From karthik085 at gmail.com Tue May 1 10:16:09 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Tue, 1 May 2007 10:16:09 -0400 Subject: [MOBY-l] REST Service registration Message-ID: Hi, I am trying to register a new service. In Service Endpoint - URL, I want to store the URL to REST service. URL is something like: http://site.com/Service?Parameter1=Value1 Site: site.com Service: Service Parameter1: parameter/name Value1: value for the parameter1 eg: http://mysite.com/Analysis?Name=phob http://mysite.com/Analysis?Name=lac In order to register the service, I have to input: - in the Service Endpoint - URL: http://mysite.com/Analysis? - in the input data, add a) Name (String) Is this right? If not, how can I register the service? -- Best Regards, Rajasekar Karthik karthik085 at gmail.com From edward.kawas at gmail.com Tue May 1 10:23:28 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 1 May 2007 07:23:28 -0700 Subject: [MOBY-l] REST Service registration In-Reply-To: References: Message-ID: <001401c78bfc$4a1de0c0$6800a8c0@notebook> Hi, That wouldn't be right (w.r.t. to moby). Personally, I think that you will have to wrap this REST service in a moby service. So, you would create a web service that takes a string name as input. This web service would then pass on the string to http://site.com/Service?Parameter1=INPUT_STRING, obtain a result and send it back to the caller of the moby service. The reason that I think that you are incorrect, is because moby has a predefined message structure that you will have follow to be compatible. Hope this makes sense! 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: Tuesday, May 01, 2007 7:16 AM > To: moby-l at biomoby.org > Subject: [MOBY-l] REST Service registration > > Hi, > > I am trying to register a new service. In Service Endpoint - URL, I want > to > store the URL to REST service. > > URL is something like: > http://site.com/Service?Parameter1=Value1 > > Site: site.com > Service: Service > Parameter1: parameter/name > Value1: value for the parameter1 > > eg: > http://mysite.com/Analysis?Name=phob > http://mysite.com/Analysis?Name=lac > > In order to register the service, I have to input: > - in the Service Endpoint - URL: http://mysite.com/Analysis? > - in the input data, add > a) Name (String) > > Is this right? If not, how can I register the service? > > -- > 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 From karthik085 at gmail.com Tue May 1 10:36:24 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Tue, 1 May 2007 10:36:24 -0400 Subject: [MOBY-l] REST Service registration In-Reply-To: <001401c78bfc$4a1de0c0$6800a8c0@notebook> References: <001401c78bfc$4a1de0c0$6800a8c0@notebook> Message-ID: Eddie, On 5/1/07, Edward Kawas wrote: > > Hi, > > That wouldn't be right (w.r.t. to moby). > > Personally, I think that you will have to wrap this REST service in a moby > service. This is what I am trying to do. Sorry, I should have explained it clearer. But, how do I do this? I already have a REST service that takes a string name as input. Can you explain in detail? So, you would create a web service that takes a string name as > input. > This web service would then pass on the string to > http://site.com/Service?Parameter1=INPUT_STRING, obtain a result and send > it > back to the caller of the moby service. > > The reason that I think that you are incorrect, is because moby has a > predefined message structure that you will have follow to be compatible. > > Hope this makes sense! > > 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: Tuesday, May 01, 2007 7:16 AM > > To: moby-l at biomoby.org > > Subject: [MOBY-l] REST Service registration > > > > Hi, > > > > I am trying to register a new service. In Service Endpoint - URL, I want > > to > > store the URL to REST service. > > > > URL is something like: > > http://site.com/Service?Parameter1=Value1 > > > > Site: site.com > > Service: Service > > Parameter1: parameter/name > > Value1: value for the parameter1 > > > > eg: > > http://mysite.com/Analysis?Name=phob > > http://mysite.com/Analysis?Name=lac > > > > In order to register the service, I have to input: > > - in the Service Endpoint - URL: http://mysite.com/Analysis? > > - in the input data, add > > a) Name (String) > > > > Is this right? If not, how can I register the service? > > > > -- > > 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 From gordonp at ucalgary.ca Tue May 1 10:21:59 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 01 May 2007 08:21:59 -0600 Subject: [MOBY-l] REST Service registration In-Reply-To: References: Message-ID: <46374D07.2000604@ucalgary.ca> Hi Rajasekar, I'm not sure what you're trying to do: MOBY is not a REST-based protocol. Can you give some more context for us? > Hi, > > I am trying to register a new service. In Service Endpoint - URL, I want to > store the URL to REST service. > > URL is something like: > http://site.com/Service?Parameter1=Value1 > > Site: site.com > Service: Service > Parameter1: parameter/name > Value1: value for the parameter1 > > eg: > http://mysite.com/Analysis?Name=phob > http://mysite.com/Analysis?Name=lac > > In order to register the service, I have to input: > - in the Service Endpoint - URL: http://mysite.com/Analysis? > - in the input data, add > a) Name (String) > > Is this right? If not, how can I register the service? > > From edward.kawas at gmail.com Tue May 1 10:44:46 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 1 May 2007 07:44:46 -0700 Subject: [MOBY-l] REST Service registration In-Reply-To: References: <001401c78bfc$4a1de0c0$6800a8c0@notebook> Message-ID: <001801c78bff$44981f50$6800a8c0@notebook> Are you planning on coding in perl or java? First, register the service using whatever method you wish (I use Dashboard). Second, create the code for the service; If you are using JAVA, http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ has information for you (under Developing jMoby services) If you are using Perl, http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/PerlMoses.html explains how to create the service. I would develop a hello world service that takes in a string and returns whatever you wish. Once you get that working, the rest would be trivial because all you would have to do instead of returning hello world is invoke your rest service and return the response. If you need further guidance, let me know. I am unsure of how much you know! Thanks, Eddie _____ From: Rajasekar Karthik [mailto:karthik085 at gmail.com] Sent: Tuesday, May 01, 2007 7:36 AM To: Edward Kawas Cc: moby-l at biomoby.org Subject: Re: [MOBY-l] REST Service registration Eddie, On 5/1/07, Edward Kawas wrote: Hi, That wouldn't be right (w.r.t. to moby). Personally, I think that you will have to wrap this REST service in a moby service. This is what I am trying to do. Sorry, I should have explained it clearer. But, how do I do this? I already have a REST service that takes a string name as input. Can you explain in detail? So, you would create a web service that takes a string name as input. This web service would then pass on the string to http://site.com/Service?Parameter1=INPUT_STRING, obtain a result and send it back to the caller of the moby service. The reason that I think that you are incorrect, is because moby has a predefined message structure that you will have follow to be compatible. Hope this makes sense! 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: Tuesday, May 01, 2007 7:16 AM > To: moby-l at biomoby.org > Subject: [MOBY-l] REST Service registration > > Hi, > > I am trying to register a new service. In Service Endpoint - URL, I want > to > store the URL to REST service. > > URL is something like: > http://site.com/Service?Parameter1=Value1 > > Site: site.com > Service: Service > Parameter1: parameter/name > Value1: value for the parameter1 > > eg: > http://mysite.com/Analysis?Name=phob > http://mysite.com/Analysis?Name=lac > > In order to register the service, I have to input: > - in the Service Endpoint - URL: http://mysite.com/Analysis? > - in the input data, add > a) Name (String) > > Is this right? If not, how can I register the service? > > -- > 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 From gordonp at ucalgary.ca Tue May 1 11:06:21 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 01 May 2007 09:06:21 -0600 Subject: [MOBY-l] REST Service registration In-Reply-To: <001801c78bff$44981f50$6800a8c0@notebook> References: <001401c78bfc$4a1de0c0$6800a8c0@notebook> <001801c78bff$44981f50$6800a8c0@notebook> Message-ID: <4637576D.6000506@ucalgary.ca> Or alternatively, you could use the MobyServlet framework http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/deployingServices.html In which case your code would be (I haven't compoiled this, but you get the point): import org.biomoby.shared.MobyDataType; import org.biomoby.shared.data.*; import org.biomoby.service.*; import java.io.*; // Annotation describing the service semantics @mobyService(name="YourServiceName", type="AppropriateServiceType", provider="auth.site.com", author="foo at site.com", in={"inputString:String"}, out={"outputHTML:text-html"}, description={"Executes service X by wrapping a REST session"}) public class YourClass extends MobyServlet{ public static final String BASE_URL = "http://site.com/Service?Parameter1="; public void processRequest(MobyDataJob request, MobyDataJob result) throws Exception{ // The input parameter matches that specified in the mobyService annotation above MobyDataString inputParam = (MobyDataString) request.get("inputString"); URL restURL = new URL(BASE_URL+inputParam); StringBuffer htmlBuffer = new StringBuffer(); LineNumberReader r = new LineNumberReader(new InputStreamReader(url.openStream())); for(String line = r.readLine(); line != null; line = r.readLine()){ htmlBuffer.append(line); } // Create the results (text-html matches mobyService annotation declaration) MobyDataComposite htmlObject = new MobyDataComposite(MobyDataType.getDataType("text-html"), null , null, htmlBuffer.toString()); // Set the result that will be passed back to the client (same name as in mobyService annotation above) result.put("outputHTML", htmlObject); } } > Are you planning on coding in perl or java? > > > > First, register the service using whatever method you wish (I use > Dashboard). > > > > Second, create the code for the service; > > > > If you are using JAVA, > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ has information > for you (under Developing jMoby services) > > > > If you are using Perl, > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/PerlMoses.html > explains how to create the service. > > > > I would develop a hello world service that takes in a string and returns > whatever you wish. Once you get that working, the rest would be trivial > because all you would have to do instead of returning hello world is invoke > your rest service and return the response. > > > > If you need further guidance, let me know. I am unsure of how much you know! > > > > Thanks, > > > > Eddie > > _____ > > From: Rajasekar Karthik [mailto:karthik085 at gmail.com] > Sent: Tuesday, May 01, 2007 7:36 AM > To: Edward Kawas > Cc: moby-l at biomoby.org > Subject: Re: [MOBY-l] REST Service registration > > > > Eddie, > > On 5/1/07, Edward Kawas wrote: > > Hi, > > That wouldn't be right (w.r.t. to moby). > > Personally, I think that you will have to wrap this REST service in a moby > service. > > > This is what I am trying to do. Sorry, I should have explained it clearer. > > But, how do I do this? I already have a REST service that takes a string > name as input. Can you explain in detail? > > > > So, you would create a web service that takes a string name as > input. > > This web service would then pass on the string to > http://site.com/Service?Parameter1=INPUT_STRING, obtain a result and send it > back to the caller of the moby service. > > The reason that I think that you are incorrect, is because moby has a > predefined message structure that you will have follow to be compatible. > > Hope this makes sense! > > 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: Tuesday, May 01, 2007 7:16 AM >> To: moby-l at biomoby.org >> Subject: [MOBY-l] REST Service registration >> >> Hi, >> >> I am trying to register a new service. In Service Endpoint - URL, I want >> to >> store the URL to REST service. >> >> URL is something like: >> http://site.com/Service?Parameter1=Value1 >> >> Site: site.com >> Service: Service >> Parameter1: parameter/name >> Value1: value for the parameter1 >> >> eg: >> http://mysite.com/Analysis?Name=phob >> http://mysite.com/Analysis?Name=lac >> >> In order to register the service, I have to input: >> - in the Service Endpoint - URL: http://mysite.com/Analysis? >> - in the input data, add >> a) Name (String) >> >> Is this right? If not, how can I register the service? >> >> -- >> 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 >> > > > > > From karthik085 at gmail.com Tue May 1 11:39:40 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Tue, 1 May 2007 11:39:40 -0400 Subject: [MOBY-l] REST Service registration In-Reply-To: <001801c78bff$44981f50$6800a8c0@notebook> References: <001401c78bfc$4a1de0c0$6800a8c0@notebook> <001801c78bff$44981f50$6800a8c0@notebook> Message-ID: Thanks Eddie. It makes sense now. I will try it today. On 5/1/07, Edward Kawas wrote: > > Are you planning on coding in perl or java? > > > > First, register the service using whatever method you wish (I use > Dashboard). > > > > Second, create the code for the service; > > > > If you are using JAVA, > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ has > information for you (under Developing jMoby services) > > > > If you are using Perl, > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/PerlMoses.htmlexplains how to create the service. > > > > I would develop a hello world service that takes in a string and returns > whatever you wish. Once you get that working, the rest would be trivial > because all you would have to do instead of returning hello world is invoke > your rest service and return the response. > > > > If you need further guidance, let me know. I am unsure of how much you > know! > > > > Thanks, > > > > Eddie > ------------------------------ > > *From:* Rajasekar Karthik [mailto:karthik085 at gmail.com] > *Sent:* Tuesday, May 01, 2007 7:36 AM > *To:* Edward Kawas > *Cc:* moby-l at biomoby.org > *Subject:* Re: [MOBY-l] REST Service registration > > > > Eddie, > > On 5/1/07, *Edward Kawas* wrote: > > Hi, > > That wouldn't be right (w.r.t. to moby). > > Personally, I think that you will have to wrap this REST service in a moby > service. > > > This is what I am trying to do. Sorry, I should have explained it clearer. > > > But, how do I do this? I already have a REST service that takes a string > name as input. Can you explain in detail? > > > > So, you would create a web service that takes a string name as > input. > > This web service would then pass on the string to > http://site.com/Service?Parameter1=INPUT_STRING, obtain a result and send > it > back to the caller of the moby service. > > The reason that I think that you are incorrect, is because moby has a > predefined message structure that you will have follow to be compatible. > > Hope this makes sense! > > 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: Tuesday, May 01, 2007 7:16 AM > > To: moby-l at biomoby.org > > Subject: [MOBY-l] REST Service registration > > > > Hi, > > > > I am trying to register a new service. In Service Endpoint - URL, I want > > > to > > store the URL to REST service. > > > > URL is something like: > > http://site.com/Service?Parameter1=Value1 > > > > Site: site.com > > Service: Service > > Parameter1: parameter/name > > Value1: value for the parameter1 > > > > eg: > > http://mysite.com/Analysis?Name=phob > > http://mysite.com/Analysis?Name=lac > > > > In order to register the service, I have to input: > > - in the Service Endpoint - URL: http://mysite.com/Analysis? > > - in the input data, add > > a) Name (String) > > > > Is this right? If not, how can I register the service? > > > > -- > > 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 From karthik085 at gmail.com Tue May 1 11:41:09 2007 From: karthik085 at gmail.com (Rajasekar Karthik) Date: Tue, 1 May 2007 11:41:09 -0400 Subject: [MOBY-l] REST Service registration In-Reply-To: <4637576D.6000506@ucalgary.ca> References: <001401c78bfc$4a1de0c0$6800a8c0@notebook> <001801c78bff$44981f50$6800a8c0@notebook> <4637576D.6000506@ucalgary.ca> Message-ID: Ok. Thanks. I will try this way too. On 5/1/07, Paul Gordon wrote: > > Or alternatively, you could use the MobyServlet framework > > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/deployingServices.html > > In which case your code would be (I haven't compoiled this, but you get > the point): > > import org.biomoby.shared.MobyDataType; > import org.biomoby.shared.data.*; > import org.biomoby.service.*; > import java.io.*; > > // Annotation describing the service semantics > @mobyService(name="YourServiceName", > type="AppropriateServiceType", > provider="auth.site.com", > author="foo at site.com" , > in={"inputString:String"}, > out={"outputHTML:text-html"}, > description={"Executes service X by wrapping a REST session"}) > > public class YourClass extends MobyServlet{ > public static final String BASE_URL = "http://site.com/Service?Parameter1=" ; > public void processRequest(MobyDataJob request, MobyDataJob result) throws Exception{ > // The input parameter matches that specified in the mobyService annotation above > MobyDataString inputParam = (MobyDataString) request.get("inputString"); > > > URL restURL = new URL(BASE_URL+inputParam); > StringBuffer htmlBuffer = new StringBuffer(); > LineNumberReader r = new LineNumberReader(new InputStreamReader( > url.openStream())); > for(String line = r.readLine(); line != null; line = r.readLine > ()){ > htmlBuffer.append(line); > } > > // Create the results (text-html matches mobyService annotation > declaration) > MobyDataComposite htmlObject = new MobyDataComposite( > MobyDataType.getDataType("text-html"), null , null, htmlBuffer.toString > ()); > > > // Set the result that will be passed back to the client (same name as in mobyService annotation above) > result.put("outputHTML", htmlObject); > > } > } > > Are you planning on coding in perl or java? > > > > First, register the service using whatever method you wish (I use > Dashboard). > > > > Second, create the code for the service; > > > > If you are using JAVA, > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ has information > for you (under Developing jMoby services) > > > > If you are using Perl, > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/PerlMoses.html > explains how to create the service. > > > > I would develop a hello world service that takes in a string and returns > whatever you wish. Once you get that working, the rest would be trivial > because all you would have to do instead of returning hello world is invoke > your rest service and return the response. > > > > If you need further guidance, let me know. I am unsure of how much you know! > > > > Thanks, > > > > Eddie > > _____ > > From: Rajasekar Karthik [mailto:karthik085 at gmail.com ] > Sent: Tuesday, May 01, 2007 7:36 AM > To: Edward Kawas > Cc: moby-l at biomoby.org > Subject: Re: [MOBY-l] REST Service registration > > > > Eddie, > > On 5/1/07, Edward Kawas wrote: > > Hi, > > That wouldn't be right (w.r.t. to moby). > > Personally, I think that you will have to wrap this REST service in a moby > service. > > > This is what I am trying to do. Sorry, I should have explained it clearer. > > But, how do I do this? I already have a REST service that takes a string > name as input. Can you explain in detail? > > > > So, you would create a web service that takes a string name as > input. > > This web service would then pass on the string to > http://site.com/Service?Parameter1=INPUT_STRING, obtain a result and send it > back to the caller of the moby service. > > The reason that I think that you are incorrect, is because moby has a > predefined message structure that you will have follow to be compatible. > > Hope this makes sense! > > 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: Tuesday, May 01, 2007 7:16 AM > To: moby-l at biomoby.org > Subject: [MOBY-l] REST Service registration > > Hi, > > I am trying to register a new service. In Service Endpoint - URL, I want > to > store the URL to REST service. > > URL is something like:http://site.com/Service?Parameter1=Value1 > > Site: site.com > Service: Service > Parameter1: parameter/name > Value1: value for the parameter1 > > eg:http://mysite.com/Analysis?Name=phob > http://mysite.com/Analysis?Name=lac > > In order to register the service, I have to input: > - in the Service Endpoint - URL: http://mysite.com/Analysis? > - in the input data, add > a) Name (String) > > Is this right? If not, how can I register the service? > > -- > 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 From darin.london at duke.edu Thu May 10 12:17:40 2007 From: darin.london at duke.edu (darin.london at duke.edu) Date: Thu, 10 May 2007 12:17:40 -0400 Subject: [MOBY-l] BOSC 2007 Second Call For Papers Message-ID: <200705101617.l4AGHebL002547@tenero.duhs.duke.edu> The BOSC Organizing Committee are proud to announce BOSC 2007, occurring in Vienna, Austria on July 19th, 20th. The conference this year promises to be exciting, as the BOSC developers attempt to define and solve currently intractable problems in Bioinformatics. Please refer to the following website for complete information, and requests for submissions. Thank you, and we hope to see you in Vienna. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. From darin.london at duke.edu Mon May 14 10:44:58 2007 From: darin.london at duke.edu (darin.london at duke.edu) Date: Mon, 14 May 2007 10:44:58 -0400 Subject: [MOBY-l] BOSC 2007 Abstract Submission Deadline Extended Message-ID: <200705141444.l4EEiw04027031@tenero.duhs.duke.edu> Due to technical difficulties in sending out the 2nd call for papers, the BOSC organizers are extending the deadline for abstract submissions to Monday May 21st. The announcement day will remain the same so that it remains before the Early Discount Date. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested.