From jones at nceas.ucsb.edu Mon May 17 18:47:42 2004 From: jones at nceas.ucsb.edu (Matt Jones) Date: Mon, 17 May 2004 17:47:42 -0800 Subject: [seek-web] Re: Development of Seek Web (public beta 2) moved to new Linux box In-Reply-To: <000f01c43c51$b8d79450$dd461881@LTERNET221> References: <000f01c43c51$b8d79450$dd461881@LTERNET221> Message-ID: <40A96B3E.7020809@nceas.ucsb.edu> Hi Steve, Thanks for the web-site update. We missed you in Edinburgh, but we'll hopefully get to meet sometime sooner than later. The site has matured a ton -- its looking nice, and I like the content additions you have done. We need to work on some of the visual appeal (we need a few pictures at least), but I like what you've got. I managed to edit some pages without crashing my browser, so it looks like you solved that problem. Thanks. Once we're ready to go we'll need to migrate the current Wiki content to the new site. Could you be sure to review all of the content at "http://seek.speciesanalyst.net" and make sure there is a sensible spot for it on the new seek web site? Most of it is internal project collaboration notes, so should not be too prominent on the seek site. Maybe it could go under "About SEEK|Teams", or maybe a specific project intranet area? I'm open to suggestions. Will those wiki pages move easily (ie, do they use the same wiki syntax) or will they need to be converted somehow? I think the site is close to being ready to be deployed. We need some more content work, and will need to install it on seek.ecoinformatics.org (a linux box) so that the URL doesn't change. What are the requirements for the installation? We currently have apache and tomcat running on that server -- need anything else? We're going to want to create an EcoGrid portal for finding data from the EcoGrid. I was hoping you could take the lead on developing the web UI for this, so you might consider how it would fit into the wiki framework (most of the UI will need to be generated from a servlet or something). An evolving developer's interface, not at all intended for end-users, to EcoGrid is here for your reference (http://129.237.201.166:8080/axis/registry.jsp). Looks like its down right now but Rod Spears can turn it back on for you. Can you produce a brief summary of what remains to be done before we can deploy the site? Once that stuff is done we should send explicitly ask for feedback from seek-web and then deploy it after addressing any concerns that arise. Thanks. Matt Steve Tekell wrote: > here's the new dev server > http://lternet-227.lternet.edu:8080/seekwiki/ > > Please do any content development and review there. > > I haven't got the server fully configured yet or setup Tomcat to run as a > daemon service. So I can't guarantee better uptime yet. Also, LDAP > security integration is turning into much more of task than originally > thought, so continue to use the temporary accounts that I gave you and let > me know if anyone else needs access. > > > Steve -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- From sroman at lternet.edu Tue May 18 05:54:52 2004 From: sroman at lternet.edu (Samantha Romanello) Date: Tue, 18 May 2004 06:54:52 -0600 Subject: [seek-web] Re: Development of Seek Web (public beta 2) moved to new Linux box In-Reply-To: <40A96B3E.7020809@nceas.ucsb.edu> References: <000f01c43c51$b8d79450$dd461881@LTERNET221> <40A96B3E.7020809@nceas.ucsb.edu> Message-ID: <40AA079C.5090607@lternet.edu> Hi Matt I have been working with steve on the content and I think we are both in need of some direction and assistance in certain areas: specifically: tools and data (specifically what tools we would like to highlight and some question like is Mysql appropriate to suggest for database solutions) and the opportunities section (specifically we would like individuals to provide additional information about: upcoming conferences, grants, jobs that could be placed on the site; a list of their publications relevant to SEEK and even current copies of presentations (like those from the e-science meeting) that could be added to the site. I was thinking that for the opportunities and document sections (i.e., information that we may not be privy to) we can email team members asking for this information and have them edit a private wiki themselves and then we (steve or I) can edit and release to the live site (this may be premature as we don't have live site) but am not sure if this approach is something that you (pl) were thinking of? Not quite sure about how to go about the tools. Once we get some of the look and feel issues agreed upon I would like to create a template for power point presentations to create a consistent unified "image" for outreach and education purposes. Also in terms of education....Dan Higgins mentioned that down loadable applets (I am assuming non-editable) could be created to highlight some of the kepler products seek dev have created -- and I think those would be great additions to the site. Thanks for the comments and I apologize in advance if you receive this message twice... Have a great day samantha Matt Jones wrote: > Hi Steve, > > Thanks for the web-site update. We missed you in Edinburgh, but we'll > hopefully get to meet sometime sooner than later. > > The site has matured a ton -- its looking nice, and I like the content > additions you have done. We need to work on some of the visual appeal > (we need a few pictures at least), but I like what you've got. I > managed to edit some pages without crashing my browser, so it looks > like you solved that problem. Thanks. > > Once we're ready to go we'll need to migrate the current Wiki content > to the new site. Could you be sure to review all of the content at > "http://seek.speciesanalyst.net" and make sure there is a sensible > spot for it on the new seek web site? Most of it is internal project > collaboration notes, so should not be too prominent on the seek site. > Maybe it could go under "About SEEK|Teams", or maybe a specific > project intranet area? I'm open to suggestions. Will those wiki pages > move easily (ie, do they use the same wiki syntax) or will they need > to be converted somehow? > > I think the site is close to being ready to be deployed. We need some > more content work, and will need to install it on > seek.ecoinformatics.org (a linux box) so that the URL doesn't change. > What are the requirements for the installation? We currently have > apache and tomcat running on that server -- need anything else? > > We're going to want to create an EcoGrid portal for finding data from > the EcoGrid. I was hoping you could take the lead on developing the > web UI for this, so you might consider how it would fit into the wiki > framework (most of the UI will need to be generated from a servlet or > something). An evolving developer's interface, not at all intended > for end-users, to EcoGrid is here for your reference > (http://129.237.201.166:8080/axis/registry.jsp). Looks like its down > right now but Rod Spears can turn it back on for you. > > Can you produce a brief summary of what remains to be done before we > can deploy the site? Once that stuff is done we should send > explicitly ask for feedback from seek-web and then deploy it after > addressing any concerns that arise. Thanks. > > Matt > > Steve Tekell wrote: > >> here's the new dev server >> http://lternet-227.lternet.edu:8080/seekwiki/ >> >> Please do any content development and review there. >> >> I haven't got the server fully configured yet or setup Tomcat to run >> as a >> daemon service. So I can't guarantee better uptime yet. Also, LDAP >> security integration is turning into much more of task than originally >> thought, so continue to use the temporary accounts that I gave you >> and let >> me know if anyone else needs access. >> >> >> Steve > > -- Nothing left to do but smile, smile, smile. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-web/attachments/20040518/ba42e27a/attachment.htm From stekell at lternet.edu Tue May 18 09:36:53 2004 From: stekell at lternet.edu (Steve Tekell) Date: Tue, 18 May 2004 10:36:53 -0600 Subject: [seek-web] Re: Development of Seek Web (public beta 2) moved to new Linux box In-Reply-To: <40A96B3E.7020809@nceas.ucsb.edu> Message-ID: <000401c43cf6$538c1fd0$dd461881@LTERNET221> > -----Original Message----- > seek.ecoinformatics.org (a linux box) so that the URL doesn't change. > What are the requirements for the installation? We currently have > apache and tomcat running on that server -- need anything else? no, that's it right now - just Tomcat (and Apache). There is a 1 WAR or webapp directory which is the engine and a directory for the data files since it is using file based versioning. There is a CVS plugin for versioning in the works, so eventually we could switch to using CVS for the wiki data files if it works for us. Until I can write a multi-org LDAP security authenticator for Tomcat, we need to use something else. I am using the simple memory-realm. So, outside the WAR, we'd need to edit the tomcat-users.xml to add accounts for any editors. Later, when I have a multi-org LDAP security authenticator that will need to be installed as a library available to Tomcat and edit the server config to make it available to applications. > We're going to want to create an EcoGrid portal for finding data from > the EcoGrid. I was hoping you could take the lead on > developing the web > UI for this, so you might consider how it would fit into the wiki In terms of technical deployment (not usability or look and feel), it won't fit _into_ the Wiki application itself. The idea was that the Wiki and new components would fit into a common larger seek portal application. If a Java portal server is used, each portlet is a webapp or WAR. Unfortunately, I haven't found a open source Java portal server which is ready for prime time yet. Still, I was thinking of deploying the new wiki as seekwiki.war or /seekwiki and just use a redirect at the root so as to protect URLs from changing when the portal server was implemented. so long term, the deployment might look like / (ROOT) - seek master portal server /seekwiki - Wiki portlet, lightweight CMS for "content" (as opposed to applications) / / / > framework (most of the UI will need to be generated from a servlet or > something). An evolving developer's interface, not at all > intended for > end-users, to EcoGrid is here for your reference > (http://129.237.201.166:8080/axis/registry.jsp). Looks like its down > right now but Rod Spears can turn it back on for you. > > Can you produce a brief summary of what remains to be done > before we can > deploy the site? determine what all graphics and additional design requirements (e.g., footer content) and implement. determine what the content requirements are for _initial_ deployment and make sure that set of content is ready. - that is, since we can develop content after launch, we only need an initial set in a complete state before launch. I don't want launch held up by everyone's ideas of what additional content could be there if it isn't really necessary for initial deployment. decide wether or not the LDAP security is a requirement for initial deployment or not and if so, then that's a dependency. > Once that stuff is done we should send > explicitly ask > for feedback from seek-web and then deploy it after addressing any > concerns that arise. Thanks. From dpennington at lternet.edu Tue May 18 10:43:09 2004 From: dpennington at lternet.edu (Deana Pennington) Date: Tue, 18 May 2004 11:43:09 -0600 Subject: [seek-web] Re: Development of Seek Web (public beta 2) moved to new Linux box In-Reply-To: <40AA079C.5090607@lternet.edu> References: <000f01c43c51$b8d79450$dd461881@LTERNET221> <40A96B3E.7020809@nceas.ucsb.edu> <40AA079C.5090607@lternet.edu> Message-ID: <40AA4B2D.1040901@lternet.edu> Really like the way the website is looking! A few comments for now... Home page: Love the glossary?great idea. Need to expand this, and make the links consistent across the website. Need a SEEK logo (still). My suggestion is that we use the Kepler pipeline logo, but add some ecology clipart to represent analysis for ecology. Other ideas? Footer should include logos for NSF, LTER, NCEAS, etc. Education: Like the organization. Like the 3 online courses. Under Informatics tools, shouldn?t this also include links for other kinds of tutorials, such as tutorials that we might do at SDSC? Opportunites. We should definitely send out a plea for information from everyone on the project. Seems like they should all have edit access to the publication page, and be able to add entries themselves, but I can also see where you might want to keep some control over it. Tools: seems like Sparrow should be here. Also GRASS GIS. Yes on R; I don?t know on MySQL. There is a website for Growl that we can link to, but we should make sure we?re going to use it before linking it. I believe Sergei came up with a separate ?ontology-for-dummies? tool that we might want to link to. Obviously needs some pictures to liven it up.... Steve: I don't think I ever got a logon from you (or I've forgotten it). Please send me a logon, and I'll help work on this. Deana Samantha Romanello wrote: > Hi Matt > > I have been working with steve on the content and I think we are both > in need of some direction and assistance in certain areas: > specifically: tools and data (specifically what tools we would like to > highlight and some question like is Mysql appropriate to suggest for > database solutions) and the opportunities section (specifically we > would like individuals to provide additional information about: > upcoming conferences, grants, jobs that could be placed on the site; a > list of their publications relevant to SEEK and even current copies of > presentations (like those from the e-science meeting) that could be > added to the site. I was thinking that for the opportunities and > document sections (i.e., information that we may not be privy to) we > can email team members asking for this information and have them edit > a private wiki themselves and then we (steve or I) can edit and > release to the live site (this may be premature as we don't have live > site) but am not sure if this approach is something that you (pl) were > thinking of? Not quite sure about how to go about the tools. > > Once we get some of the look and feel issues agreed upon I would like > to create a template for power point presentations to create a > consistent unified "image" for outreach and education purposes. Also > in terms of education....Dan Higgins mentioned that down loadable > applets (I am assuming non-editable) could be created to highlight > some of the kepler products seek dev have created -- and I think those > would be great additions to the site. > > Thanks for the comments and I apologize in advance if you receive this > message twice... > Have a great day > samantha > > > > Matt Jones wrote: > >> Hi Steve, >> >> Thanks for the web-site update. We missed you in Edinburgh, but we'll >> hopefully get to meet sometime sooner than later. >> >> The site has matured a ton -- its looking nice, and I like the >> content additions you have done. We need to work on some of the >> visual appeal (we need a few pictures at least), but I like what >> you've got. I managed to edit some pages without crashing my browser, >> so it looks like you solved that problem. Thanks. >> >> Once we're ready to go we'll need to migrate the current Wiki content >> to the new site. Could you be sure to review all of the content at >> "http://seek.speciesanalyst.net" and make sure there is a sensible >> spot for it on the new seek web site? Most of it is internal project >> collaboration notes, so should not be too prominent on the seek site. >> Maybe it could go under "About SEEK|Teams", or maybe a specific >> project intranet area? I'm open to suggestions. Will those wiki pages >> move easily (ie, do they use the same wiki syntax) or will they need >> to be converted somehow? >> >> I think the site is close to being ready to be deployed. We need some >> more content work, and will need to install it on >> seek.ecoinformatics.org (a linux box) so that the URL doesn't change. >> What are the requirements for the installation? We currently have >> apache and tomcat running on that server -- need anything else? >> >> We're going to want to create an EcoGrid portal for finding data from >> the EcoGrid. I was hoping you could take the lead on developing the >> web UI for this, so you might consider how it would fit into the wiki >> framework (most of the UI will need to be generated from a servlet or >> something). An evolving developer's interface, not at all intended >> for end-users, to EcoGrid is here for your reference >> (http://129.237.201.166:8080/axis/registry.jsp). Looks like its down >> right now but Rod Spears can turn it back on for you. >> >> Can you produce a brief summary of what remains to be done before we >> can deploy the site? Once that stuff is done we should send >> explicitly ask for feedback from seek-web and then deploy it after >> addressing any concerns that arise. Thanks. >> >> Matt >> >> Steve Tekell wrote: >> >>> here's the new dev server >>> http://lternet-227.lternet.edu:8080/seekwiki/ >>> >>> Please do any content development and review there. >>> >>> I haven't got the server fully configured yet or setup Tomcat to run >>> as a >>> daemon service. So I can't guarantee better uptime yet. Also, LDAP >>> security integration is turning into much more of task than originally >>> thought, so continue to use the temporary accounts that I gave you >>> and let >>> me know if anyone else needs access. >>> >>> >>> Steve >> >> > > > -- > > Nothing left to do but smile, smile, smile. > -- ******** Deana D. Pennington, PhD Long-term Ecological Research Network Office UNM Biology Department MSC03 2020 1 University of New Mexico Albuquerque, NM 87131-0001 505-272-7288 (office) 505 272-7080 (fax) From jones at nceas.ucsb.edu Wed May 19 13:45:07 2004 From: jones at nceas.ucsb.edu (Matt Jones) Date: Wed, 19 May 2004 12:45:07 -0800 Subject: [seek-web] [Fwd: Seek website - suggestions #1] Message-ID: <40ABC753.7000303@nceas.ucsb.edu> Steve, Suggestions for the new web site from our local graphics expert. Its mostly just cleanup stuff, but I think implementing his proposed changes will make a much crisper site. Thanks, Matt -- ------------------------------------------------------------------- Matt Jones jones at nceas.ucsb.edu http://www.nceas.ucsb.edu/ Fax: 425-920-2439 Ph: 907-789-0496 National Center for Ecological Analysis and Synthesis (NCEAS) University of California Santa Barbara Interested in ecological informatics? http://www.ecoinformatics.org ------------------------------------------------------------------- -------------- next part -------------- An embedded message was scrubbed... From: Matthew Brooke Subject: Seek website - suggestions #1 Date: Wed, 19 May 2004 12:35:38 -0700 Size: 4468 Url: http://mercury.nceas.ucsb.edu/ecoinformatics/pipermail/seek-web/attachments/20040519/ee6c0151/Seekwebsite-suggestions1.eml From jones at nceas.ucsb.edu Mon May 24 10:11:18 2004 From: jones at nceas.ucsb.edu (Matt Jones) Date: Mon, 24 May 2004 09:11:18 -0800 Subject: [seek-web] web site progress Message-ID: <40B22CB6.8020403@nceas.ucsb.edu> Hi Steve, The web site is looking good. I was looking it over this morning, and I think the content is close enough to ready that we can go ahead and deploy. As its a dynamic site, we can continue to improve the content incrementally as needed. Here's a brief list of the things I think still need to be done before we go production: 1) Create accounts for all SEEK project members Hopefully this will utilize LDAP, but ok if not 2) Move all material from old SEEK Wiki at Kansas to new site 3) Move meeting pages from the old seek site to the new wiki Once we move the old site away, the links will no longer work, so we need to fully update the external links here: http://lternet-227.lternet.edu:8080/seekwiki/Wiki.jsp?page=Calendar 4) Images: we need some. I tried uploading a png, but got an error when trying to atttach it. Any idea why? Are there other items that you think need to be finished before we move the server into production mode? Thanks, Matt From stekell at lternet.edu Mon May 24 12:52:05 2004 From: stekell at lternet.edu (Steve Tekell) Date: Mon, 24 May 2004 13:52:05 -0600 Subject: [seek-web] web site progress In-Reply-To: <40B22CB6.8020403@nceas.ucsb.edu> Message-ID: <000501c441c8$96e4d3e0$dd461881@LTERNET221> > -----Original Message----- > Hi Steve, > > The web site is looking good. I was looking it over this > morning, and I > think the content is close enough to ready that we can go ahead and > deploy. As its a dynamic site, we can continue to improve the content > incrementally as needed. Here's a brief list of the things I > think still > need to be done before we go production: > > 1) Create accounts for all SEEK project members > Hopefully this will utilize LDAP, but ok if not I haven't yet made any progress with an multi-org LDAP authenticator. So if you want to deploy soon, we should go with creating accounts. Is there a complete/up-to-date list with email addresses that I can use to create accounts from? > 2) Move all material from old SEEK Wiki at Kansas to new site well I guess we won't be using now, but I did create a InterWiki link definition for OldSeekWiki --> http://seek.speciesanalyst.net/ow.asp?%s > 3) Move meeting pages from the old seek site to the new wiki > Once we move the old site away, the links will no longer > work, so we > need to fully update the external links here: > > http://lternet-227.lternet.edu:8080/seekwiki/Wiki.jsp?page=Calendar > 4) Images: we need some. I tried uploading a png, but got an error when trying to atttach it. Any idea why? It appears to be something related to Linux as it works fine on my Windows box. I just don't have a clue what. Tomcat is only logging an NPE. From stekell at lternet.edu Mon May 24 13:04:37 2004 From: stekell at lternet.edu (Steve Tekell) Date: Mon, 24 May 2004 14:04:37 -0600 Subject: [seek-web] web site progress Message-ID: <000601c441ca$5723a6d0$dd461881@LTERNET221> > > 1) Create accounts for all SEEK project members > > Hopefully this will utilize LDAP, but ok if not > > I haven't yet made any progress with an multi-org LDAP > authenticator. So if you want to deploy soon, we should go > with creating accounts. Is there a complete/up-to-date list > with email addresses that I can use to create accounts from? BTW I was assuming by LDAP you meant existing accounts and that we'd just create Tomcat accounts until those can be used. Although, I guess you could use LDAP for the temporary accounts as long as they were all in one place (not mult-org) AND didn't use referrals. Then we should be able to use the standard Tomcat JNDI authenticator. From stekell at lternet.edu Mon May 24 14:27:52 2004 From: stekell at lternet.edu (Steve Tekell) Date: Mon, 24 May 2004 15:27:52 -0600 Subject: [seek-web] web site progress Message-ID: <000701c441d5$f842bfa0$dd461881@LTERNET221> > > 4) Images: we need some. I tried uploading a png, but got an error > when trying to atttach it. Any idea why? > > It appears to be something related to Linux as it works fine > on my Windows box. I just don't have a clue what. Tomcat is > only logging an NPE. FYI I am talking about Linux server versus Windows server not clients. And so far I am stumped. The actually NPE is happening on Error.jsp trying to say what the error is as if there is none. ugghhh