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From: Rutger V. <rut...@gm...> - 2012-02-07 10:21:05
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I agree that the search results could be sexed up, but that's a separate issue. > - it doesn't seem to recognise DOIs, e.g. 10.1016/j.ympev.2009.07.011 > No, this is just a proof of concept. It only distinguishes between treebase identifiers and "other words", to do that we would just need to expand inferType() to include 'doi' as a return value, and create another mapping from 'doi' to the underlying query predicate (which should be prism.doi) in the predicates map. > -how about interpreting numbers as study ids, NCBI tax ids, or PubMed ids > All numbers are now treated as identifiers. In this prototype for study searches that's only tb.identifier.study but on the taxon search page we would map from 'id' to 'tb.identifier.ubio' and/or 'tb.identifier.ncbi'. We don't store PubMed ids. > -doe sit support "standard" identifier abbreviations, "doi:", "pmid:", > etc.? > Not yet, but it would be easy. > Is there a full text index underlying the search (e.g., something like > Solr or Elastic search)? That would make the search more powerful. > No. > On 7 Feb 2012, at 09:53, Rutger Vos wrote: > > Hi all, > > here's a prototype of a simplified search interface: > http://dl.dropbox.com/u/4180059/treebase/query.html > > It gives users the ability to just type any words, and the javascript > infers whether the terms are identifiers or something else. It then turns > the terms into a PhyloWS query and calls that. It would need some > configuration to use the right predicates for each search page, but it > would simplify things for users, and if power users want to see (and edit) > the underlying query they can still do so. > > Rutger > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the > Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > > --------------------------------------------------------- > Roderic Page > Professor of Taxonomy > Institute of Biodiversity, Animal Health and Comparative Medicine > College of Medical, Veterinary and Life Sciences > Graham Kerr Building > University of Glasgow > Glasgow G12 8QQ, UK > > Email: r....@bi... > Tel: +44 141 330 4778 > Fax: +44 141 330 2792 > AIM: rod...@ai... > Facebook: http://www.facebook.com/profile.php?id=1112517192 > Twitter: http://twitter.com/rdmpage > Blog: http://iphylo.blogspot.com > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Roderic P. <r....@bi...> - 2012-02-07 10:09:41
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Nice, but (Vince Smith used to say "nice, but" to me all the time, drove me nuts). The list of results could be sexed up a bit: 1. show a thumbnail of the tree 2. show a thumbnail of the taxon the tree is about (via Wikipedia, EOL, etc.) 3. have facets so I can filter by taxa, date, author, etc. OK, so that's maybe the next step. Regarding the search box itself - it doesn't seem to recognise DOIs, e.g. 10.1016/j.ympev.2009.07.011 -how about interpreting numbers as study ids, NCBI tax ids, or PubMed ids -doe sit support "standard" identifier abbreviations, "doi:", "pmid:", etc.? Is there a full text index underlying the search (e.g., something like Solr or Elastic search)? That would make the search more powerful. Regards Rod On 7 Feb 2012, at 09:53, Rutger Vos wrote: > Hi all, > > here's a prototype of a simplified search interface: http://dl.dropbox.com/u/4180059/treebase/query.html > > It gives users the ability to just type any words, and the javascript infers whether the terms are identifiers or something else. It then turns the terms into a PhyloWS query and calls that. It would need some configuration to use the right predicates for each search page, but it would simplify things for users, and if power users want to see (and edit) the underlying query they can still do so. > > Rutger > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r....@bi... Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rod...@ai... Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html |
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From: Rutger V. <rut...@gm...> - 2012-02-07 09:53:12
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Hi all, here's a prototype of a simplified search interface: http://dl.dropbox.com/u/4180059/treebase/query.html It gives users the ability to just type any words, and the javascript infers whether the terms are identifiers or something else. It then turns the terms into a PhyloWS query and calls that. It would need some configuration to use the right predicates for each search page, but it would simplify things for users, and if power users want to see (and edit) the underlying query they can still do so. Rutger -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Rutger V. <rut...@gm...> - 2012-02-06 10:54:40
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Hi all, I have done some refactorings on the NeXML generation this weekend, which also involved some changes to the nexml.jar. The upshot is two-fold: * generation of character state matrices should go faster now, though that recent study with an nchar ~40k amino acids still hangs things. Perhaps we need to make nexml output more modular, such that in the entire study dump we don't put the full matrices, but instead an xinclude directive that points to the matrix's purl? * row objects can now be annotated in a way that fits more with our data model where different segments can be annotated separately. What we can now do is attach an annotation to a row, and then annotate that annotation. So you'd get on a row multiple annotations "tb:rowSegment" and each of these segments is in turn annotated with its start and end index and whichever other metadata the submitter has supplied (e.g. georeferencing and GenBank accession numbers). Here is a recent example that demonstrates this: http://treebase-dev.nescent.org/treebase-web/search/downloadAStudy.html?id=12335&format=nexml There's still a couple of little commits that need to happen (among which are: TreebaseIDString needs to store a prefix for MatrixRow objects so that we can attach the ID to the <row> element) before I would suggest pushing this to production, by the way. Cheers, Rutger -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Roderic P. <r....@bi...> - 2012-02-03 15:58:43
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It's a pity about the NSF ABI grant. I've not read the proposal in detail, but my gut feeling is the link between TreeBASE and ToLWeb is a mistake. The former matters, the later is basically moribund (let EOL have the aggregation space). I'd like a usable database of trees that gives us an overview of what we know, provides a platform for people to do science, and exploits existing social networks and citation/provenance metrics to engage users. That's it. I've no particular desire for NEXML, CDAO, PHYLWS, etc., or integration with TolWeb (I'd be much more excited by integration with PhyLoTA). Just show me the trees, let me find them by taxon, by geography, make it trivial to find my trees, and see what others have done with them (or the data I used). Regards Rod On 3 Feb 2012, at 14:36, Hilmar Lapp wrote: > > On Feb 3, 2012, at 3:00 AM, Roderic Page wrote: > >> I'm reading this thread with a growing sense of horror. > > Actually I'm glad others outside the project are finally getting horrified too. That should help with prioritization :-) > >> At some point TreeBASE needs a radical rethink. A nonSQL document store would make life so much easier, as would cleanly separating the data entry stuff from the data storage and output. > > > A wholehearted +1. In fact this is part of what we proposed in the 2011 NSF ABI grant (posted on the evoio.org wiki if you are curious) that was just declined from funding. And I also agree that there are significant barriers in the TreeBASE architecture to engendering outside participation, but I'm afraid the architecture is so entangled right now that it takes dedicated effort to break that up right now, i.e., grant funding. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r....@bi... Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rod...@ai... Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html |
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From: Hilmar L. <hl...@ne...> - 2012-02-03 14:36:36
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On Feb 3, 2012, at 3:00 AM, Roderic Page wrote: > I'm reading this thread with a growing sense of horror. Actually I'm glad others outside the project are finally getting horrified too. That should help with prioritization :-) > At some point TreeBASE needs a radical rethink. A nonSQL document store would make life so much easier, as would cleanly separating the data entry stuff from the data storage and output. A wholehearted +1. In fact this is part of what we proposed in the 2011 NSF ABI grant (posted on the evoio.org wiki if you are curious) that was just declined from funding. And I also agree that there are significant barriers in the TreeBASE architecture to engendering outside participation, but I'm afraid the architecture is so entangled right now that it takes dedicated effort to break that up right now, i.e., grant funding. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2012-02-03 13:52:18
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On Feb 3, 2012, at 3:00 AM, Roderic Page wrote: > When I harvest for projects like the TreeBASE browser I pause between requests, but still get time outs. Its driving us all completely nuts too, I might add. TreeBASE is capable of delivering all of its NeXML files -- at least initially. But throughout the day, even with a modest string of NeXML requests (basically, it has just been you and Enrico over the last couple of days), performance steadily degrades, threads proliferate, the CPU maxes out, and ultimately it starts failing to fulfill at all -- java/tomcat gets hung up with a backlog of requests, and even very minor requests spawn treads that are blocked. Surely Hibernate -- an industry standard -- is capable of better, more robust performance. The problem, then, is figuring out the source of the leaks (memory, threads, etc), the cause of the blockages, and the reason for inadequate trash collecting. bp |
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From: Rutger V. <rut...@gm...> - 2012-02-03 09:43:12
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> > In some ways I'd be less worried about all this if I could get the data > out of TreeBASE 2 easily so I could build a local version with the kind of > interface features I want. So, the argument that people who complain about > the interface are free to build their own using the API has some merit, > but collapses because it's so hard to get all the data (and annotations) > out. > The key thing now is that we must be able to get valid, sane and richly annotated NeXML documents for all studies. If we have those we can fill up document stores with different representations (data files, HTML, tree pictures) and experiment with different searches and front ends. I'm doing what I can to improve NeXML serialization, creating character state matrices is the big bug bear (and has been for TreeBASE2 from day one). Rutger -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Roderic P. <r....@bi...> - 2012-02-03 08:55:13
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> > At some point TreeBASE needs a radical rethink. A nonSQL document store would make life so much easier, as would cleanly separating the data entry stuff from the data storage and output. > > I tend to agree except that I don't see how TreeBASE3.0 is going to get built by all volunteers. Will you actively contribute? What, instead of sit on the sidelines and complain? Where's the fun in that? ;) I don't think being built by volunteers is the problem, almost the reverse. TreeBASE 2 has just about the worst set of technologies if you want people to get involved. There's no way I'd touch PostgreSQL, Tomcat, Java, Hibernate, etc. with a 10 foot barge pole. The cost of participating is just too high. But if it's re-engineered using, say, HTML, SVG, Javascript, a document store, and a little server-side scripting, then things become much more tractable. A search engine like Elastic Search would add some nice features as well. I've not submitted anything to TreeBASE 2 so I can't comment much on that, but again I'm sure this could engineered using the above tools quite simply (and no passwords! let people use Google/Facebook/Twitter/Mendeley to log in). I guess I'd want a focus on users, particularly people wanting to get data out of TreeBASE. The current interface metaphor is unusable. In some ways I'd be less worried about all this if I could get the data out of TreeBASE 2 easily so I could build a local version with the kind of interface features I want. So, the argument that people who complain about the interface are free to build their own using the API has some merit, but collapses because it's so hard to get all the data (and annotations) out. Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r....@bi... Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rod...@ai... Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html |
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From: Rutger V. <rut...@gm...> - 2012-02-03 08:25:06
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On Fri, Feb 3, 2012 at 9:00 AM, Roderic Page <r....@bi...> wrote: > I'm reading this thread with a growing sense of horror. In this day and > age there is no reason to store user passwords, see Jeff Atwood's > http://www.codinghorror.com/blog/2010/12/the-dirty-truth-about-web-passwords.html(and > http://www.codinghorror.com/blog/2010/11/your-internet-drivers-license.html). > We are aware of that, which is why we are having this discussion. > There seems to be something seriously wrong with TreeBASE's architecture > that it times out generating NEXML files. Apart from caching the output > (+1), perhaps intermediate views could be created to cache key elements of > the data structure to support creating NEXML files, rather than generating > the whole thing from scratch. > > The issue with NEXML continues to be a source of grief for me, especially > when I ended up with out of date and broken NEXML (which I'd cached locally > to avoid hitting TreeBASE). When I harvest for projects like the TreeBASE > browser I pause between requests, but still get time outs. > > At some point TreeBASE needs a radical rethink. A nonSQL document store > would make life so much easier, as would cleanly separating the data entry > stuff from the data storage and output. > I tend to agree except that I don't see how TreeBASE3.0 is going to get built by all volunteers. Will you actively contribute? Rutger > On 2 Feb 2012, at 22:44, Hilmar Lapp wrote: > > > On Feb 2, 2012, at 5:28 PM, Rutger Vos wrote: > > I had no idea we were under attack by brute-force rainbow tables. > > > That's what an intruder would use if they got ahold of our (encrypted) > user/password table. (For obvious reasons, one doesn't have to go there if > the password isn't encrypted.) > > http://en.wikipedia.org/wiki/Rainbow_table > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > > http://p.sf.net/sfu/learndevnow-d2d_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > --------------------------------------------------------- > Roderic Page > Professor of Taxonomy > Institute of Biodiversity, Animal Health and Comparative Medicine > College of Medical, Veterinary and Life Sciences > Graham Kerr Building > University of Glasgow > Glasgow G12 8QQ, UK > > Email: r....@bi... > Tel: +44 141 330 4778 > Fax: +44 141 330 2792 > AIM: rod...@ai... > Facebook: http://www.facebook.com/profile.php?id=1112517192 > Twitter: http://twitter.com/rdmpage > Blog: http://iphylo.blogspot.com > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Roderic P. <r....@bi...> - 2012-02-03 08:00:58
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I'm reading this thread with a growing sense of horror. In this day and age there is no reason to store user passwords, see Jeff Atwood's http://www.codinghorror.com/blog/2010/12/the-dirty-truth-about-web-passwords.html (and http://www.codinghorror.com/blog/2010/11/your-internet-drivers-license.html ). There seems to be something seriously wrong with TreeBASE's architecture that it times out generating NEXML files. Apart from caching the output (+1), perhaps intermediate views could be created to cache key elements of the data structure to support creating NEXML files, rather than generating the whole thing from scratch. The issue with NEXML continues to be a source of grief for me, especially when I ended up with out of date and broken NEXML (which I'd cached locally to avoid hitting TreeBASE). When I harvest for projects like the TreeBASE browser I pause between requests, but still get time outs. At some point TreeBASE needs a radical rethink. A nonSQL document store would make life so much easier, as would cleanly separating the data entry stuff from the data storage and output. Regards Rod On 2 Feb 2012, at 22:44, Hilmar Lapp wrote: > > On Feb 2, 2012, at 5:28 PM, Rutger Vos wrote: > >> I had no idea we were under attack by brute-force rainbow tables. > > That's what an intruder would use if they got ahold of our (encrypted) user/password table. (For obvious reasons, one doesn't have to go there if the password isn't encrypted.) > > http://en.wikipedia.org/wiki/Rainbow_table > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r....@bi... Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rod...@ai... Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html |
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From: Hilmar L. <hl...@ne...> - 2012-02-02 22:44:23
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On Feb 2, 2012, at 5:28 PM, Rutger Vos wrote: > I had no idea we were under attack by brute-force rainbow tables. That's what an intruder would use if they got ahold of our (encrypted) user/password table. (For obvious reasons, one doesn't have to go there if the password isn't encrypted.) http://en.wikipedia.org/wiki/Rainbow_table -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2012-02-02 22:28:45
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> > That sounds about right. I'd strongly recommend SHA1 in favor of MD5 > (computationally harder for brute-force rainbow tables, and programming > support should be equal to MD5), the comparison to a retyped password could > also be done entirely client-side (JavaScript), and the password reset > function could initially be written to reset the password to a randomly > generated one, which could then be emailed to the user, if changing to a > token-based system for reset is more effort than we can or want to afford > for now. (A randomly generated password being sent over email is still > hugely better than storing passwords in clear text in the database.) > Yes that's probably easier to do initially. I had no idea we were under attack by brute-force rainbow tables. > BTW you didn't cc the list - intention? If not, feel free to forward this > one back to the list. > Ah, thanks for catching - I was trying out gmail offline for chrome and I'm not crazy about it. More below: On Feb 2, 2012, at 12:59 PM, Rutger Vos wrote: > > So based on the above I'm still hoping this could be done in a way that >> isn't a major thing, or equivalent to redoing the authentication system. >> >> Either way, I agree it's worthwhile to consider whether we can use the >> emergency funds for this. One difficulty here is obviously how we'd do this >> without adding Yale's 60% overhead rate - perhaps we can hire Harry on an >> outside contractor basis for this task if he does work on the side? Could >> you or Harry give me an estimate of effort in number of hours? >> > > So what are the steps involved in this? I think what needs to happen is: > > * encrypt the passwords in the database (SHA? MD5?) > * make sure the passwords that users enter, either when logging in, > creating an account or updating their password, are encrypted in the same > way as early as possible > > I looked at User.getPassword() and User.setPassword() and there's only a > couple of points in the call hierarchy that interact with those methods > (AbstractUserController, PasswordFormController and > RegisterUserController). The behavior at those points would need to be > altered. In particular: > > * AbstractUserController can't simply compare the HTTP parameter > "retypedpassword" with what's in the database: the "retypedpassword" needs > to be encrypted first. > * PasswordFormController can no longer echo the password back in plain > text. This controller can only provide password change functionality since > the plain text password is no longer available anywhere. > > Or as Hilmar suggests: email a randomly generated password that is only stored in encrypted form and that the user most then change. > * RegisterUserController needs to behave such that when it calls > UserService.createUser() the user object has its password already > encrypted. This won't require the controller to change though: it's > probably better if setPassword() encrypts its argument before assigning it > to a local field. > > All in all this doesn't seem like that much work, but it needs to be > coordinated carefully. Especially when we pull the trigger on encrypting > the passwords in the database and committing the code that handles them. > > Rutger > > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Rutger V. <rut...@gm...> - 2012-02-02 12:27:43
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> > Either way, I agree it's worthwhile to consider whether we can use the > emergency funds for this. One difficulty here is obviously how we'd do this > without adding Yale's 60% overhead rate - perhaps we can hire Harry on an > outside contractor basis for this task if he does work on the side? Could > you or Harry give me an estimate of effort in number of hours? > As far as I can see the changes would be relatively minor, though they are scary because if we F this up it locks everyone out of their accounts. I think we would need to make the following changes in principle: * encrypt all the passwords in the database (SHA?) * make it so that any password strings that enter into the code base are encrypted at the earliest point I searched in eclipse where in the call hierarchy the methods User.getPassword() and User.setPassword() are interacted with, and it's mercifully limited: 1. in RegisterUserController.onSubmit() when we create the user, this user's password should already be encrypted. Right now, we simply coerce the command Object into a User (line 42), which means that the password is treated as an ordinary object property which we obtain out of the session variables. Here we would have to do the encryption and pass that into User.setPassword() - we can't do the encryption inside the body of setPassword() because that would mean the encryption is done twice when User objects are created out of the database (where the passwords are already encrypted) rather than out of session variables. 2. in AbstractUserController.checkPasswords() we compare User.getPassword() with the HTTP parameter "retypedpassword". Here getPassword() should return the encrypted string, and the HTTP parameter should be encrypted for comparison. 3. in PasswordFormController.onSubmit() we send a reminder email with the password in plain text back to the user. We can't do that because we won't have the unencrypted password anywhere in the system. Instead we should send a password change email. If we first do only 1. and then ask for the reminder email we can check to see if a new dummy user is successfully created with an encrypted password. We then do the encryption of all other passwords in the database and 2. change checkPasswords() to compare with an encrypted "retypedpassword". At this point the reminder email is no longer useful, because it will return an encrypted string that will be encrypted again before the comparison is done, so then we have to 3. change the reminder email to a password change email. That's a bit tricky because we would have to send a special link that sets the user to "authenticated" on our end so we can send them to the updateProfile page, but it's functionality that's more or less separate from everything else so we can start thinking about how to do that, perhaps in parallel. Anyway, all in all this should be doable, but I'm worried about missing something. What do you guys think? Rutger -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@ne...> - 2012-02-01 19:14:44
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On Feb 1, 2012, at 12:17 PM, William Piel wrote: > The only "missing" functionality is when the admin person needs to create a new submission for someone else -- in some cases because they can't seem to do *anything* for themselves. I see. And the problem here would only be if the user for whom you want to create a submission has already an account. (Because otherwise you could also create the account for them, and when done with your part, ask them to reset the password if they want to polish up anything.) > In other cases because I discover that a submission is corrupt in some way, and the most efficient solution is for me to create a new submission for them, re-upoad non-corrupting data, and then delete the old one. So here the user would indeed already have an account. > the ability for the admin person to move a submission from one user to a different user. > > I don't think it would be significant work -- at least the SQL is pretty minor -- just two updates within the same transaction: > > UPDATE submission SET user_id = <new user> WHERE study_id = 10; > UPDATE study SET user_id = <new user> WHERE study_id = 10; That looks fairly minor indeed - and presumably you can do that already now, no? > Harry isn't funded for TreeBASE, so while minor tweaks might be okay (out of the kindness of his heart), major thinks like redoing the authentication system need to be budgeted. But perhaps this is the ideal use for the emergency funds (the one ones that Karen is now dipping into regarding the student worker) ? So based on the above I'm still hoping this could be done in a way that isn't a major thing, or equivalent to redoing the authentication system. Either way, I agree it's worthwhile to consider whether we can use the emergency funds for this. One difficulty here is obviously how we'd do this without adding Yale's 60% overhead rate - perhaps we can hire Harry on an outside contractor basis for this task if he does work on the side? Could you or Harry give me an estimate of effort in number of hours? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2012-02-01 17:17:21
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On Feb 1, 2012, at 11:01 AM, Hilmar Lapp wrote: > Yes, there'd have to be admin privileges that override all other access permissions. Are you saying that such a role does currently not exist in TreeBASE? Introducing it would then likely mean a quite significant change, I would imagine. Maybe this could be accomplished in the short term by having a "super-password" that allows logging in as any user. Admin users can edit any existing submission, even if it does not belong to them. So that's not a problem. The only "missing" functionality is when the admin person needs to create a new submission for someone else -- in some cases because they can't seem to do *anything* for themselves. In other cases because I discover that a submission is corrupt in some way, and the most efficient solution is for me to create a new submission for them, re-upoad non-corrupting data, and then delete the old one. It's in these cases that I need to login as the user. A super password, like the one you mention, would accomplish this -- but another feature would also accomplish it while providing additional benefits: the ability for the admin person to move a submission from one user to a different user. I don't think it would be significant work -- at least the SQL is pretty minor -- just two updates within the same transaction: UPDATE submission SET user_id = <new user> WHERE study_id = 10; UPDATE study SET user_id = <new user> WHERE study_id = 10; So, instead of spoofing another user, the Admin person can create a new submission in his/her own account, and then transfer it to the other user. Also, this would solve other issues, like the request from Susanne Renner (below). She wanted to edit/update some citations, but these and been submitted by prior students who have since moved on. So she wanted to "repatriate" these submissions under her own account username -- something I could not do for her. Another example is with the student worker that Karen has just advertised. This student will be creating new submissions for data belonging to other scientists, so therefore parking them under this students own account. Which is fine, but maybe in the future these other scientists will (finally) be creating their own user accounts on TreeBASE, and they may (like Susanne Renner) want to repatriate their own submissions from the student account. On Feb 1, 2012, at 11:01 AM, Hilmar Lapp wrote: > The assignment to Vladimir, if it is still there, was from the time of the public release and post-release. Where we're currently at with grant funding I don't see much sense in him investing the time in digging through the code, acquiring enough understanding of it, and then implementing it. So consider this task unassigned. Is Harry in a position to take it on? Harry isn't funded for TreeBASE, so while minor tweaks might be okay (out of the kindness of his heart), major thinks like redoing the authentication system need to be budgeted. But perhaps this is the ideal use for the emergency funds (the one ones that Karen is now dipping into regarding the student worker) ? bp > From: "Susanne Renner via RT" <he...@tr...> > Date: January 5, 2012 6:26:17 AM EST > To: undisclosed-recipients:; > Subject: [treebase-help #12703] Up-dating citations > Reply-To: he...@tr... > > > Thu Jan 05 06:26:17 2012: Request 12703 was acted upon. > Transaction: Ticket created by re...@lr... > Queue: Treebase-help > Subject: Up-dating citations > Owner: Nobody > Requestors: re...@lr... > Status: new > Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=12703 > > > > Dear Bill, > > All but one of my "in progress" submissions are now solved. > > Could I get permission to update the citations of all the matrices associated with my paper? There are 19 or 20, many not up-dated. I understand that only the original submitter can make changes, but often these were graduate students, who have long moved on. > > Best regards, > > Susanne |
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From: Hilmar L. <hl...@ne...> - 2012-02-01 16:02:08
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Yes, there'd have to be admin privileges that override all other access permissions. Are you saying that such a role does currently not exist in TreeBASE? Introducing it would then likely mean a quite significant change, I would imagine. Maybe this could be accomplished in the short term by having a "super-password" that allows logging in as any user. The assignment to Vladimir, if it is still there, was from the time of the public release and post-release. Where we're currently at with grant funding I don't see much sense in him investing the time in digging through the code, acquiring enough understanding of it, and then implementing it. So consider this task unassigned. Is Harry in a position to take it on? -hilmar On Jan 31, 2012, at 10:18 PM, William Piel wrote: > > On Jan 31, 2012, at 10:00 PM, Hilmar Lapp wrote: > >> Indeed. Which reminds me to ask whether we can get anyone to finally implement the storing encrypted passwords functionality. It's a ticking time bomb, and I would hate it to explode. >> >> -hilmar > > I think the ticket was assigned to Vladimir. > > If that happens, btw, we need to include one additional functionality (aside from also changing the password recovery system): the ability for an admin person to move/park submissions under another account ID. (For really hopeless submitters, I sometimes have to resort to logging in under their credentials to create a submission for them, etc. -- so being able to transfer a submission that I have created under my own account is valuable). > > bp > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2012-02-01 10:59:42
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Mmmm... nothing seems to point towards any of the changes I've made, and the build is successful in any case. Can we somehow clean up and do a fresh rebuild, because this seems weird? The only thing that's changed since everything was working is Bill's commit but I don't see how a SQL file could break things. Rutger On Wed, Feb 1, 2012 at 5:35 AM, William Piel <wil...@ya...> wrote: > > On Jan 31, 2012, at 5:27 PM, Rutger Vos wrote: > > It could but that is not obvious from the stack trace. Could you post a > full one? > > Rutger > > > Below is the entire message I received. > > bp > > > > > > See <http://localhost:8888/job/Treebase-dev/291/changes> > > Changes: > > [sfrgpiel] Update SQL statement to fix older TB1 citations that are still > called "in prep" when they are likely to be published > > > ------------------------------------------ > Started by an SCM change > Updating https://treebase.svn.sourceforge.net/svnroot/treebase/trunk > A treebase-core/db/cleaning/2012-01-31_Update_TB1_citation_status > A > treebase-core/db/cleaning/2012-01-31_Update_TB1_citation_status/update_citation_status.sql > At revision 1028 > > [trunk] $ /usr/local/apache-maven/apache-maven-2.2.0/bin/mvn clean package > -Dmaven.test.skip=true > [INFO] Scanning for projects... > [INFO] Reactor build order: > [INFO] Treebase > [INFO] treebase-core > [INFO] treebase-web > [INFO] > ------------------------------------------------------------------------ > [INFO] Building Treebase > [INFO] task-segment: [clean, package] > [INFO] > ------------------------------------------------------------------------ > [INFO] [clean:clean {execution: default-clean}] > [INFO] [site:attach-descriptor {execution: default-attach-descriptor}] > [INFO] > ------------------------------------------------------------------------ > [INFO] Building treebase-core > [INFO] task-segment: [clean, package] > [INFO] > ------------------------------------------------------------------------ > [INFO] [clean:clean {execution: default-clean}] > [INFO] Deleting directory > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target > [INFO] [resources:resources {execution: default-resources}] > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered > resources, i.e. build is platform dependent! > [INFO] Copying 16 resources > [INFO] snapshot org.nexml.model:nexml:1.5-SNAPSHOT: checking for updates > from repository.jboss.org > [WARNING] repository metadata for: 'snapshot > org.nexml.model:nexml:1.5-SNAPSHOT' could not be retrieved from repository: > repository.jboss.org due to an error: Authorization failed: Access denied > to: > http://repository.jboss.org/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/maven-metadata.xml > [INFO] Repository 'repository.jboss.org' will be blacklisted > Downloading: > http://repo1.maven.org/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom > [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' in > repository maven2 (http://repo1.maven.org/maven2) > Downloading: > http://treebase.sourceforge.net/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom > [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' in > repository m2.remote.repos (http://treebase.sourceforge.net/maven2) > Downloading: > http://nexml-dev.nescent.org/.m2/repository/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom > [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' in > repository m2.nexml.repos (http://nexml-dev.nescent.org/.m2/repository) > [INFO] [compiler:compile {execution: default-compile}] > [INFO] Compiling 382 source files to > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target/classes > [INFO] [resources:testResources {execution: default-testResources}] > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered > resources, i.e. build is platform dependent! > [INFO] Copying 16 resources > [INFO] [compiler:testCompile {execution: default-testCompile}] > [INFO] Not compiling test sources > [INFO] [surefire:test {execution: default-test}] > [INFO] Tests are skipped. > [INFO] [jar:jar {execution: default-jar}] > [INFO] Building jar: > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target/treebase-core-1.0-SNAPSHOT.jar > [INFO] > ------------------------------------------------------------------------ > [INFO] Building treebase-web > [INFO] task-segment: [clean, package] > [INFO] > ------------------------------------------------------------------------ > [INFO] [clean:clean {execution: default-clean}] > [INFO] Deleting directory > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target > [INFO] [resources:resources {execution: default-resources}] > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered > resources, i.e. build is platform dependent! > [INFO] Copying 1 resource > [INFO] [compiler:compile {execution: default-compile}] > [INFO] Compiling 160 source files to > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/classes > [INFO] [resources:testResources {execution: default-testResources}] > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered > resources, i.e. build is platform dependent! > [INFO] skip non existing resourceDirectory > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/src/test/resources > [INFO] [compiler:testCompile {execution: default-testCompile}] > [INFO] Not compiling test sources > [INFO] [surefire:test {execution: default-test}] > [INFO] Tests are skipped. > [INFO] [war:war {execution: default-war}] > [INFO] Packaging webapp > [INFO] Assembling webapp[treebase-web] in > [/home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/treebase-web] > [INFO] Processing war project > [INFO] Copying webapp > resources[/home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/src/main/webapp] > [INFO] Webapp assembled in[1248 msecs] > > [INFO] Building war: > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/treebase-web.war > [INFO] > [INFO] > [INFO] > ------------------------------------------------------------------------ > [INFO] Reactor Summary: > [INFO] > ------------------------------------------------------------------------ > [INFO] Treebase .............................................. SUCCESS > [3.210s] > [INFO] treebase-core ......................................... SUCCESS > [23.292s] > [INFO] treebase-web .......................................... SUCCESS > [12.708s] > > [INFO] > ------------------------------------------------------------------------ > [INFO] > ------------------------------------------------------------------------ > [INFO] BUILD SUCCESSFUL > [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: 40 seconds > [INFO] Finished at: Tue Jan 31 17:12:22 EST 2012 > [INFO] Final Memory: 53M/351M > > [INFO] > ------------------------------------------------------------------------ > Deploying < > http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war> > to container Tomcat 5.x Remote > [< > http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war]> > is not deployed. Doing a fresh deployment. > > Deploying [< > http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war] > > > ERROR: Publisher hudson.plugins.deploy.DeployPublisher aborted due to > exception > org.codehaus.cargo.container.ContainerException: Failed to deploy [< > http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war] > > > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:111) > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.redeploy(AbstractTomcatManagerDeployer.java:187) > at > hudson.plugins.deploy.CargoContainerAdapter.deploy(CargoContainerAdapter.java:60) > at > hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:86) > at > hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:73) > at hudson.FilePath.act(FilePath.java:785) > at hudson.FilePath.act(FilePath.java:767) > at > hudson.plugins.deploy.CargoContainerAdapter.redeploy(CargoContainerAdapter.java:73) > at hudson.plugins.deploy.DeployPublisher.perform(DeployPublisher.java:45) > at hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:36) > at > hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:694) > at > hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:669) > at > hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:647) > at hudson.model.Build$RunnerImpl.post2(Build.java:162) > at hudson.model.AbstractBuild$AbstractRunner.post(AbstractBuild.java:616) > at hudson.model.Run.run(Run.java:1429) > at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46) > at hudson.model.ResourceController.execute(ResourceController.java:88) > at hudson.model.Executor.run(Executor.java:230) > Caused by: > org.codehaus.cargo.container.tomcat.internal.TomcatManagerException: FAIL - > Failed to deploy application at context path /treebase-web > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.invoke(TomcatManager.java:507) > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deployImpl(TomcatManager.java:547) > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:273) > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:256) > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:240) > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:107) > ... 18 more > org.codehaus.cargo.container.tomcat.internal.TomcatManagerException: FAIL > - Failed to deploy application at context path /treebase-web > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.invoke(TomcatManager.java:507) > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deployImpl(TomcatManager.java:547) > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:273) > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:256) > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:240) > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:107) > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.redeploy(AbstractTomcatManagerDeployer.java:187) > at > hudson.plugins.deploy.CargoContainerAdapter.deploy(CargoContainerAdapter.java:60) > at > hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:86) > at > hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:73) > at hudson.FilePath.act(FilePath.java:785) > at hudson.FilePath.act(FilePath.java:767) > at > hudson.plugins.deploy.CargoContainerAdapter.redeploy(CargoContainerAdapter.java:73) > at hudson.plugins.deploy.DeployPublisher.perform(DeployPublisher.java:45) > at hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:36) > at > hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:694) > at > hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:669) > at > hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:647) > at hudson.model.Build$RunnerImpl.post2(Build.java:162) > at hudson.model.AbstractBuild$AbstractRunner.post(AbstractBuild.java:616) > at hudson.model.Run.run(Run.java:1429) > at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46) > at hudson.model.ResourceController.execute(ResourceController.java:88) > at hudson.model.Executor.run(Executor.java:230) > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2012-02-01 04:35:42
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On Jan 31, 2012, at 5:27 PM, Rutger Vos wrote: > It could but that is not obvious from the stack trace. Could you post a full one? > > Rutger Below is the entire message I received. bp See <http://localhost:8888/job/Treebase-dev/291/changes> Changes: [sfrgpiel] Update SQL statement to fix older TB1 citations that are still called "in prep" when they are likely to be published ------------------------------------------ Started by an SCM change Updating https://treebase.svn.sourceforge.net/svnroot/treebase/trunk A treebase-core/db/cleaning/2012-01-31_Update_TB1_citation_status A treebase-core/db/cleaning/2012-01-31_Update_TB1_citation_status/update_citation_status.sql At revision 1028 [trunk] $ /usr/local/apache-maven/apache-maven-2.2.0/bin/mvn clean package -Dmaven.test.skip=true [INFO] Scanning for projects... [INFO] Reactor build order: [INFO] Treebase [INFO] treebase-core [INFO] treebase-web [INFO] ------------------------------------------------------------------------ [INFO] Building Treebase [INFO] task-segment: [clean, package] [INFO] ------------------------------------------------------------------------ [INFO] [clean:clean {execution: default-clean}] [INFO] [site:attach-descriptor {execution: default-attach-descriptor}] [INFO] ------------------------------------------------------------------------ [INFO] Building treebase-core [INFO] task-segment: [clean, package] [INFO] ------------------------------------------------------------------------ [INFO] [clean:clean {execution: default-clean}] [INFO] Deleting directory /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target [INFO] [resources:resources {execution: default-resources}] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 16 resources [INFO] snapshot org.nexml.model:nexml:1.5-SNAPSHOT: checking for updates from repository.jboss.org [WARNING] repository metadata for: 'snapshot org.nexml.model:nexml:1.5-SNAPSHOT' could not be retrieved from repository: repository.jboss.org due to an error: Authorization failed: Access denied to: http://repository.jboss.org/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/maven-metadata.xml [INFO] Repository 'repository.jboss.org' will be blacklisted Downloading: http://repo1.maven.org/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' in repository maven2 (http://repo1.maven.org/maven2) Downloading: http://treebase.sourceforge.net/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' in repository m2.remote.repos (http://treebase.sourceforge.net/maven2) Downloading: http://nexml-dev.nescent.org/.m2/repository/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' in repository m2.nexml.repos (http://nexml-dev.nescent.org/.m2/repository) [INFO] [compiler:compile {execution: default-compile}] [INFO] Compiling 382 source files to /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target/classes [INFO] [resources:testResources {execution: default-testResources}] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 16 resources [INFO] [compiler:testCompile {execution: default-testCompile}] [INFO] Not compiling test sources [INFO] [surefire:test {execution: default-test}] [INFO] Tests are skipped. [INFO] [jar:jar {execution: default-jar}] [INFO] Building jar: /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target/treebase-core-1.0-SNAPSHOT.jar [INFO] ------------------------------------------------------------------------ [INFO] Building treebase-web [INFO] task-segment: [clean, package] [INFO] ------------------------------------------------------------------------ [INFO] [clean:clean {execution: default-clean}] [INFO] Deleting directory /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target [INFO] [resources:resources {execution: default-resources}] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 1 resource [INFO] [compiler:compile {execution: default-compile}] [INFO] Compiling 160 source files to /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/classes [INFO] [resources:testResources {execution: default-testResources}] [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] skip non existing resourceDirectory /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/src/test/resources [INFO] [compiler:testCompile {execution: default-testCompile}] [INFO] Not compiling test sources [INFO] [surefire:test {execution: default-test}] [INFO] Tests are skipped. [INFO] [war:war {execution: default-war}] [INFO] Packaging webapp [INFO] Assembling webapp[treebase-web] in [/home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/treebase-web] [INFO] Processing war project [INFO] Copying webapp resources[/home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/src/main/webapp] [INFO] Webapp assembled in[1248 msecs] [INFO] Building war: /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/treebase-web.war [INFO] [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] ------------------------------------------------------------------------ [INFO] Treebase .............................................. SUCCESS [3.210s] [INFO] treebase-core ......................................... SUCCESS [23.292s] [INFO] treebase-web .......................................... SUCCESS [12.708s] [INFO] ------------------------------------------------------------------------ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESSFUL [INFO] ------------------------------------------------------------------------ [INFO] Total time: 40 seconds [INFO] Finished at: Tue Jan 31 17:12:22 EST 2012 [INFO] Final Memory: 53M/351M [INFO] ------------------------------------------------------------------------ Deploying <http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war> to container Tomcat 5.x Remote [<http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war]> is not deployed. Doing a fresh deployment. Deploying [<http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war]> ERROR: Publisher hudson.plugins.deploy.DeployPublisher aborted due to exception org.codehaus.cargo.container.ContainerException: Failed to deploy [<http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war]> at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:111) at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.redeploy(AbstractTomcatManagerDeployer.java:187) at hudson.plugins.deploy.CargoContainerAdapter.deploy(CargoContainerAdapter.java:60) at hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:86) at hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:73) at hudson.FilePath.act(FilePath.java:785) at hudson.FilePath.act(FilePath.java:767) at hudson.plugins.deploy.CargoContainerAdapter.redeploy(CargoContainerAdapter.java:73) at hudson.plugins.deploy.DeployPublisher.perform(DeployPublisher.java:45) at hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:36) at hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:694) at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:669) at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:647) at hudson.model.Build$RunnerImpl.post2(Build.java:162) at hudson.model.AbstractBuild$AbstractRunner.post(AbstractBuild.java:616) at hudson.model.Run.run(Run.java:1429) at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46) at hudson.model.ResourceController.execute(ResourceController.java:88) at hudson.model.Executor.run(Executor.java:230) Caused by: org.codehaus.cargo.container.tomcat.internal.TomcatManagerException: FAIL - Failed to deploy application at context path /treebase-web at org.codehaus.cargo.container.tomcat.internal.TomcatManager.invoke(TomcatManager.java:507) at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deployImpl(TomcatManager.java:547) at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:273) at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:256) at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:240) at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:107) ... 18 more org.codehaus.cargo.container.tomcat.internal.TomcatManagerException: FAIL - Failed to deploy application at context path /treebase-web at org.codehaus.cargo.container.tomcat.internal.TomcatManager.invoke(TomcatManager.java:507) at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deployImpl(TomcatManager.java:547) at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:273) at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:256) at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:240) at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:107) at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.redeploy(AbstractTomcatManagerDeployer.java:187) at hudson.plugins.deploy.CargoContainerAdapter.deploy(CargoContainerAdapter.java:60) at hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:86) at hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:73) at hudson.FilePath.act(FilePath.java:785) at hudson.FilePath.act(FilePath.java:767) at hudson.plugins.deploy.CargoContainerAdapter.redeploy(CargoContainerAdapter.java:73) at hudson.plugins.deploy.DeployPublisher.perform(DeployPublisher.java:45) at hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:36) at hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:694) at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:669) at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:647) at hudson.model.Build$RunnerImpl.post2(Build.java:162) at hudson.model.AbstractBuild$AbstractRunner.post(AbstractBuild.java:616) at hudson.model.Run.run(Run.java:1429) at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46) at hudson.model.ResourceController.execute(ResourceController.java:88) at hudson.model.Executor.run(Executor.java:230) |
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From: William P. <wil...@ya...> - 2012-02-01 03:19:05
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On Jan 31, 2012, at 10:00 PM, Hilmar Lapp wrote: > Indeed. Which reminds me to ask whether we can get anyone to finally implement the storing encrypted passwords functionality. It's a ticking time bomb, and I would hate it to explode. > > -hilmar I think the ticket was assigned to Vladimir. If that happens, btw, we need to include one additional functionality (aside from also changing the password recovery system): the ability for an admin person to move/park submissions under another account ID. (For really hopeless submitters, I sometimes have to resort to logging in under their credentials to create a submission for them, etc. -- so being able to transfer a submission that I have created under my own account is valuable). bp |
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From: Hilmar L. <hl...@ne...> - 2012-02-01 03:00:54
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Indeed. Which reminds me to ask whether we can get anyone to finally implement the storing encrypted passwords functionality. It's a ticking time bomb, and I would hate it to explode. -hilmar On Jan 31, 2012, at 2:08 PM, William Piel wrote: > > Yup -- worth doing something like this. > > Note that all personal info for user accounts (emails, passwords) would need to be erased; and all unpublished submissions would need to be erased. > > bp > > > On Jan 31, 2012, at 1:49 PM, Hilmar Lapp wrote: >> Well, yeah, that's I was suggesting with the AMI. -hilmar > >>> On Jan 31, 2012, at 1:18 PM, Rutger Vos wrote: >>> >>> By the way, wouldn't it a good idea if instead we could simply share an image of the entire treebase environment? I heard PFAM has just started doing that and it might be a good idea if we want to entice volunteer developers. > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2012-01-31 22:27:40
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It could but that is not obvious from the stack trace. Could you post a full one? Rutger On Tue, Jan 31, 2012 at 11:17 PM, William Piel <wil...@ya...>wrote: > > This seems to say that my data curation change is to blame for Hudson not > building -- but that's probably not it. Perhaps it's the authorization > failure for fetch NeXML code? > > bp > > > > On Jan 31, 2012, at 5:03 PM, sys...@ne... wrote: > > > See <http://localhost:8888/job/Treebase-dev/290/changes> > > > > Changes: > > > > [sfrgpiel] Script and data file for updating TB1 citations > > > > ------------------------------------------ > > Started by an SCM change > > Updating https://treebase.svn.sourceforge.net/svnroot/treebase/trunk > > A treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations > > A > treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/citationdata.txt > > A treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/ > update_citations.pl > > A > treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/README > > At revision 1027 > > [trunk] $ /usr/local/apache-maven/apache-maven-2.2.0/bin/mvn clean > package -Dmaven.test.skip=true > > [INFO] Scanning for projects... > > [INFO] Reactor build order: > > [INFO] Treebase > > [INFO] treebase-core > > [INFO] treebase-web > > [INFO] > ------------------------------------------------------------------------ > > [INFO] Building Treebase > > [INFO] task-segment: [clean, package] > > [INFO] > ------------------------------------------------------------------------ > > [INFO] [clean:clean {execution: default-clean}] > > [INFO] [site:attach-descriptor {execution: default-attach-descriptor}] > > [INFO] > ------------------------------------------------------------------------ > > [INFO] Building treebase-core > > [INFO] task-segment: [clean, package] > > [INFO] > ------------------------------------------------------------------------ > > [INFO] [clean:clean {execution: default-clean}] > > [INFO] Deleting directory > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target > > [INFO] [resources:resources {execution: default-resources}] > > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered > resources, i.e. build is platform dependent! > > [INFO] Copying 16 resources > > [INFO] snapshot org.nexml.model:nexml:1.5-SNAPSHOT: checking for updates > from repository.jboss.org > > [WARNING] repository metadata for: 'snapshot > org.nexml.model:nexml:1.5-SNAPSHOT' could not be retrieved from repository: > repository.jboss.org due to an error: Authorization failed: Access denied > to: > http://repository.jboss.org/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/maven-metadata.xml > > [INFO] Repository 'repository.jboss.org' will be blacklisted > > Downloading: > http://repo1.maven.org/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom > > [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' > in repository maven2 (http://repo1.maven.org/maven2) > > Downloading: > http://treebase.sourceforge.net/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom > > [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' > in repository m2.remote.repos (http://treebase.sourceforge.net/maven2) > > Downloading: > http://nexml-dev.nescent.org/.m2/repository/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom > > [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' > in repository m2.nexml.repos (http://nexml-dev.nescent.org/.m2/repository) > > [INFO] [compiler:compile {execution: default-compile}] > > [INFO] Compiling 382 source files to > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target/classes > > [INFO] [resources:testResources {execution: default-testResources}] > > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered > resources, i.e. build is platform dependent! > > [INFO] Copying 16 resources > > [INFO] [compiler:testCompile {execution: default-testCompile}] > > [INFO] Not compiling test sources > > [INFO] [surefire:test {execution: default-test}] > > [INFO] Tests are skipped. > > [INFO] [jar:jar {execution: default-jar}] > > [INFO] Building jar: > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target/treebase-core-1.0-SNAPSHOT.jar > > [INFO] > ------------------------------------------------------------------------ > > [INFO] Building treebase-web > > [INFO] task-segment: [clean, package] > > [INFO] > ------------------------------------------------------------------------ > > [INFO] [clean:clean {execution: default-clean}] > > [INFO] Deleting directory > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target > > [INFO] [resources:resources {execution: default-resources}] > > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered > resources, i.e. build is platform dependent! > > [INFO] Copying 1 resource > > [INFO] [compiler:compile {execution: default-compile}] > > [INFO] Compiling 160 source files to > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/classes > > [INFO] [resources:testResources {execution: default-testResources}] > > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered > resources, i.e. build is platform dependent! > > [INFO] skip non existing resourceDirectory > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/src/test/resources > > [INFO] [compiler:testCompile {execution: default-testCompile}] > > [INFO] Not compiling test sources > > [INFO] [surefire:test {execution: default-test}] > > [INFO] Tests are skipped. > > [INFO] [war:war {execution: default-war}] > > [INFO] Packaging webapp > > [INFO] Assembling webapp[treebase-web] in > [/home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/treebase-web] > > [INFO] Processing war project > > [INFO] Copying webapp > resources[/home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/src/main/webapp] > > [INFO] Webapp assembled in[1437 msecs] > > [INFO] Building war: > /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/treebase-web.war > > [INFO] > > [INFO] > > [INFO] > ------------------------------------------------------------------------ > > [INFO] Reactor Summary: > > [INFO] > ------------------------------------------------------------------------ > > [INFO] Treebase .............................................. SUCCESS > [2.801s] > > [INFO] treebase-core ......................................... SUCCESS > [12.292s] > > [INFO] treebase-web .......................................... SUCCESS > [17.017s] > > [INFO] > ------------------------------------------------------------------------ > > [INFO] > ------------------------------------------------------------------------ > > [INFO] BUILD SUCCESSFUL > > [INFO] > ------------------------------------------------------------------------ > > [INFO] Total time: 32 seconds > > [INFO] Finished at: Tue Jan 31 17:02:12 EST 2012 > > [INFO] Final Memory: 53M/382M > > [INFO] > ------------------------------------------------------------------------ > > Deploying < > http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war> > to container Tomcat 5.x Remote > > Redeploying [< > http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war > ]> > > Undeploying [< > http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war > ]> > > Deploying [< > http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war > ]> > > ERROR: Publisher hudson.plugins.deploy.DeployPublisher aborted due to > exception > > org.codehaus.cargo.container.ContainerException: Failed to deploy [< > http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war > ]> > > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:111) > > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.redeploy(AbstractTomcatManagerDeployer.java:187) > > at > hudson.plugins.deploy.CargoContainerAdapter.deploy(CargoContainerAdapter.java:60) > > at > hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:86) > > at > hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:73) > > at hudson.FilePath.act(FilePath.java:785) > > at hudson.FilePath.act(FilePath.java:767) > > at > hudson.plugins.deploy.CargoContainerAdapter.redeploy(CargoContainerAdapter.java:73) > > at > hudson.plugins.deploy.DeployPublisher.perform(DeployPublisher.java:45) > > at > hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:36) > > at > hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:694) > > at > hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:669) > > at > hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:647) > > at hudson.model.Build$RunnerImpl.post2(Build.java:162) > > at > hudson.model.AbstractBuild$AbstractRunner.post(AbstractBuild.java:616) > > at hudson.model.Run.run(Run.java:1429) > > at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46) > > at > hudson.model.ResourceController.execute(ResourceController.java:88) > > at hudson.model.Executor.run(Executor.java:230) > > Caused by: > org.codehaus.cargo.container.tomcat.internal.TomcatManagerException: FAIL - > Failed to deploy application at context path /treebase-web > > > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.invoke(TomcatManager.java:507) > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deployImpl(TomcatManager.java:547) > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:273) > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:256) > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:240) > > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:107) > > ... 18 more > > org.codehaus.cargo.container.tomcat.internal.TomcatManagerException: > FAIL - Failed to deploy application at context path /treebase-web > > > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.invoke(TomcatManager.java:507) > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deployImpl(TomcatManager.java:547) > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:273) > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:256) > > at > org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:240) > > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:107) > > at > org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.redeploy(AbstractTomcatManagerDeployer.java:187) > > at > hudson.plugins.deploy.CargoContainerAdapter.deploy(CargoContainerAdapter.java:60) > > at > hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:86) > > at > hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:73) > > at hudson.FilePath.act(FilePath.java:785) > > at hudson.FilePath.act(FilePath.java:767) > > at > hudson.plugins.deploy.CargoContainerAdapter.redeploy(CargoContainerAdapter.java:73) > > at > hudson.plugins.deploy.DeployPublisher.perform(DeployPublisher.java:45) > > at > hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:36) > > at > hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:694) > > at > hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:669) > > at > hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:647) > > at hudson.model.Build$RunnerImpl.post2(Build.java:162) > > at > hudson.model.AbstractBuild$AbstractRunner.post(AbstractBuild.java:616) > > at hudson.model.Run.run(Run.java:1429) > > at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46) > > at > hudson.model.ResourceController.execute(ResourceController.java:88) > > at hudson.model.Executor.run(Executor.java:230) > > > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2012-01-31 22:17:48
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This seems to say that my data curation change is to blame for Hudson not building -- but that's probably not it. Perhaps it's the authorization failure for fetch NeXML code? bp On Jan 31, 2012, at 5:03 PM, sys...@ne... wrote: > See <http://localhost:8888/job/Treebase-dev/290/changes> > > Changes: > > [sfrgpiel] Script and data file for updating TB1 citations > > ------------------------------------------ > Started by an SCM change > Updating https://treebase.svn.sourceforge.net/svnroot/treebase/trunk > A treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations > A treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/citationdata.txt > A treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/update_citations.pl > A treebase-core/db/cleaning/2012-01-31_Update_TB1_Citations/README > At revision 1027 > [trunk] $ /usr/local/apache-maven/apache-maven-2.2.0/bin/mvn clean package -Dmaven.test.skip=true > [INFO] Scanning for projects... > [INFO] Reactor build order: > [INFO] Treebase > [INFO] treebase-core > [INFO] treebase-web > [INFO] ------------------------------------------------------------------------ > [INFO] Building Treebase > [INFO] task-segment: [clean, package] > [INFO] ------------------------------------------------------------------------ > [INFO] [clean:clean {execution: default-clean}] > [INFO] [site:attach-descriptor {execution: default-attach-descriptor}] > [INFO] ------------------------------------------------------------------------ > [INFO] Building treebase-core > [INFO] task-segment: [clean, package] > [INFO] ------------------------------------------------------------------------ > [INFO] [clean:clean {execution: default-clean}] > [INFO] Deleting directory /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target > [INFO] [resources:resources {execution: default-resources}] > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! > [INFO] Copying 16 resources > [INFO] snapshot org.nexml.model:nexml:1.5-SNAPSHOT: checking for updates from repository.jboss.org > [WARNING] repository metadata for: 'snapshot org.nexml.model:nexml:1.5-SNAPSHOT' could not be retrieved from repository: repository.jboss.org due to an error: Authorization failed: Access denied to: http://repository.jboss.org/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/maven-metadata.xml > [INFO] Repository 'repository.jboss.org' will be blacklisted > Downloading: http://repo1.maven.org/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom > [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' in repository maven2 (http://repo1.maven.org/maven2) > Downloading: http://treebase.sourceforge.net/maven2/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom > [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' in repository m2.remote.repos (http://treebase.sourceforge.net/maven2) > Downloading: http://nexml-dev.nescent.org/.m2/repository/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.pom > [INFO] Unable to find resource 'org.nexml.model:nexml:pom:1.5-SNAPSHOT' in repository m2.nexml.repos (http://nexml-dev.nescent.org/.m2/repository) > [INFO] [compiler:compile {execution: default-compile}] > [INFO] Compiling 382 source files to /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target/classes > [INFO] [resources:testResources {execution: default-testResources}] > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! > [INFO] Copying 16 resources > [INFO] [compiler:testCompile {execution: default-testCompile}] > [INFO] Not compiling test sources > [INFO] [surefire:test {execution: default-test}] > [INFO] Tests are skipped. > [INFO] [jar:jar {execution: default-jar}] > [INFO] Building jar: /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-core/target/treebase-core-1.0-SNAPSHOT.jar > [INFO] ------------------------------------------------------------------------ > [INFO] Building treebase-web > [INFO] task-segment: [clean, package] > [INFO] ------------------------------------------------------------------------ > [INFO] [clean:clean {execution: default-clean}] > [INFO] Deleting directory /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target > [INFO] [resources:resources {execution: default-resources}] > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! > [INFO] Copying 1 resource > [INFO] [compiler:compile {execution: default-compile}] > [INFO] Compiling 160 source files to /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/classes > [INFO] [resources:testResources {execution: default-testResources}] > [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! > [INFO] skip non existing resourceDirectory /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/src/test/resources > [INFO] [compiler:testCompile {execution: default-testCompile}] > [INFO] Not compiling test sources > [INFO] [surefire:test {execution: default-test}] > [INFO] Tests are skipped. > [INFO] [war:war {execution: default-war}] > [INFO] Packaging webapp > [INFO] Assembling webapp[treebase-web] in [/home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/treebase-web] > [INFO] Processing war project > [INFO] Copying webapp resources[/home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/src/main/webapp] > [INFO] Webapp assembled in[1437 msecs] > [INFO] Building war: /home/hudson/jobs/Treebase-dev/workspace/trunk/treebase-web/target/treebase-web.war > [INFO] > [INFO] > [INFO] ------------------------------------------------------------------------ > [INFO] Reactor Summary: > [INFO] ------------------------------------------------------------------------ > [INFO] Treebase .............................................. SUCCESS [2.801s] > [INFO] treebase-core ......................................... SUCCESS [12.292s] > [INFO] treebase-web .......................................... SUCCESS [17.017s] > [INFO] ------------------------------------------------------------------------ > [INFO] ------------------------------------------------------------------------ > [INFO] BUILD SUCCESSFUL > [INFO] ------------------------------------------------------------------------ > [INFO] Total time: 32 seconds > [INFO] Finished at: Tue Jan 31 17:02:12 EST 2012 > [INFO] Final Memory: 53M/382M > [INFO] ------------------------------------------------------------------------ > Deploying <http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war> to container Tomcat 5.x Remote > Redeploying [<http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war]> > Undeploying [<http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war]> > Deploying [<http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war]> > ERROR: Publisher hudson.plugins.deploy.DeployPublisher aborted due to exception > org.codehaus.cargo.container.ContainerException: Failed to deploy [<http://localhost:8888/job/Treebase-dev/ws/trunk/treebase-web/target/treebase-web.war]> > at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:111) > at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.redeploy(AbstractTomcatManagerDeployer.java:187) > at hudson.plugins.deploy.CargoContainerAdapter.deploy(CargoContainerAdapter.java:60) > at hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:86) > at hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:73) > at hudson.FilePath.act(FilePath.java:785) > at hudson.FilePath.act(FilePath.java:767) > at hudson.plugins.deploy.CargoContainerAdapter.redeploy(CargoContainerAdapter.java:73) > at hudson.plugins.deploy.DeployPublisher.perform(DeployPublisher.java:45) > at hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:36) > at hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:694) > at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:669) > at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:647) > at hudson.model.Build$RunnerImpl.post2(Build.java:162) > at hudson.model.AbstractBuild$AbstractRunner.post(AbstractBuild.java:616) > at hudson.model.Run.run(Run.java:1429) > at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46) > at hudson.model.ResourceController.execute(ResourceController.java:88) > at hudson.model.Executor.run(Executor.java:230) > Caused by: org.codehaus.cargo.container.tomcat.internal.TomcatManagerException: FAIL - Failed to deploy application at context path /treebase-web > > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.invoke(TomcatManager.java:507) > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deployImpl(TomcatManager.java:547) > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:273) > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:256) > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:240) > at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:107) > ... 18 more > org.codehaus.cargo.container.tomcat.internal.TomcatManagerException: FAIL - Failed to deploy application at context path /treebase-web > > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.invoke(TomcatManager.java:507) > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deployImpl(TomcatManager.java:547) > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:273) > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:256) > at org.codehaus.cargo.container.tomcat.internal.TomcatManager.deploy(TomcatManager.java:240) > at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.deploy(AbstractTomcatManagerDeployer.java:107) > at org.codehaus.cargo.container.tomcat.internal.AbstractTomcatManagerDeployer.redeploy(AbstractTomcatManagerDeployer.java:187) > at hudson.plugins.deploy.CargoContainerAdapter.deploy(CargoContainerAdapter.java:60) > at hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:86) > at hudson.plugins.deploy.CargoContainerAdapter$1.invoke(CargoContainerAdapter.java:73) > at hudson.FilePath.act(FilePath.java:785) > at hudson.FilePath.act(FilePath.java:767) > at hudson.plugins.deploy.CargoContainerAdapter.redeploy(CargoContainerAdapter.java:73) > at hudson.plugins.deploy.DeployPublisher.perform(DeployPublisher.java:45) > at hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:36) > at hudson.model.AbstractBuild$AbstractRunner.perform(AbstractBuild.java:694) > at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:669) > at hudson.model.AbstractBuild$AbstractRunner.performAllBuildSteps(AbstractBuild.java:647) > at hudson.model.Build$RunnerImpl.post2(Build.java:162) > at hudson.model.AbstractBuild$AbstractRunner.post(AbstractBuild.java:616) > at hudson.model.Run.run(Run.java:1429) > at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46) > at hudson.model.ResourceController.execute(ResourceController.java:88) > at hudson.model.Executor.run(Executor.java:230) > |
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From: Roderic P. <r....@bi...> - 2012-01-31 21:48:31
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I'm parsing NEXML from TreeBASE as part of a project to build a TreeBASE browser. In some cases I'm getting files where the OTU labels (in the <otus> tags) don't match the trees. I'm using XML files a grabbed late last year so I'm not sure if the issue ahs been fixed, but I can't get a more recent verison from TreeBASE - http://treebase.org/treebase-web/search/downloadAStudy.html?id=2048&format=nexml keeps timing out (sigh). The file for S2048 has three trees and three <otus> blocks. These don't seem to match. For example, tree #trees663275 claims it's OTUs are labelled by otus650205, but these otus only partially match the tree, leaving large gaps when I draw the tree. Something has gone badly amiss. It's been a hassle to get to the bottom of this partly because of the verbosity of NEXML, and partly because the labels are separated from the tree, making it a hassle to extract the two sets of labels and discover that there's a problem. Any thoughts on why the list of <otus> referred to by a tree would lack all the labels? I've attached the file that I'm working with. Regards Rod |
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From: William P. <met...@gm...> - 2012-01-31 19:09:03
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Yup -- worth doing something like this. Note that all personal info for user accounts (emails, passwords) would need to be erased; and all unpublished submissions would need to be erased. bp On Jan 31, 2012, at 1:49 PM, Hilmar Lapp wrote: > Well, yeah, that's I was suggesting with the AMI. -hilmar >> On Jan 31, 2012, at 1:18 PM, Rutger Vos wrote: >> >> By the way, wouldn't it a good idea if instead we could simply share an image of the entire treebase environment? I heard PFAM has just started doing that and it might be a good idea if we want to entice volunteer developers. |
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