration of new objects, >> service types, or namespaces. That's because the ontologies are assumed >> to be canonical, and can only exist in one place - >> mobycentral.icapture.ubc.ca - if you create your own registry and chose >> to >> run your own ontologies there is NO guarantee that you will continue to >> be >> interoperable with any other services in the world. >> >> Having said that, for other calls (like findService and registerService) >> you should be able to run as many registries as you wish. >> >> ... caveat emptor... I don't think anyone has EVER tried to do this, so >> the code might not work... >> >> M >> >> >> >> >> >> On Sun, 11 Feb 2007 19:20:56 -0800, Rajasekar Karthik >> wrote: >> >> > Hi, >> > >> > Is it possible to setup multiple local centrals on a same server? With >> > the >> > databases, there can be multiple ones created. All the executables >> like >> > MOBY-Central.PL, OntologyServer.cgi....can be moved into two >> directories >> > of >> > webserver cgi-bin folder. But, what about httpd.conf configuration >> file >> > in >> > apache? How do I modify that? >> > >> >> >> >> -- >> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ >> > > > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From markw at illuminae.com Sun Feb 11 22:43:43 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 11 Feb 2007 19:43:43 -0800 Subject: [MOBY-l] Multiple Centrals on Same server In-Reply-To: References: Message-ID: In addition to that comment - just last week Eddie and I discovered a bug in the code that was supposed to allow MOBY::Client::Central to refer to another *single* registry by another name. That may have been the only bug, and it may work perfectly from now on, but... say a prayer before you try it :-) M On Sun, 11 Feb 2007 19:40:17 -0800, Mark Wilkinson wrote: > Hi Karthik! > > Actually, I didn't express myself clearly. Running multiple MOBY > Centrals > on the same machine is fine - I know from personal experience that I can > run up to three instances on the same server. It is the CLIENT libraries > that I am not sure about. I have never tried "in the real world" to use > the Perl client libraries to talk to more than one instance of MOBY at > the > same time. I wrote them such that they SHOULD be able to do this, but I > have never thoroughly tested this functionality, so I am not certain that > it will work for you. > > I can assure you, however, that running multiple instances of teh > registry > on the same machine in different instances of Apache works just fine :-) > > M > > > > > On Sun, 11 Feb 2007 19:35:51 -0800, Rajasekar Karthik > wrote: > >> Mark, >> >> You are right. I will just setup multiple central on different machine. >> After I am more comfortable with MOBY, I will try it. >> >> On 2/11/07, Mark Wilkinson wrote: >>> >>> As far as I know, nobody has ever tried this, so you are breaking new >>> ground (and as someone new to MOBY, that might not be the easiest thing >>> to >>> do :-) ) >>> >>> But the answer to your question is that you can only run one instance >>> of >>> MOBY Central per instance of the Apache server. You can run multiple >>> instances of Apache, each with their own config file, where each config >>> file points to a different mobycentral.config file. On the client side >>> (in Perl, I don't know about Java) you can create an instance of >>> MOBY::Client::Central that connects to two different MOBY Centrals by >>> name >>> (you create the name when you assign the URL during creation of the >>> object), and you have to specify the name of the MOBY Central you are >>> addressing when you make your MOBY Central call using the "Registry => >>> "somename"" parameter. >>> >>> Some MOBY::Client::Central calls don't allow you to address more than >>> one >>> registry. In particular, ones that involve registration of new >>> objects, >>> service types, or namespaces. That's because the ontologies are >>> assumed >>> to be canonical, and can only exist in one place - >>> mobycentral.icapture.ubc.ca - if you create your own registry and chose >>> to >>> run your own ontologies there is NO guarantee that you will continue to >>> be >>> interoperable with any other services in the world. >>> >>> Having said that, for other calls (like findService and >>> registerService) >>> you should be able to run as many registries as you wish. >>> >>> ... caveat emptor... I don't think anyone has EVER tried to do this, so >>> the code might not work... >>> >>> M >>> >>> >>> >>> >>> >>> On Sun, 11 Feb 2007 19:20:56 -0800, Rajasekar Karthik >>> wrote: >>> >>> > Hi, >>> > >>> > Is it possible to setup multiple local centrals on a same server? >>> With >>> > the >>> > databases, there can be multiple ones created. All the executables >>> like >>> > MOBY-Central.PL, OntologyServer.cgi....can be moved into two >>> directories >>> > of >>> > webserver cgi-bin folder. But, what about httpd.conf configuration >>> file >>> > in >>> > apache? How do I modify that? >>> > >>> >>> >>> >>> -- >>> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ >>> >> >> >> > > > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From karthik085 at gmail.com Sun Feb 11 22:46:57 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 22:46:57 -0500 Subject: [MOBY-l] Multiple Centrals on Same server In-Reply-To: References: Message-ID: Hi Mark, Thanks for making it more clear. I misunderstood from the earlier mail. On 2/11/07, Mark Wilkinson wrote: > > Hi Karthik! > > Actually, I didn't express myself clearly. Running multiple MOBY Centrals > on the same machine is fine - I know from personal experience that I can > run up to three instances on the same server. It is the CLIENT libraries > that I am not sure about. I have never tried "in the real world" to use > the Perl client libraries to talk to more than one instance of MOBY at the > same time. I wrote them such that they SHOULD be able to do this, but I > have never thoroughly tested this functionality, so I am not certain that > it will work for you. > > I can assure you, however, that running multiple instances of teh registry > on the same machine in different instances of Apache works just fine :-) > > M > > > > > On Sun, 11 Feb 2007 19:35:51 -0800, Rajasekar Karthik > wrote: > > > Mark, > > > > You are right. I will just setup multiple central on different machine. > > After I am more comfortable with MOBY, I will try it. > > > > On 2/11/07, Mark Wilkinson wrote: > >> > >> As far as I know, nobody has ever tried this, so you are breaking new > >> ground (and as someone new to MOBY, that might not be the easiest thing > >> to > >> do :-) ) > >> > >> But the answer to your question is that you can only run one instance > of > >> MOBY Central per instance of the Apache server. You can run multiple > >> instances of Apache, each with their own config file, where each config > >> file points to a different mobycentral.config file. On the client side > >> (in Perl, I don't know about Java) you can create an instance of > >> MOBY::Client::Central that connects to two different MOBY Centrals by > >> name > >> (you create the name when you assign the URL during creation of the > >> object), and you have to specify the name of the MOBY Central you are > >> addressing when you make your MOBY Central call using the "Registry => > >> "somename"" parameter. > >> > >> Some MOBY::Client::Central calls don't allow you to address more than > >> one > >> registry. In particular, ones that involve registration of new > objects, > >> service types, or namespaces. That's because the ontologies are > assumed > >> to be canonical, and can only exist in one place - > >> mobycentral.icapture.ubc.ca - if you create your own registry and chose > >> to > >> run your own ontologies there is NO guarantee that you will continue to > >> be > >> interoperable with any other services in the world. > >> > >> Having said that, for other calls (like findService and > registerService) > >> you should be able to run as many registries as you wish. > >> > >> ... caveat emptor... I don't think anyone has EVER tried to do this, so > >> the code might not work... > >> > >> M > >> > >> > >> > >> > >> > >> On Sun, 11 Feb 2007 19:20:56 -0800, Rajasekar Karthik > >> wrote: > >> > >> > Hi, > >> > > >> > Is it possible to setup multiple local centrals on a same server? > With > >> > the > >> > databases, there can be multiple ones created. All the executables > >> like > >> > MOBY-Central.PL, OntologyServer.cgi....can be moved into two > >> directories > >> > of > >> > webserver cgi-bin folder. But, what about httpd.conf configuration > >> file > >> > in > >> > apache? How do I modify that? > >> > > >> > >> > >> > >> -- > >> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > >> > > > > > > > > > > -- > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From markw at illuminae.com Sun Feb 11 22:50:53 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 11 Feb 2007 19:50:53 -0800 Subject: [MOBY-l] Multiple Centrals on Same server In-Reply-To: References: Message-ID: Super - sorry for muddying the waters on your first day :-) Welcome to MOBY! I hope the rest of your time here is easier than today! M On Sun, 11 Feb 2007 19:46:57 -0800, Rajasekar Karthik wrote: > Hi Mark, > > Thanks for making it more clear. I misunderstood from the earlier mail. > > On 2/11/07, Mark Wilkinson wrote: >> >> Hi Karthik! >> >> Actually, I didn't express myself clearly. Running multiple MOBY >> Centrals >> on the same machine is fine - I know from personal experience that I can >> run up to three instances on the same server. It is the CLIENT >> libraries >> that I am not sure about. I have never tried "in the real world" to use >> the Perl client libraries to talk to more than one instance of MOBY at >> the >> same time. I wrote them such that they SHOULD be able to do this, but I >> have never thoroughly tested this functionality, so I am not certain >> that >> it will work for you. >> >> I can assure you, however, that running multiple instances of teh >> registry >> on the same machine in different instances of Apache works just fine :-) >> >> M >> >> >> >> >> On Sun, 11 Feb 2007 19:35:51 -0800, Rajasekar Karthik >> wrote: >> >> > Mark, >> > >> > You are right. I will just setup multiple central on different >> machine. >> > After I am more comfortable with MOBY, I will try it. >> > >> > On 2/11/07, Mark Wilkinson wrote: >> >> >> >> As far as I know, nobody has ever tried this, so you are breaking new >> >> ground (and as someone new to MOBY, that might not be the easiest >> thing >> >> to >> >> do :-) ) >> >> >> >> But the answer to your question is that you can only run one instance >> of >> >> MOBY Central per instance of the Apache server. You can run multiple >> >> instances of Apache, each with their own config file, where each >> config >> >> file points to a different mobycentral.config file. On the client >> side >> >> (in Perl, I don't know about Java) you can create an instance of >> >> MOBY::Client::Central that connects to two different MOBY Centrals by >> >> name >> >> (you create the name when you assign the URL during creation of the >> >> object), and you have to specify the name of the MOBY Central you are >> >> addressing when you make your MOBY Central call using the "Registry >> => >> >> "somename"" parameter. >> >> >> >> Some MOBY::Client::Central calls don't allow you to address more than >> >> one >> >> registry. In particular, ones that involve registration of new >> objects, >> >> service types, or namespaces. That's because the ontologies are >> assumed >> >> to be canonical, and can only exist in one place - >> >> mobycentral.icapture.ubc.ca - if you create your own registry and >> chose >> >> to >> >> run your own ontologies there is NO guarantee that you will continue >> to >> >> be >> >> interoperable with any other services in the world. >> >> >> >> Having said that, for other calls (like findService and >> registerService) >> >> you should be able to run as many registries as you wish. >> >> >> >> ... caveat emptor... I don't think anyone has EVER tried to do this, >> so >> >> the code might not work... >> >> >> >> M >> >> >> >> >> >> >> >> >> >> >> >> On Sun, 11 Feb 2007 19:20:56 -0800, Rajasekar Karthik >> >> wrote: >> >> >> >> > Hi, >> >> > >> >> > Is it possible to setup multiple local centrals on a same server? >> With >> >> > the >> >> > databases, there can be multiple ones created. All the executables >> >> like >> >> > MOBY-Central.PL, OntologyServer.cgi....can be moved into two >> >> directories >> >> > of >> >> > webserver cgi-bin folder. But, what about httpd.conf configuration >> >> file >> >> > in >> >> > apache? How do I modify that? >> >> > >> >> >> >> >> >> >> >> -- >> >> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ >> >> >> > >> > >> > >> >> >> >> -- >> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ >> > > > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From karthik085 at gmail.com Sun Feb 11 22:55:36 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 22:55:36 -0500 Subject: [MOBY-l] Multiple Centrals on Same server In-Reply-To: References: Message-ID: Mark, You have been very helpful. Without your help, I couldn't have setup my local installation. Thank you very much. On 2/11/07, Mark Wilkinson wrote: > > Super - sorry for muddying the waters on your first day :-) > > Welcome to MOBY! I hope the rest of your time here is easier than today! > > M > > > > On Sun, 11 Feb 2007 19:46:57 -0800, Rajasekar Karthik > wrote: > > > Hi Mark, > > > > Thanks for making it more clear. I misunderstood from the earlier mail. > > > > On 2/11/07, Mark Wilkinson wrote: > >> > >> Hi Karthik! > >> > >> Actually, I didn't express myself clearly. Running multiple MOBY > >> Centrals > >> on the same machine is fine - I know from personal experience that I > can > >> run up to three instances on the same server. It is the CLIENT > >> libraries > >> that I am not sure about. I have never tried "in the real world" to > use > >> the Perl client libraries to talk to more than one instance of MOBY at > >> the > >> same time. I wrote them such that they SHOULD be able to do this, but > I > >> have never thoroughly tested this functionality, so I am not certain > >> that > >> it will work for you. > >> > >> I can assure you, however, that running multiple instances of teh > >> registry > >> on the same machine in different instances of Apache works just fine > :-) > >> > >> M > >> > >> > >> > >> > >> On Sun, 11 Feb 2007 19:35:51 -0800, Rajasekar Karthik > >> wrote: > >> > >> > Mark, > >> > > >> > You are right. I will just setup multiple central on different > >> machine. > >> > After I am more comfortable with MOBY, I will try it. > >> > > >> > On 2/11/07, Mark Wilkinson wrote: > >> >> > >> >> As far as I know, nobody has ever tried this, so you are breaking > new > >> >> ground (and as someone new to MOBY, that might not be the easiest > >> thing > >> >> to > >> >> do :-) ) > >> >> > >> >> But the answer to your question is that you can only run one > instance > >> of > >> >> MOBY Central per instance of the Apache server. You can run > multiple > >> >> instances of Apache, each with their own config file, where each > >> config > >> >> file points to a different mobycentral.config file. On the client > >> side > >> >> (in Perl, I don't know about Java) you can create an instance of > >> >> MOBY::Client::Central that connects to two different MOBY Centrals > by > >> >> name > >> >> (you create the name when you assign the URL during creation of the > >> >> object), and you have to specify the name of the MOBY Central you > are > >> >> addressing when you make your MOBY Central call using the "Registry > >> => > >> >> "somename"" parameter. > >> >> > >> >> Some MOBY::Client::Central calls don't allow you to address more > than > >> >> one > >> >> registry. In particular, ones that involve registration of new > >> objects, > >> >> service types, or namespaces. That's because the ontologies are > >> assumed > >> >> to be canonical, and can only exist in one place - > >> >> mobycentral.icapture.ubc.ca - if you create your own registry and > >> chose > >> >> to > >> >> run your own ontologies there is NO guarantee that you will continue > >> to > >> >> be > >> >> interoperable with any other services in the world. > >> >> > >> >> Having said that, for other calls (like findService and > >> registerService) > >> >> you should be able to run as many registries as you wish. > >> >> > >> >> ... caveat emptor... I don't think anyone has EVER tried to do this, > >> so > >> >> the code might not work... > >> >> > >> >> M > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> On Sun, 11 Feb 2007 19:20:56 -0800, Rajasekar Karthik > >> >> wrote: > >> >> > >> >> > Hi, > >> >> > > >> >> > Is it possible to setup multiple local centrals on a same server? > >> With > >> >> > the > >> >> > databases, there can be multiple ones created. All the executables > >> >> like > >> >> > MOBY-Central.PL, OntologyServer.cgi....can be moved into two > >> >> directories > >> >> > of > >> >> > webserver cgi-bin folder. But, what about httpd.conf configuration > >> >> file > >> >> > in > >> >> > apache? How do I modify that? > >> >> > > >> >> > >> >> > >> >> > >> >> -- > >> >> Using Opera's revolutionary e-mail client: > http://www.opera.com/mail/ > >> >> > >> > > >> > > >> > > >> > >> > >> > >> -- > >> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > >> > > > > > > > > > > -- > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From karthik085 at gmail.com Sun Feb 11 22:57:25 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 22:57:25 -0500 Subject: [MOBY-l] OntologyServer synchronization Message-ID: Hi, Currently, I have OntologyServer setup locally. How can I synchronize this with the main OntologyServer? Do I just download new version of OntologyServer.cgi? Is it possible to have MOBY setup locally, MOBY_SERVER and MOBY_URI pointing to localhost and MOBY_ONTOLOGYSERVER pointing to mobycentral.icapture.ubc.ca? -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From markw at illuminae.com Sun Feb 11 22:59:10 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 11 Feb 2007 19:59:10 -0800 Subject: [MOBY-l] Multiple Centrals on Same server In-Reply-To: References: Message-ID: My pleasure! I hope you find that Moby does what you need it to do! The mailing list is very welcoming and very helpful, so please continue to post your questions there and somone will always be around to help :-) Mark On Sun, 11 Feb 2007 19:55:36 -0800, Rajasekar Karthik wrote: > Mark, > > You have been very helpful. Without your help, I couldn't have setup my > local installation. Thank you very much. > > On 2/11/07, Mark Wilkinson wrote: >> >> Super - sorry for muddying the waters on your first day :-) >> >> Welcome to MOBY! I hope the rest of your time here is easier than >> today! >> >> M >> >> >> >> On Sun, 11 Feb 2007 19:46:57 -0800, Rajasekar Karthik >> wrote: >> >> > Hi Mark, >> > >> > Thanks for making it more clear. I misunderstood from the earlier >> mail. >> > >> > On 2/11/07, Mark Wilkinson wrote: >> >> >> >> Hi Karthik! >> >> >> >> Actually, I didn't express myself clearly. Running multiple MOBY >> >> Centrals >> >> on the same machine is fine - I know from personal experience that I >> can >> >> run up to three instances on the same server. It is the CLIENT >> >> libraries >> >> that I am not sure about. I have never tried "in the real world" to >> use >> >> the Perl client libraries to talk to more than one instance of MOBY >> at >> >> the >> >> same time. I wrote them such that they SHOULD be able to do this, >> but >> I >> >> have never thoroughly tested this functionality, so I am not certain >> >> that >> >> it will work for you. >> >> >> >> I can assure you, however, that running multiple instances of teh >> >> registry >> >> on the same machine in different instances of Apache works just fine >> :-) >> >> >> >> M >> >> >> >> >> >> >> >> >> >> On Sun, 11 Feb 2007 19:35:51 -0800, Rajasekar Karthik >> >> wrote: >> >> >> >> > Mark, >> >> > >> >> > You are right. I will just setup multiple central on different >> >> machine. >> >> > After I am more comfortable with MOBY, I will try it. >> >> > >> >> > On 2/11/07, Mark Wilkinson wrote: >> >> >> >> >> >> As far as I know, nobody has ever tried this, so you are breaking >> new >> >> >> ground (and as someone new to MOBY, that might not be the easiest >> >> thing >> >> >> to >> >> >> do :-) ) >> >> >> >> >> >> But the answer to your question is that you can only run one >> instance >> >> of >> >> >> MOBY Central per instance of the Apache server. You can run >> multiple >> >> >> instances of Apache, each with their own config file, where each >> >> config >> >> >> file points to a different mobycentral.config file. On the client >> >> side >> >> >> (in Perl, I don't know about Java) you can create an instance of >> >> >> MOBY::Client::Central that connects to two different MOBY Centrals >> by >> >> >> name >> >> >> (you create the name when you assign the URL during creation of >> the >> >> >> object), and you have to specify the name of the MOBY Central you >> are >> >> >> addressing when you make your MOBY Central call using the >> "Registry >> >> => >> >> >> "somename"" parameter. >> >> >> >> >> >> Some MOBY::Client::Central calls don't allow you to address more >> than >> >> >> one >> >> >> registry. In particular, ones that involve registration of new >> >> objects, >> >> >> service types, or namespaces. That's because the ontologies are >> >> assumed >> >> >> to be canonical, and can only exist in one place - >> >> >> mobycentral.icapture.ubc.ca - if you create your own registry and >> >> chose >> >> >> to >> >> >> run your own ontologies there is NO guarantee that you will >> continue >> >> to >> >> >> be >> >> >> interoperable with any other services in the world. >> >> >> >> >> >> Having said that, for other calls (like findService and >> >> registerService) >> >> >> you should be able to run as many registries as you wish. >> >> >> >> >> >> ... caveat emptor... I don't think anyone has EVER tried to do >> this, >> >> so >> >> >> the code might not work... >> >> >> >> >> >> M >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Sun, 11 Feb 2007 19:20:56 -0800, Rajasekar Karthik >> >> >> wrote: >> >> >> >> >> >> > Hi, >> >> >> > >> >> >> > Is it possible to setup multiple local centrals on a same >> server? >> >> With >> >> >> > the >> >> >> > databases, there can be multiple ones created. All the >> executables >> >> >> like >> >> >> > MOBY-Central.PL, OntologyServer.cgi....can be moved into two >> >> >> directories >> >> >> > of >> >> >> > webserver cgi-bin folder. But, what about httpd.conf >> configuration >> >> >> file >> >> >> > in >> >> >> > apache? How do I modify that? >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Using Opera's revolutionary e-mail client: >> http://www.opera.com/mail/ >> >> >> >> >> > >> >> > >> >> > >> >> >> >> >> >> >> >> -- >> >> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ >> >> >> > >> > >> > >> >> >> >> -- >> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ >> > > > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From karthik085 at gmail.com Sun Feb 11 23:06:45 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Sun, 11 Feb 2007 23:06:45 -0500 Subject: [MOBY-l] Multiple Centrals on Same server In-Reply-To: References: Message-ID: Mark, So far, I like it. I heard the moby user community is increasing - making it popular. I will try to help too. This week, I am going to try creating .deb packages from the source and see if I can get it just working by just copying the same to a new machine and a script to configure the necessary files. I will post the same here or create a debian/ubuntu repository on my machine. On 2/11/07, Mark Wilkinson wrote: > > My pleasure! I hope you find that Moby does what you need it to do! The > mailing list is very welcoming and very helpful, so please continue to > post your questions there and somone will always be around to help :-) > > Mark > > > > On Sun, 11 Feb 2007 19:55:36 -0800, Rajasekar Karthik > wrote: > > > Mark, > > > > You have been very helpful. Without your help, I couldn't have setup my > > local installation. Thank you very much. > > > > On 2/11/07, Mark Wilkinson wrote: > >> > >> Super - sorry for muddying the waters on your first day :-) > >> > >> Welcome to MOBY! I hope the rest of your time here is easier than > >> today! > >> > >> M > >> > >> > >> > >> On Sun, 11 Feb 2007 19:46:57 -0800, Rajasekar Karthik > >> wrote: > >> > >> > Hi Mark, > >> > > >> > Thanks for making it more clear. I misunderstood from the earlier > >> mail. > >> > > >> > On 2/11/07, Mark Wilkinson wrote: > >> >> > >> >> Hi Karthik! > >> >> > >> >> Actually, I didn't express myself clearly. Running multiple MOBY > >> >> Centrals > >> >> on the same machine is fine - I know from personal experience that I > >> can > >> >> run up to three instances on the same server. It is the CLIENT > >> >> libraries > >> >> that I am not sure about. I have never tried "in the real world" to > >> use > >> >> the Perl client libraries to talk to more than one instance of MOBY > >> at > >> >> the > >> >> same time. I wrote them such that they SHOULD be able to do this, > >> but > >> I > >> >> have never thoroughly tested this functionality, so I am not certain > >> >> that > >> >> it will work for you. > >> >> > >> >> I can assure you, however, that running multiple instances of teh > >> >> registry > >> >> on the same machine in different instances of Apache works just fine > >> :-) > >> >> > >> >> M > >> >> > >> >> > >> >> > >> >> > >> >> On Sun, 11 Feb 2007 19:35:51 -0800, Rajasekar Karthik > >> >> wrote: > >> >> > >> >> > Mark, > >> >> > > >> >> > You are right. I will just setup multiple central on different > >> >> machine. > >> >> > After I am more comfortable with MOBY, I will try it. > >> >> > > >> >> > On 2/11/07, Mark Wilkinson wrote: > >> >> >> > >> >> >> As far as I know, nobody has ever tried this, so you are breaking > >> new > >> >> >> ground (and as someone new to MOBY, that might not be the easiest > >> >> thing > >> >> >> to > >> >> >> do :-) ) > >> >> >> > >> >> >> But the answer to your question is that you can only run one > >> instance > >> >> of > >> >> >> MOBY Central per instance of the Apache server. You can run > >> multiple > >> >> >> instances of Apache, each with their own config file, where each > >> >> config > >> >> >> file points to a different mobycentral.config file. On the > client > >> >> side > >> >> >> (in Perl, I don't know about Java) you can create an instance of > >> >> >> MOBY::Client::Central that connects to two different MOBY > Centrals > >> by > >> >> >> name > >> >> >> (you create the name when you assign the URL during creation of > >> the > >> >> >> object), and you have to specify the name of the MOBY Central you > >> are > >> >> >> addressing when you make your MOBY Central call using the > >> "Registry > >> >> => > >> >> >> "somename"" parameter. > >> >> >> > >> >> >> Some MOBY::Client::Central calls don't allow you to address more > >> than > >> >> >> one > >> >> >> registry. In particular, ones that involve registration of new > >> >> objects, > >> >> >> service types, or namespaces. That's because the ontologies are > >> >> assumed > >> >> >> to be canonical, and can only exist in one place - > >> >> >> mobycentral.icapture.ubc.ca - if you create your own registry and > >> >> chose > >> >> >> to > >> >> >> run your own ontologies there is NO guarantee that you will > >> continue > >> >> to > >> >> >> be > >> >> >> interoperable with any other services in the world. > >> >> >> > >> >> >> Having said that, for other calls (like findService and > >> >> registerService) > >> >> >> you should be able to run as many registries as you wish. > >> >> >> > >> >> >> ... caveat emptor... I don't think anyone has EVER tried to do > >> this, > >> >> so > >> >> >> the code might not work... > >> >> >> > >> >> >> M > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> On Sun, 11 Feb 2007 19:20:56 -0800, Rajasekar Karthik > >> >> >> wrote: > >> >> >> > >> >> >> > Hi, > >> >> >> > > >> >> >> > Is it possible to setup multiple local centrals on a same > >> server? > >> >> With > >> >> >> > the > >> >> >> > databases, there can be multiple ones created. All the > >> executables > >> >> >> like > >> >> >> > MOBY-Central.PL, OntologyServer.cgi....can be moved into two > >> >> >> directories > >> >> >> > of > >> >> >> > webserver cgi-bin folder. But, what about httpd.conf > >> configuration > >> >> >> file > >> >> >> > in > >> >> >> > apache? How do I modify that? > >> >> >> > > >> >> >> > >> >> >> > >> >> >> > >> >> >> -- > >> >> >> Using Opera's revolutionary e-mail client: > >> http://www.opera.com/mail/ > >> >> >> > >> >> > > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> >> -- > >> >> Using Opera's revolutionary e-mail client: > http://www.opera.com/mail/ > >> >> > >> > > >> > > >> > > >> > >> > >> > >> -- > >> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > >> > > > > > > > > > > -- > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ > -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From karthik085 at gmail.com Fri Feb 16 11:19:12 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Fri, 16 Feb 2007 11:19:12 -0500 Subject: [MOBY-l] Registration and CVS Message-ID: Hi, I like dashboard. It is good - lets me register/deregister, browse...lot of other functionalities. But, there are few problems I am facing: 1. Update registration: Once I register an object/service..., how can I update it? Currently once I register, if I have to unregister and re-register back. Is there an easy way to do this? 2. Roll-back to previous version: Let's say I register/unregister/re-register an object N times. I want to use an earlier version, say, 2nd one. How can I discard the current one and use the one I wanted? I understand dashboard doesn't let you do this. But, are there other ways...tie dashboard with cvs or something like that. I have all my versions of objects stored as XML in cvs. Are there any other clients that lets me do this beside dashboard? -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From martin.senger at gmail.com Fri Feb 16 11:38:12 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 16 Feb 2007 16:38:12 +0000 Subject: [MOBY-l] Registration and CVS In-Reply-To: References: Message-ID: <4d93f07c0702160838x4a2df648j5cfab0e07a4cb6f6@mail.gmail.com> Hi, 1. Update registration: Once I register an object/service..., how can I > update it? You cannot - the BioMoby API does not allow it. You have to unregister and register again. Dashboard, however, helps you to do it: 1) Let display all service info in the 'service registration' panel (by checking 'Fill new service when selected in browser panel' and selecting a service you are interested in). 2) Unregister (by clicking a button). 3) Make changes in the srevice description. 4) Register again (by clicking another button). The procedure is slightly more complex if you are using Signature RDF (you need to call the RDF agent (there is a button for it) after you manually remove your RDF file...). 2. Roll-back to previous version Rolling back does not exist in the BioMoby API. Sorry... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From karthik085 at gmail.com Fri Feb 16 14:35:54 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Fri, 16 Feb 2007 14:35:54 -0500 Subject: [MOBY-l] Registration and CVS In-Reply-To: <4d93f07c0702160838x4a2df648j5cfab0e07a4cb6f6@mail.gmail.com> References: <4d93f07c0702160838x4a2df648j5cfab0e07a4cb6f6@mail.gmail.com> Message-ID: On 2/16/07, Martin Senger wrote: > > Hi, > > 1. Update registration: Once I register an object/service..., how can I > > update it? > > > You cannot - the BioMoby API does not allow it. You have to unregister and > register again. Dashboard, however, helps you to do it: > > 1) Let display all service info in the 'service registration' panel (by > checking 'Fill new service when selected in browser panel' and selecting a > service you are interested in). > > 2) Unregister (by clicking a button). > > 3) Make changes in the srevice description. > > 4) Register again (by clicking another button). > That's what I have been doing till now. Since our XML is changing all the time, including for the base objects, it is time-consuming task to unregister and re-register the base objects and all the dependents on it. As I am experimenting with local central, I can always run SQL queries against mobyobject database. But, for a biologist in our team, the above using dashboard might be a painful task. The procedure is slightly more complex if you are using Signature RDF (you > need to call the RDF agent (there is a button for it) after you manually > remove your RDF file...). > > 2. Roll-back to previous version > > > Rolling back does not exist in the BioMoby API. Sorry... > > Cheers, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From karthik085 at gmail.com Fri Feb 16 14:59:23 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Fri, 16 Feb 2007 14:59:23 -0500 Subject: [MOBY-l] Registration and CVS In-Reply-To: <009f01c75204$04aad5c0$6900a8c0@notebook> References: <005e01c751e6$e374a970$6900a8c0@notebook> <009701c75202$21a2fb50$6900a8c0@notebook> <009f01c75204$04aad5c0$6900a8c0@notebook> Message-ID: Thanks, that's what I am planning to do. I might just create a simple gui that does this. If you have any advice how I can integrate this with dashboard, let me know. I am going to look at dashboard for developers page. On 2/16/07, Edward Kawas wrote: > > Oh. I didn't understand before, but now its more clear. My only advice to > you would be then to create a gui that does the whole update process as an > atomic process. > > > > Sorry that I cant be of more help. > > > > Eddie > > > ------------------------------ > > *From:* Rajasekar Karthik [mailto:karthik085 at gmail.com] > *Sent:* Friday, February 16, 2007 11:47 AM > *To:* Edward Kawas > *Subject:* Re: [MOBY-l] Registration and CVS > > > > Eddie, > > Our team has not finalized XML schema for the object/services. So, it > keeps getting changing often - new attributes gets added or existing ones > are removed/changed. Since even the very base ones are not finalized, all > the dependents on it needs to be re-registered, if I have to change the base > ones. > > On 2/16/07, *Edward Kawas* wrote: > > Why would your XML change all the time? > > > > Eddie > > > ------------------------------ > > *From:* Rajasekar Karthik [mailto:karthik085 at gmail.com] > *Sent:* Friday, February 16, 2007 11:38 AM > *To:* Edward Kawas > *Subject:* Re: [MOBY-l] Registration and CVS > > > > Hi, > > I am facing that problem.....Since our XML is changing all the time, > including for the base objects, it is time-consuming task to unregister and > re-register the base objects and all the dependents on it. > > On 2/16/07, *Edward Kawas* wrote: > > Hi, > > Updating will require a register/deregister command, since the MOBY api > doesn't have an update command. Note that you could create a client that > had > an 'update' method that did all the work for you. Dashboard doesn't do > this. > Also, you have to be careful, because as soon as a service provider has > referred to a specific datatype, that datatype cannot be removed from the > ontology until the service is removed. > > As far as I know, there are no other clients that behave like dashboard. > > Eddie > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Rajasekar Karthik > Sent: Friday, February 16, 2007 8:19 AM > To: moby-l at biomoby.org > Subject: [MOBY-l] Registration and CVS > > Hi, > > I like dashboard. It is good - lets me register/deregister, browse...lot > of > other functionalities. But, there are few problems I am facing: > 1. Update registration: Once I register an object/service..., how can I > update it? Currently once I register, if I have to unregister and > re-register back. Is there an easy way to do this? > 2. Roll-back to previous version: Let's say I > register/unregister/re-register an object N times. I want to use an > earlier > version, say, 2nd one. How can I discard the current one and use the one I > wanted? I understand dashboard doesn't let you do this. But, are there > other > ways...tie dashboard with cvs or something like that. I have all my > versions > of objects stored as XML in cvs. > > Are there any other clients that lets me do this beside dashboard? > > -- > Best Regards, > Rajasekar Karthik > karthik085 at gmail.com > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > > > > > -- > Best Regards, > Rajasekar Karthik > karthik085 at gmail.com > > > > > -- > Best Regards, > Rajasekar Karthik > karthik085 at gmail.com > -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From paolo.romano at istge.it Mon Feb 19 08:01:26 2007 From: paolo.romano at istge.it (Paolo Romano) Date: Mon, 19 Feb 2007 14:01:26 +0100 Subject: [MOBY-l] Final Call for Papers NETTAB 2007 Message-ID: <7.0.1.0.0.20070219140119.01dd3870@istge.it> ================================= Apologies, if you're receiving multiple copies ================================= Final Call for Papers 7th International Workshop NETTAB 2007 June 12-15, 2006 Department of Computer Science, University of Pisa, Pisa http://www.nettab.org/2007/ FOCUS THEME A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications ADJUNCT THEMES Algorithms in bioinformatics Formal Methods for Systems Biology Network Tools and Applications in Bioinformatics AIMS This workshop aims at getting together biologists, bioinformaticians, computer scientists and linguists to try to answer the following questions: - Is the Semantic Web of some use for Bioinformatics? - Which goals should have a Semantic Web for Bioinformatics? - Which standards, technologies and tools of the Semantic Web can most profitably be used in Bioinformatics? - Which application did the Semantic Web already find in Bioinformatics? - Which current Bioinformatics research problems can be solved by the Semantic Web? - Which are the short, medium and long term perspectives in applying Semantic Web technologies to Bionformatics? The workshop also intends to: - introduce the basic knowledge of related standards and technologies, in a non trivial way through invited lectures and tutorials - outline the promising features of the Semantic Web in bioinformatics through invited lectures and open discussion - show some valuable examples in bioinformatics through invited lectures, oral communications and posters - support as much discussion as possible through open discussions and a panel discussion - practically demonstrate "how it works" through tutorials INVITED SPEAKERS We are extremely glad to inform you that four excellent speakers have accepted to give an invited lecture at next NETTAB workshop. + Session on Goals of the Semantic Web in Bioinformatics Invited speaker: Eric Neumann, Co-chair of the Health Care and Life Science Interest Group of the Semantic Web Activity at W3C & Teranode Inc., USA + Session on Semantic Web Standards and Technologies Invited speaker: Guus Schreiber, Chair of Semantic Web Deployment Interest Group at W3C & University of Amsterdam, The Netherlands + Session on Semantic Web Tools Invited speaker: Olivier Bodenreider, Medical Ontology Research, National Library of Medicine, USA + Session on Applications of Semantic Web in Bioinformatics Invited speakers: Michael Schroeder, Biotec TU Dresden, Germany, and Albert Burger, Heriot-Watt University, Scotland, UK Titles of the lectures will soon be announced. TOPICS NETTAB workshops also include general sessions on Network Tools and Applications in Biology and adjunct focus topics selected by local organizers. You are therefore welcome to submit your work on any of the followings topics: Goals of a Semantic Web for Bioinformatics: Standards, Technologies, Tools for the Semantic Web Systems for a Semantic Web for Bioinformatics: Existing and perspective applications of the Semantic Web for Bioinformatics Algorithms in Bioinformatics Formal Methods for Systems Biology Network Tools and Applications in Bioinformatics DEADLINES Submission of oral communications: March 16, 2007 Proposals for tutorials: March 16, 2007 Submission of posters: April 20, 2007 Early Registration Deadline: April 27, 2007 SUBMISSION OF CONTRIBUTIONS You are welcome to submit your contributions through the MyReview system at the following URL: http://www.nettab.org/2007/myreview/ . This is a two steps submission procedure. You will have to submit first an abstract and later the paper. You are invited to prepare your contribution according to instructions available at http://www.biomedcentral.com/bmcbioinformatics/ifora/ (specially, see "Preparing main manuscript text" section). See the workshop's web site for more details about the preparation of the papers. PUBLICATION OF PAPERS AND POSTERS All accepted oral communications and posters will be published in the Workshop's Proceedings that will be distributed to all participants. Selected papers will be published by BMC Bioinformatics as a Supplement Issue. When submitting, you will be asked if your submission is intended for the workshop only or for the publication in BMC Bioinformatics too. The papers will be reviewed by the members of the Programme Committee. They will decide whether the papers are accepted for the workshop only or for the publication in BMC Bioinformatics as well. The workshop will engage itself to pay part of the cost of the publication, but please be advised that depending on the final budget of the workshop you could be requested to contribute to publication costs which has been set to 600 British pounds per paper. For any further information or clarification, please contact the organization by email at info at nettab.org . CHAIRS P. Romano, Bioinformatics, Natl Cancer Research Inst., Italy M. Schr?der, Biotechnology Centre, TU Dresden, Germany N. Cannata, Mathematics & Computer Science Dept, Univ. of Camerino, Italy O. Signore, ISTI, National Research Council, Italy PROGRAMME COMMITTEE G. Armano, Electrical and Electronic Engineering Dept, Univ. of Cagliari, IT C. Baker, Institute for Infocomm Research (I2R), SG P. Barahona, Department of Informatics, New University of Lisboa, PT L. Barrio-Alvers, Transinsight GmbH, DE O. Bodenreider, National Library of Medicine, USA A. Burger, Department of Computer Science, Heriot-Watt University, UK M. Cannataro, Experimental and Clinical Medicine Dept, Univ. of Catanzaro "Magna Graecia", IT W. Ceusters, Bioinformatics and Life Sciences, University at Buffalo, USA M. Cockerill, BioMed Central, UK M.-D. Devignes, LORIA, Vandoeuvre les Nancy, FR R. Dieng, INRIA, Sophia Antipolis, FR L. Grivell, European Molecular Biology Organisation, DE M. Harris, European Bioinformatics Institute, UK M. Helmer-Citterich, Biology Dept, University of Rome "Tor Vergata", IT C. M. Keet, Computer Science Faculty, Free University of Bozen-Bolzano, IT J. Koehler, Biomathematics and Bioinformatics, Rothamsted Research, UK M. Krallinger, Spanish National Cancer Research Center (CNIO), ES L. Krippahl, Department of Informatics, New University of Lisboa, PT P. Lambrix, Computer and Information Science Dept, Link?ping University, SE U. Leser, Institute for Computer Science, Humboldt-University of Berlin, DE J. Luciano, Department of Genetics, Harvard Medical School, USA R. Marangoni, Computer Science Department, University of Pisa, IT M. Marchiori, Pure and Applied Mathematics Dept, University of Padua, IT M. Masseroli, Department of BioEngineering, Polytechnic of Milan, IT G. Mauri, Informatics Systems and Communication Dept, Univ. Milan "Bicocca", IT E. Merelli, Mathematics and Computer Science Dept, University of Camerino, IT S. Moeller, Institute of Neuro- and Bioinformatics, University of L?beck, DE S. Philippi, Institute for Software Technology, Univ. of Koblenz-Landau, DE D. Quann, IBM Software Group, USA D. Rubin, Stanford Medical Informatics, Stanford University Medical Center, USA S.-A. Sansone, European Bioinformatics Institute, UK M. Senger, International Rice Research Institute, PH D. Turi, School of Computer Science, University of Manchester, UK G. Vetere, IBM Center for Advanced Studies of Rome, IT D. Zaccagnini, Language and Computing, USA Looking forward to seeing you all in Tuscany. Best regards. On behalf of the Chairs and of the Organizing Committee Paolo Romano Paolo Romano (paolo.romano at istge.it) Bioinformatics and Structural Proteomics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 From chris at bioteam.net Thu Feb 22 13:35:09 2007 From: chris at bioteam.net (Chris Dagdigian) Date: Thu, 22 Feb 2007 13:35:09 -0500 Subject: [MOBY-l] I need a primer on how moby uses DNS Message-ID: Hi folks, portal.open-bio.org crashed today right around the time our intrusion detection / firewall was reporting a massive "UDP Flood Attack" against the server. Looking at the actual logs, all the UDP traffic is originating from port 53 on the remote IP addresses which is the standard port that DNS queries go over. Since all OBF DNS except for biomoby.org is outsourced to a third party provider I'm wondering if our security tools are interpreting some MOBY type action or service lookup as "UDP flood". I'm looking for reasons/explanations as to why remote DNS servers would be hammering us with UDP traffic. Any info on how MOBY clients or services may be using DNS would be appreciated so I can see if there is a correlation. Thanks! Regards, Chris open-bio.org From robert.stevens at manchester.ac.uk Thu Feb 22 11:28:17 2007 From: robert.stevens at manchester.ac.uk (Robert Stevens) Date: Thu, 22 Feb 2007 16:28:17 +0000 Subject: [MOBY-l] Tenth bio-Ontologies Meeting; ISMB 2007 Message-ID: <6.2.5.6.2.20070222162809.03a643b0@manchester.ac.uk> ** Apologies for cross posting ** CALL FOR PAPERS and POSTER ABSTRACTS *^**^***^****^****^****^****^****^****^****^****^****^****^***^**^* Bio-Ontologies Meting Vienna, Austria: July 19th 2007 "Bio-Ontologies: ten years past and looking to the future" *^**^***^****^****^***^**^* 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria: July 18-25, 2007 *^**^***^****^****^****^****^****^****^****^****^****^****^****^****^****^***^**^* CALL FOR PAPERS and POSTER ABSTRACTS The long-standing ISMB Bio-Ontologies SIG is in its tenth consecutive year. This year the workshop will have a celebratory and reflective discussion on "Bio-Ontologies: ten years past and looking to the future". Program chairs: Robert Stevens (1), Phillip Lord (2), Robin McEntire (3), Susanna-Assunta Sansone (4) Websites: Bio-Ontologies SIG workshop http://bio-ontologies.org.uk ISMB/ECCB main conference website http://www.iscb.org/ismbeccb2007/ About the Bio-Ontologies SIG Meeting The meeting will continue to offer an informal environment for presentation and discussion of ontologies and their role in providing a mechanism for describing biology as well as organising, sharing and reconciling data. This year, to celebrate its tenth anniversary, we have invited four presenters from the first bio-ontologies tutorial and meeting organisers to sit on a panel, namely: Mark Musen Peter Karp Russ Altman Steffen Schulze-Kremer They will be asked to present positions on the following questions: List of 4 items 1.What has been the best thing to have happened in bio-ontologies in the past ten years? 2.What has been the worst thing to have happened in bio-ontologies in the past ten years? 3.How must bio-ontologies progress in the next ten years? 4.How must bio-ontologies not progress in the next ten years list end Call for papers and poster abstract: We are inviting two types of submissions: SHORT PAPER papers (up to 4 pages) and POSTER ABSTRACT (up to 1/2 page) from any aspect doing bio-ontology research or using bio-ontologies to do bioinformatics research. Topics include, but are not restricted to: *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 *The implications of Bio-Ontologies or the Semantic Web for the drug discovery process * Current Research In Ontology Languages and its implication for Bio-Ontologies DETAILS AND DEADLINE FOR SUBMISSIONS: May 1st, 2007 Full submission details will be soon available at http://bio-ontologies.org.uk/submissions.php From simont at hmgc.mcw.edu Mon Feb 26 15:21:46 2007 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Mon, 26 Feb 2007 14:21:46 -0600 Subject: [MOBY-l] Nature Rev. Genetics paper on dynamic software infrastructures Message-ID: <8702AF42-B513-4300-A1B9-58E33ADD974A@hmgc.mcw.edu> I came across this today via another mailing list and thought it would be of interest to those who can get at it... http://www.nature.com/nrg/journal/v8/n3/abs/nrg2048.html "Abstract | Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate mechanisms to support variation are currently lacking. We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that ?systems biologists really want to have?. Mentions MOBY and other things but I havent had a chance to read it all as yet. Simo. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw