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From: Hilmar L. <hl...@ne...> - 2009-07-04 17:20:14
|
On Jul 3, 2009, at 6:13 PM, William Piel wrote: > cool stuff. I agree - the API is definitely heading in the right direction. I suggest some tweaks: > > I notice that this departs a bit from the phylows that is proposed > here. For example, the proposed phylows puts "/find/" before "/ > tree/", whereas you have it the other way. Right, this is not in compliance with the spec. find/ comes first as it changes the resource from a record and its URI to a finder. I.e., although it's possible that we change the spec, I don't see the reason that would justify that. In general, note that REST APIs at present aren't formally declared in a descriptor document that a general purpose validator could use and validate compliance. So really extra care needs to be taken to comply with the spec, or otherwise it's not a spec but a loose prescription. It seems like we should also implement a PhyloWS validator that uncovers violations quickly. > And the other major difference is that the proposed phylows suggest > that to search on trees you do something like: > > /phylows/find/tree/?name=Primates > > whereas you are implementing: > > /phylows/taxon/find/?name=Primates&recordSchema=tree Note BTW that a taxon finder is a custom addition to the API. Which is fine in principle, except that I'd suggest you conform to the pattern in the API spec and put find/ first. Also, find/taxon/ would imply that you are finding (and returning) taxa, which if I understand correctly is not the case - rather it seems you have one query parameter in the URI path (namely that you are searching by taxon?) and one in the query string. So if this is searching trees, it needs to be find/tree/, and if you are matching against taxon names, the query parameter needs to be tb.taxon.name or whatever the blessed metadata term for this purpose is. Third, recordSchema=tree means that you want records back in the tree schema. Unless you have invented that schema meanwhile, this is in all likelihood not what you want. Rather, the value should be nexml I suppose. find/tree already implies that you are finding (and returning) trees, so there is no point in expressing that redundantly in the query string. You might want to specify that you only want the tree and not also the matrix, but that would be a separate query parameter and should not be confounded with the return format. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2009-07-04 17:20:07
|
On Jul 4, 2009, at 3:24 AM, William Piel wrote: > Could you try adding "<?xml version="1.0" encoding="utf-8"?>" as a > header? BTW the <?xml> line is required to be present for it to be valid XML. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2009-07-04 01:25:21
|
On Jul 3, 2009, at 6:16 PM, Rutger Vos wrote: >> I notice that while the following produces a hit of one record: >> http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo >> ...yet I'm unable to get any results via rss: >> http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo&format=rss1 >> Is my syntax incorrect? > > I don't know - I *am* getting an rss feed with a single item returned. > Maybe you should "view source" to see it? Ah... indeed, it works for FireFox and Camino, but it does not work for Safari (says "zero articles"). >> Also, I believe that this should give me a list of trees: >> http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo&recordSchema=tree >> but instead it gives me a list of taxa. Perhaps my syntax is wrong? > > The recordSchema switch is only used in combination with format=rss1, > the thinking being that the web interface behaviour should stay the > same (we can switch tabs anyway to project a result set into a > different context) but for programmatic access we do need recordSchema > (because - no tabs). Ok. Although perhaps this could be a low-priority feature to be added later. (I can imagine this being a useful feature for web sites like tolweb.org and eol.org, in which for each species page they can have a simple hyperlink called "trees in TreeBASE with taxon x" -- thus avoiding users to have to make another mouse-click on a tab once they get to TreeBASE. I can't figure out why your rss does not work in Safari. For example, these two urls produce, more or less, the same content since they are making the same query: http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo&recordSchema=tree&format=rss1 http://purl.org/phylo/treebase/phylows/find/tree/?query=taxon_name+any+Homo&operation=searchRetrieve&recordSchema=pc ...by yours says "0 articles" in Safari while mine says "25 articles". Could you try adding "<?xml version="1.0" encoding="utf-8"?>" as a header? Thats the only substantive difference between the two, as far as I can tell. (also, it would be cool if yours included some other human-readable metadata -- like tree name, tree title, article citation, etc -- just a little synopsis so that people can use this in an RSS client) bp |
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From: Rutger V. <rut...@gm...> - 2009-07-03 22:17:05
|
Hi Bill, glad you like it. I think I will use this on one of the days in Lisbon to have students download data and process it. On Fri, Jul 3, 2009 at 9:13 AM, William Piel<wil...@ya...> wrote: > cool stuff. > I notice that this departs a bit from the phylows that is proposed here. > For example, the proposed phylows puts "/find/" before "/tree/", whereas > you have it the other way. And the other major difference is that the > proposed phylows suggest that to search on trees you do something like: > /phylows/find/tree/?name=Primates > whereas you are implementing: > /phylows/taxon/find/?name=Primates&recordSchema=tree The former, "standard" way to me seems very ambiguous. I would interpret it to mean the name of the tree, not of a taxon in the tree. > Your method is probably better and clearer -- in that it makes more sense > that we're doing a find on a taxon with the result being a tree (only the > taxon label is inherently part of the tree object), but perhaps we should > get the other PhyloWS developers in agreement (i.e. Ryan Scherle), and then > modify the wiki accordingly. > I notice that while the following produces a hit of one record: > http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo > ...yet I'm unable to get any results via rss: > http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo&format=rss1 > Is my syntax incorrect? I don't know - I *am* getting an rss feed with a single item returned. Maybe you should "view source" to see it? > Also, I believe that this should give me a list of trees: > http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo&recordSchema=tree > but instead it gives me a list of taxa. Perhaps my syntax is wrong? The recordSchema switch is only used in combination with format=rss1, the thinking being that the web interface behaviour should stay the same (we can switch tabs anyway to project a result set into a different context) but for programmatic access we do need recordSchema (because - no tabs). Cheers, Rutger > On Jul 2, 2009, at 9:40 PM, Rutger Vos wrote: > > erm, please substitute 8ball.sdsc.edu:6666 for localhost:8080 in the > examples below. > > On Thu, Jul 2, 2009 at 4:10 PM, Rutger Vos<rut...@gm...> wrote: > > Hi, > > I've implemented nexml export on treebase2, and made the serializer > > attach predicates from this list > > (http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw) in > > the indicated locations. The predicates with asterisks can be used as > > search predicates through the PhyloWS architecture as described here: > > http://localhost:8080/treebase-web/help/urlAPI.jsp > > In addition, CQL searches can be tried out on the main search tabs by > > clicking the "Advanced search..." links, e.g. see: > > http://localhost:8080/treebase-web/search/studySearch.html > > Rutger > > -- > > Dr. Rutger A. Vos > > Department of zoology > > University of British Columbia > > http://www.nexml.org > > http://rutgervos.blogspot.com > > > > -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
|
From: William P. <wil...@ya...> - 2009-07-03 16:14:57
|
cool stuff. I notice that this departs a bit from the phylows that is proposed here. For example, the proposed phylows puts "/find/" before "/ tree/", whereas you have it the other way. And the other major difference is that the proposed phylows suggest that to search on trees you do something like: /phylows/find/tree/?name=Primates whereas you are implementing: /phylows/taxon/find/?name=Primates&recordSchema=tree Your method is probably better and clearer -- in that it makes more sense that we're doing a find on a taxon with the result being a tree (only the taxon label is inherently part of the tree object), but perhaps we should get the other PhyloWS developers in agreement (i.e. Ryan Scherle), and then modify the wiki accordingly. I notice that while the following produces a hit of one record: http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo ...yet I'm unable to get any results via rss: http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo&format=rss1 Is my syntax incorrect? Also, I believe that this should give me a list of trees: http://8ball.sdsc.edu:6666/treebase-web/phylows/taxon/find?query=tb.title.taxon==Homo&recordSchema=tree but instead it gives me a list of taxa. Perhaps my syntax is wrong? bp On Jul 2, 2009, at 9:40 PM, Rutger Vos wrote: > erm, please substitute 8ball.sdsc.edu:6666 for localhost:8080 in the > examples below. > > On Thu, Jul 2, 2009 at 4:10 PM, Rutger Vos<rut...@gm...> > wrote: >> Hi, >> >> I've implemented nexml export on treebase2, and made the serializer >> attach predicates from this list >> (http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw) in >> the indicated locations. The predicates with asterisks can be used as >> search predicates through the PhyloWS architecture as described here: >> http://localhost:8080/treebase-web/help/urlAPI.jsp >> >> In addition, CQL searches can be tried out on the main search tabs by >> clicking the "Advanced search..." links, e.g. see: >> http://localhost:8080/treebase-web/search/studySearch.html >> >> Rutger >> >> -- >> Dr. Rutger A. Vos >> Department of zoology >> University of British Columbia >> http://www.nexml.org >> http://rutgervos.blogspot.com >> |
|
From: Rutger V. <rut...@gm...> - 2009-07-03 02:55:35
|
erm, please substitute 8ball.sdsc.edu:6666 for localhost:8080 in the examples below. On Thu, Jul 2, 2009 at 4:10 PM, Rutger Vos<rut...@gm...> wrote: > Hi, > > I've implemented nexml export on treebase2, and made the serializer > attach predicates from this list > (http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw) in > the indicated locations. The predicates with asterisks can be used as > search predicates through the PhyloWS architecture as described here: > http://localhost:8080/treebase-web/help/urlAPI.jsp > > In addition, CQL searches can be tried out on the main search tabs by > clicking the "Advanced search..." links, e.g. see: > http://localhost:8080/treebase-web/search/studySearch.html > > Rutger > > -- > Dr. Rutger A. Vos > Department of zoology > University of British Columbia > http://www.nexml.org > http://rutgervos.blogspot.com > -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
|
From: Rutger V. <rut...@gm...> - 2009-07-02 23:10:13
|
Hi, I've implemented nexml export on treebase2, and made the serializer attach predicates from this list (http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw) in the indicated locations. The predicates with asterisks can be used as search predicates through the PhyloWS architecture as described here: http://localhost:8080/treebase-web/help/urlAPI.jsp In addition, CQL searches can be tried out on the main search tabs by clicking the "Advanced search..." links, e.g. see: http://localhost:8080/treebase-web/search/studySearch.html Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
|
From: Rutger V. <rut...@gm...> - 2009-06-27 07:25:04
|
Dear Ewald, > I am trying to link my taxon labels to the names in uBio using the > above-mentioned page in the new version of the TreeBASE submission tool. > However, for many of the names I encounter the attached error page when I > enter the NameBankID manually after looking it up on the uBio web site. I investigated the issue using the nexus file you sent me, and it turned out that the errors occurred in cases where we need to process a response from the uBio web services, and the response does not contain an NCBI identifier. I fixed this as per code revision 133, which should appear on the web site the next time we reload our server. > Also, many of my taxon names (e.g. Blastacervulus eucalypti) I can find back > easily in uBio but they do not automatically appear as options in TreeBASE > when I click on "Taxon Label Editor" pencil button. There is unfortunately very little we can do about this. The issue is caused by the discrepancy between the uBio web site output and that of its web services: we know certain names exist on the uBio website but we can't get to them because they aren't being produced in a way that our server can process. > I am using a Macbook Pro running and up-to-date version of OS 10.5 with > Firefox 3.0.3 as browser. > > Please let me know if I need to supply more information. I believe we have addressed the issues you have encountered - to the extent that we have control over them - thanks to the supporting information (input file, stack trace) you have already provided. Your feedback is what we need to improve the TreeBASE web site, so if anything else comes up don't hesitate to contact us. > Kind regards, > Ewald > > J.Z. (Ewald) Groenewald, PhD > Researcher: Evolutionary Phytopathology Group > > CBS-KNAW Fungal Biodiversity Centre > An Institute of the Royal Netherlands Academy of Arts and Sciences (KNAW) > > Visiting address: > Uppsalalaan 8, Room C1.51 > 3584 CT Utrecht, The Netherlands > Postal address: > P.O. Box 85167 > 3508 AD Utrecht, The Netherlands > > work tel: +31 (0)30 212 2600 (reception) > +31 (0)30 212 2686 (direct) > work fax: +31 (0)30 251 2097 > mobile: +31 (0)65 497 4428 > e-mail: e.g...@cb... > > > > Best wishes, Rutger Vos -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
|
From: Hilmar L. <hl...@du...> - 2009-06-24 16:26:07
|
I suppose most here have seen this: Ranwez et al (2009) PhyloExplorer: a web server to validate, explore and query phylogenetic trees. BMC Evolutionary Biology 2009, 9:108 http://dx.doi.org/10.1186/1471-2148-9-108 Might be nice for getting some ideas for how the taxon name validation UI and implementation might be improved further. It's also open source :-) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu : =========================================================== |
|
From: Wayne M. <wma...@in...> - 2009-06-24 01:05:34
|
Dear Bill,
At 5:24 PM -0400 23.6.2009, William Halliday Piel wrote:
>Dear David and Wayne,
>
>As you know, TreeBASE is using a headless version of Mesquite to
>parse all incoming data.
>
>I've noticed that although Mesquite is happy parsing a tree with a
>translation table (but without a taxon block), for some reason it
>doesn't like trees that lack a translation table and a taxon block.
>
>For these tree files (e.g. the default tree file produced by MrBayes
>-- see attached), I get the following message:
>
>A block of trees has been read for which no corresponding block of
>taxa has been found, and no block of taxa could be created for it.
>If you had expected that the trees would have applied to an existing
>block of taxa, it is possible that the taxa no longer correspond
>because of changes in names or in which taxa are included.
>
>However, if a translation table exists, I get the following message
>-- which is similar, but has a much happier outcome (i.e., the tree
>gets parsed):
>
>A block of trees has been read for which no corresponding block of
>taxa is available; a new block of taxa has been created for it. If
>you had expected that the trees would have applied to an existing
>block of taxa, it is possible that the taxa no longer correspond
>because of changes in names or in which taxa are included.
>
>How is it that in one case a new block of taxa is created, but in
>the other case "no block" could be created?
The translation table is easy to parse and reinterpret as if a taxa
block. Without a translation table, Mesquite is forced to invent
taxa on the fly as it is reading a tree. Not a pretty scenario...
We can look into a change to make this work; it will take some
programming. But I seem to remember we've done this sort of thing
somewhere in the code.
Wayne
>
>Is there a workaround (e.g. a preferences flag?) that we can use so
>that Mesquite will parse MrBayes tree files without taxon blocks?
>
>thanks,
>
>Bill
>
>
>Dear David and Wayne,
>
>As you know, TreeBASE is using a headless version of Mesquite to
>parse all incoming data.
>
>I've noticed that although Mesquite is happy parsing a tree with a
>translation table (but without a taxon block), for some reason it
>doesn't like trees that lack a translation table and a taxon block.
>
>For these tree files (e.g. the default tree file produced by MrBayes
>-- see attached), I get the following message:
>
>A block of trees has been read for which no corresponding block of
>taxa has been found, and no block of taxa could be created for it.
>If you had expected that the trees wo isting block of taxa, it is
>possible that the taxa no longer correspond because of changes in
>names or in which taxa are included.
>
>
>However, if a translation table exists, I get the following message
>-- which is similar, but has a much happier outcome (i.e., the tree
>gets parsed):
>
>A block of trees has been read for which no corresponding block of
>taxa is available; a new block of taxa has been created for it. If
>you had expected that the trees would have applied to an existing
>block of taxa, it is possible that the taxa no longer correspond
>because of changes in names or in which taxa are included.
>
>
>How is it that in one case a new block of taxa is created, but in
>the other case "no block" could be created?
>
>thanks,
>
>Bill
>
>
>Attachment converted: Thrandina:RNF213IRBPMLLRhodomin3.zip
>(pZIP/«IC») (00260B04)
--
--------------------------------------------------------
Wayne Maddison
Professor and Canada Research Chair
Depts. of Zoology and Botany and
Biodiversity Research Centre
& Director
Beaty Biodiversity Museum
6270 University Boulevard
University of British Columbia
Vancouver, BC V6T 1Z4 Canada
email: wma...@in... FAX: +1 604 822-2416
Mesquite: http://mesquiteproject.org
MacClade: http://macclade.org
Salticidae: http://salticidae.org
Tree of Life: http://tolweb.org
Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
Home page: http://salticidae.org/wpm/home.html
|
|
From: William H. P. <pi...@tr...> - 2009-06-23 21:40:22
|
Dear David and Wayne, As you know, TreeBASE is using a headless version of Mesquite to parse all incoming data. I've noticed that although Mesquite is happy parsing a tree with a translation table (but without a taxon block), for some reason it doesn't like trees that lack a translation table and a taxon block. For these tree files (e.g. the default tree file produced by MrBayes -- see attached), I get the following message: A block of trees has been read for which no corresponding block of taxa has been found, and no block of taxa could be created for it. If you had expected that the trees would have applied to an existing block of taxa, it is possible that the taxa no longer correspond because of changes in names or in which taxa are included. However, if a translation table exists, I get the following message -- which is similar, but has a much happier outcome (i.e., the tree gets parsed): A block of trees has been read for which no corresponding block of taxa is available; a new block of taxa has been created for it. If you had expected that the trees would have applied to an existing block of taxa, it is possible that the taxa no longer correspond because of changes in names or in which taxa are included. How is it that in one case a new block of taxa is created, but in the other case "no block" could be created? Is there a workaround (e.g. a preferences flag?) that we can use so that Mesquite will parse MrBayes tree files without taxon blocks? thanks, Bill |
|
From: Hilmar L. <hl...@ne...> - 2009-06-16 02:06:52
|
PostgreSQL is case-insensitive for table and column names, so it doesn't really matter which case you use. It also shouldn't matter whether the Hibernate code and the schema DDL code use different case. The convention for PostgreSQL schemas and SQL code is to use lower- case for tables and columns, but if doing so is work then it shouldn't be necessary to bother. When I write SQL (whether DDL or queries) for PostgreSQL I typically use the convention of writing all SQL reserved words in all-caps whereas all tables, columns, and aliases are in all-lower. But that's only for increased readability - you can mix it wildly and it should still be syntactically correct. -hilmar On Jun 15, 2009, at 3:50 PM, Rutger Vos wrote: > Hi Hilmar, > > what would you recommend for the postgres schema: either change the > case of all table names and column names to lower case (which seems to > be more postgres-y) but then having to change the hibernate > annotations or leave as is and be "weird" w.r.t. postgres practices? > > Rutger > > > > -- > Dr. Rutger A. Vos > Department of zoology > University of British Columbia > http://www.nexml.org > http://rutgervos.blogspot.com |
|
From: Rutger V. <rut...@gm...> - 2009-06-15 22:50:26
|
Hi Hilmar, what would you recommend for the postgres schema: either change the case of all table names and column names to lower case (which seems to be more postgres-y) but then having to change the hibernate annotations or leave as is and be "weird" w.r.t. postgres practices? Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
|
From: Hayden, K. M. <KH...@be...> - 2009-06-15 19:16:19
|
Hey Rutger, Finally figured this out and I have an alternative to suggest. Instead of adding predicateHandlerMapping.properties to the JVM classpath, you could just recompile and load that source up, so that predicateHandlerMapping.properties is copied to the bin folder for anyone who checks out nexml. That way anyone setting up nexml would only have to put a path to the nexml bin in classpaths.xml and not have to worry about adding a path to predicateHandlerMapping.properties to their JVM classpath. Otherwise, adding a path to predicateHandlerMapping's directory in my .bashrc file (along with a path to nexml's bin in classpaths.xml) worked. Kasia Katherine "Kasia" Hayden Bennington College, Class of 2011 312.576.8175 kh...@be... -----Original Message----- From: Rutger Vos [mailto:rut...@gm...] Sent: Wed 6/10/2009 5:48 PM To: Hayden, Katherine M. Cc: Wayne Maddison; TreeBASE Developers; Enrico Pontelli; ju...@ig...; nex...@li...; ph...@go... Subject: Re: [Nexml-discuss] CDAO term inclusion community process Hi Kasia, you don't want to have the properties file listed in your classpaths.xml. All you need in there is the path to the root of the compiled nexml classes, i.e. <classpath>../../nexmltest/java/bin</classpath> or wherever the root of the folder structure is that contains org/nexml/model/Annotatable.class (and all other core nexml classes) and mesquite/nexml/InterpretNEXML/HyperlinkHandler.class (and all other mesquite/nexml classes). Under a clean mesquite install that path is all you need to have in your classpaths.xml, you don't need to point to the nexml source, or the mesquite source, or your Mesquite_Folder, or your properties file. The properties file needs to be in the jvm classpath (NOT in the classpaths.xml) such that it can be read from within InterpretNEXML.class. Please have a look at the code for java/src/mesquite/nexml/InterpretNEXML/InterpretNEXML.java for where that properties file is read (lines 65 and 81) and try to figure out why it's not working - reading a properties file is pretty standard so I'm a little bit at the end of my wits as to why this isn't working. Once you think you have it figured out, try loading the attached file and send me the mesquite log. The first log you sent me you were basically there except that the properties file couldn't be found. Rutger On Wed, Jun 10, 2009 at 2:07 PM, Hayden, Katherine M.<KH...@be...> wrote: > Hi Rutger, > > Thanks for spending all this time working through this! > > When I've used the url > https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java for > checkout, rather than > https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/ I don't have > the Examples folder that the hyperlink.xml file is in, so I can't read that. > > But about using the first url, I now have the problem that when I try to > export in Nexml I no longer get the default hyperlink.xml that treated > hyperlink as a predicate; instead it crashes, with the log file reproduced > below. What's odd is that for Mesquite to even load nexml now, > predicateHandlerMapping.properties must be commented out. > > So, two log files. The fist is where the .properties file is commented out > in my classpaths.xml file and thus Mesquite loads the nexml module, provides > exporting as NeXml as an option, but crashes when I try to export. The > second is when the .properties file isn't commented out in my classpaths.xml > file, but not you don't see that Mesquite loads nexml in the log. > > Error message when I try to export with nexml. Log: > > > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/dom4j-1.6.1.jar > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/JSci.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/pal.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/Jama-1.0.1.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/iText.jar > Mesquite version 2.6+ (build 499) > Copyright (c) 1997-2009 W. Maddison and D. Maddison > The basic Mesquite package (class library and basic modules) is free > software; you can redistribute it and/or modify it under the terms of the > GNU Lesser General Public License. Mesquite is distributed in the hope > that it will be useful, but WITHOUT ANY WARRANTY. For details on license > and lack of warranty see the GNU Lesser General Public License by selecting > "Display License" from the Window menu or at www.gnu.org > > Principal Authors: Wayne Maddison & David Maddison > Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver > Development Team Alumnus: Danny Mandel > > > Wed Jun 10 16:25:01 EDT 2009 > Running under Java 1.6.0_13; virtual machine by Sun Microsystems Inc. on > Linux 2.6.28-13-generic (architecture: i386) > User: kasia > > Incorporated from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/ > dom4j-1.6.1.jar JSci.zip pal.zip Jama-1.0.1.zip iText.jar > > > Mesquite directory: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/ > Log file located in: /home/kasia/Mesquite_Support_Files > Prefs directory: /home/kasia/Mesquite_Support_Files/Mesquite_Prefs > > Modules loading from directory /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/mesquite/ > > ancstates basic categ charMatrices charts cont genesis io lists minimal > parsimony stochchar trees align assoc batchArch coalesce consensus correl > distance diverse dmanager mb meristic molec ornamental pairwise rhetenor > search tol treefarm iText jama jsci pal trunk > > Additional modules loaded from > /home/kasia/workspace/MesquiteGSoC/Mesquite_Folder > > > Additional modules loaded from /home/kasia/workspace/nexmltest/java/bin > nexml > > 687 modules installed. > 1 prerelease substantive modules installed. > > Mesquite makes use of BrowserLauncher by Eric Albert, corejava.Format by > Horstmann & Cornell, and iText by Lowagie & Soares > > ------------------------------ > > > > > THIS IS A PRERELEASE (BETA) VERSION: Please do not publish results from this > version without permission of authors. > > Loading manual for searching..... manual ready. > Mesquite > openGeneral "Open_URL" > Opening external > at Wed Jun 10 16:25:13 EDT 2009 > Dialog box shown. Title: Open URL > > For console choice use component numbers > 1 <blank> > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a editable text, enter > both number of component and the text within it > (e.g. if you want to specify the text for component 1 to be "100.0", > enter "1 100.0" > > (Open URL) # > (Mesquite) # Dialog closed > Location: > http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex > > Reading NEXUS file hyperlink.nex > Reading block: TAXA > Reading block: TREES > Reading block: NOTES > Reading block: MESQUITE > File reading complete (file hyperlink.nex) > Basic File Coordinator > export > Dialog box shown. Title: Export format > > For console choice use component numbers > Export part or all of the information as a file of the following > format > -------------- > 1 List > 1 *Export NEXUS Tree File > 2 Export NEXUS Tree File from Tree Source > 3 Phylip (trees) > 4 Export Taxa Distance Matrix > 5 NeXML (taxa, matrices, trees and annotations) > -------------- > Exports NEXUS file with a tree block, and optionally a taxa block. > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a list or choice menu, enter > both number of component and number of item within it to choose > (e.g. if a list is component 1, and you want to select its item 2, enter "1 > 2" > > > (Export format) # > (Mesquite) # Dialog closed > (Following stack trace from object of class: class > mesquite.lib.PendingCommand) > java.lang.NullPointerException > at java.util.Properties$LineReader.readLine(Properties.java:418) > at java.util.Properties.load0(Properties.java:337) > at java.util.Properties.load(Properties.java:325) > at mesquite.nexml.InterpretNEXML.InterpretNEXML.exportFile(Unknown > Source) > at > mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator.export(BasicFileCoordinator.java:1003) > at > mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator.doCommand(BasicFileCoordinator.java:1488) > at mesquite.lib.PendingCommand.go(PendingCommand.java:205) > at mesquite.lib.MainThread.run(MainThread.java:116) > > Dialog box shown. Title: Crash > > For console choice use component numbers > A command could not be completed because an exception occurred (i.e. a > crash; class java.lang.NullPointerException ). WARNING: there is a chance > this crash could have corrupted your data. Please check your data > carefully. If you save any files, you might best use Save As... in case > file saving doesn't work properly. > > Please send a report of this crash to the Mesquite server, to help us debug > it and improve Mesquite. None of your data will be sent, but your log file > up to this point will be sent. > 1 (Close without sending) > 2 (OK, Send and Force Quit) > 3 (OK, Send Report and Continue) > Enter number of component to select. > > (Crash) # > (Mesquite) # Dialog closed > > > > > - Curiously, when I change my classpaths.xml file so that > predicateHandlerMapping isn't commented out, the nexml module doesn't even > load and exporting as NeXml isn't an option. classpaths.xml: > > <?xml version="1.0"?> > <mesquite> > <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath> > <classpath>predicateHandlerMapping.properties</classpath> > <!-- classpath>../../nexml/java</classpath--> > <!--classpath>../..nexml/java/src</classpath--> > > <!--classpath>../../teest/java/bin</classpath> < The test that > worked to bring up nexml option again, but crashed. Only needed this > classpath. --> > <!--classpath>../../nexmltest3/nexml/java/bin</classpath--> > <classpath>../../nexmltest/java/bin</classpath> > > </mesquite> > > > Log: > > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/dom4j-1.6.1.jar > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/JSci.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/pal.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/Jama-1.0.1.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/iText.jar > Mesquite version 2.6+ (build 499) > Copyright (c) 1997-2009 W. Maddison and D. Maddison > The basic Mesquite package (class library and basic modules) is free > software; you can redistribute it and/or modify it under the terms of the > GNU Lesser General Public License. Mesquite is distributed in the hope > that it will be useful, but WITHOUT ANY WARRANTY. For details on license > and lack of warranty see the GNU Lesser General Public License by selecting > "Display License" from the Window menu or at www.gnu.org > > Principal Authors: Wayne Maddison & David Maddison > Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver > Development Team Alumnus: Danny Mandel > > > Wed Jun 10 16:30:03 EDT 2009 > Running under Java 1.6.0_13; virtual machine by Sun Microsystems Inc. on > Linux 2.6.28-13-generic (architecture: i386) > User: kasia > > Incorporated from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/ > dom4j-1.6.1.jar JSci.zip pal.zip Jama-1.0.1.zip iText.jar > > > Mesquite directory: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/ > Log file located in: /home/kasia/Mesquite_Support_Files > Prefs directory: /home/kasia/Mesquite_Support_Files/Mesquite_Prefs > > Modules loading from directory /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/mesquite/ > > ancstates basic categ charMatrices charts cont genesis io lists minimal > parsimony stochchar trees align assoc batchArch coalesce consensus correl > distance diverse dmanager mb meristic molec ornamental pairwise rhetenor > search tol treefarm iText jama jsci pal trunk > > Additional modules loaded from > /home/kasia/workspace/MesquiteGSoC/Mesquite_Folder > > > Additional modules loaded from /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/predicateHandlerMapping.properties > > > 686 modules installed. > 1 prerelease substantive modules installed. > > Mesquite makes use of BrowserLauncher by Eric Albert, corejava.Format by > Horstmann & Cornell, and iText by Lowagie & Soares > > --------------------- > > > THIS IS A PRERELEASE (BETA) VERSION: Please do not publish results from this > version without permission of authors. > > Loading manual for searching..... manual ready. > Mesquite > openGeneral "Open_URL" > Opening external > at Wed Jun 10 16:31:08 EDT 2009 > Dialog box shown. Title: Open URL > > For console choice use component numbers > 1 <blank> > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a editable text, enter > both number of component and the text within it > (e.g. if you want to specify the text for component 1 to be "100.0", > enter "1 100.0" > > (Open URL) # > (Mesquite) # Dialog closed > Mesquite > openGeneral "Open_URL" > Opening external > at Wed Jun 10 16:31:25 EDT 2009 > Dialog box shown. Title: Open URL > > For console choice use component numbers > 1 <blank> > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a editable text, enter > both number of component and the text within it > (e.g. if you want to specify the text for component 1 to be "100.0", > enter "1 100.0" > > (Open URL) # > (Mesquite) # Dialog closed > Location: > http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex > > Reading NEXUS file hyperlink.nex > Reading block: TAXA > Reading block: TREES > Reading block: NOTES > Reading block: MESQUITE > File reading complete (file hyperlink.nex) > Basic File Coordinator > export > Dialog box shown. Title: Export format > > For console choice use component numbers > Export part or all of the information as a file of the following > format > -------------- > 1 List > 1 *Export NEXUS Tree File > 2 Export NEXUS Tree File from Tree Source > 3 Phylip (trees) > 4 Export Taxa Distance Matrix > -------------- > Exports NEXUS file with a tree block, and optionally a taxa block. > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a list or choice menu, enter > both number of component and number of item within it to choose > (e.g. if a list is component 1, and you want to select its item 2, enter "1 > 2" > > > (Export format) # > (Mesquite) # Dialog closed > > > Kasia > > > > Katherine "Kasia" Hayden > Bennington College, Class of 2011 > 312.576.8175 > kh...@be... > > > > -----Original Message----- > From: Rutger Vos [mailto:rut...@gm...] > Sent: Wed 6/10/2009 3:52 PM > To: Hayden, Katherine M. > Cc: Wayne Maddison; TreeBASE Developers; Enrico Pontelli; ju...@ig...; > nex...@li...; ph...@go... > Subject: Re: [Nexml-discuss] CDAO term inclusion community process > > Ok, so now that you have nexml as an export option, could you send the > log for when you're reading the hyperlink.xml file? > > On Wed, Jun 10, 2009 at 8:41 AM, Hayden, Katherine > M.<KH...@be...> wrote: >> Hi Rutger, >> >> I couldn't get NeXml as an export option with these new instructions, but >> when I made a test directory and used the old checkout url >> (https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java) the >> option to export as NeXml was back. Still trying to figure out the >> difference. >> >> Kasia >> >> >> >> Katherine "Kasia" Hayden >> Bennington College, Class of 2011 >> 312.576.8175 >> kh...@be... >> >> >> >> -----Original Message----- >> From: Rutger Vos [mailto:rut...@gm...] >> Sent: Wed 6/10/2009 7:07 AM >> To: Wayne Maddison >> Cc: Hayden, Katherine M.; TreeBASE Developers; Enrico Pontelli; >> ju...@ig...; nex...@li...; >> ph...@go... >> Subject: Re: [Nexml-discuss] CDAO term inclusion community process >> >> Hi, >> >> Wayne, thanks for chiming in - I changed the way the properties file >> is loaded a little bit (sorry I left the absolute paths in >> previously!). Kasia, could you try the following, >> >> - assuming $NEXMLTRUNK is your local equivalent for >> https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/ >> - assuming $MESQUITE_FOLDER is your local equivalent for >> >> http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/Mesquite%20Project/Mesquite_Folder/ >> >> * cd $NEXMLTRUNK/java >> * export CLASSPATH=$CLASSPATH:"$MESQUITE_FOLDER" >> * ant mesquite >> * pico "$MESQUITE_FOLDER/classpaths.xml" >> * add an entry in classpaths.xml: >> <classpath>$NEXMLTRUNK/java/bin/</classpath>, where $NEXMLTRUNK must >> be substituted for the real path (either relative or absolute) to the >> bin folder in which ant placed the compiled classes. Attached is how I >> have it, which works when you check the mesquite trunk and the full >> nexml code (trunk and branches) in the same folder (for me that's >> ~/Documents/workspace but it shouldn't matter) >> >> Now, when Mesquite starts up, could you copy and paste what happens in >> the log window when you read the local version of this file: >> $NEXMLTRUNK/examples/translations/hyperlink.xml >> >> Hope this helps! >> >> Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
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From: Mark D. <mj...@ge...> - 2009-06-15 15:39:17
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Rutger Vos wrote: > Mark, do you know what Val is talking about? Check out org.cipres.treebase.dao.jdbc. |
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From: <rut...@gm...> - 2009-06-13 02:10:24
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Hi, I'm sharing a google docs spreadsheet with you. It contains candidate search predicates we would like to expose through a TreeBASE web service interface. In addition, it contains the subjects they may apply to, the value space of the objects, where/how they would be expressed and retrieved in nexml and a short description of the application of each of these predicates. All implementation details aside, we imagine one should be able to search for example on dc.title='foo' and get a result set where the study titles match 'foo'. The list of predicates is a combination of dublin core/prism (for publication metadata) and a tb (TreeBASE) prefix. As a request for team CDAO, are any of the tb predicates in the spreadsheet concepts in CDAO? Could they be? To everyone else, please comment on the naming scheme. For example, it seems redundant to have taxonID and taxaID and treeID (etc.), on the other hand, it disambiguates the subject of the query. Should things be renamed? Does it make sense as is? Thanks, Rutger TreeBASE search predicates http://spreadsheets.google.com/ccc?key=rL--O7pyhR8FcnnG5-ofAlw |
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From: Rutger V. <rut...@gm...> - 2009-06-13 02:04:55
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Hi, On Fri, Jun 12, 2009 at 5:24 PM, Karen Cranston<kar...@gm...> wrote: > Can I make one initial request? Can we make this a little less TreeBASE > specific? I assume that we want to be friendly to other existing or future > databases of trees, so when we make this public, we may want to have a core > group of predicates that apply to trees in general and then examples of how > to extend to a specific implementation (e.g. the tb.matrixTB1ID, which is > pretty specific for this project). Absolutely 100% correct. I was hoping this discussion would start, because I think many of the predicates I now pushed into the tb: namespace can be moved up either to a PhyloWS vocabulary that defines generic search fields for phylogenetic web services (e.g. to lookup things by their IDs or labels) or even to CDAO (assuming the fields are relevant to CDAO's mission). Ideally only the distinction between the TreeBASE1 and TreeBASE2 identifiers would be something for the tb: vocabulary namespace. > There does seem to be a fair bit of redundancy, as well as labels whose > meaning aren't really that clear (the difference between treeKind and > treeType or matrixID and matrixLabel is not immediately obvious). treeKind and treeType are ambiguous, but that's how they are called in the treebase schema. The treeType is meant to indicate whether the tree is an atomic result (e.g. a single, optimal topology) or some kind of summary (e.g. a supertree, a consensus tree). TreeKind says something about what we assume the tips to mean (species or single sequences), which in turn says something about how the data are homologized. matrixID and matrixLabel should be obvious - they're just like taxonID and taxonLabel, or treeID and treeLabel etc. An ID is an identifier (e.g. "TreeBASE:M21313"), a Label is a human readable string (e.g. "Cytochrome B matrix, aligned using ClustalW"). > Does it > make more sense to split these into separate predicates? For example, have > matrix.xxx and tree.xxx. The matrix labels could then be used by projects > that only have data matrices (e.g. benchmark data sets for alignment or > phylogeny reconstruction) without having to worry about tree-specific terms. I think the goal is that we can run queries such as: select * from matrices where tb.matrixID='TreeBASE:M21313'; ...which implies that there is a vocabulary, identified by the tb prefix, that explains what a 'matrixID' is. I agree that it might seem less redundant to do something like: select * from matrices where matrix.id='TreeBASE:M21313'; ...but all that does is imply a separate vocabulary with a matrix prefix. This in turn implies that there would have to be vocabularies for matrix, taxon, taxa, tree, trees (etc.?) which would all have to be developed and maintained, and whose namespaces would need to be imported by whoever is formulating the query (imagine this as a SPARQL query, for example). I believe the end result is actually *more* redundancy and *longer* queries, so nothing much would be gained that way. > I'd like to see some simplification and renaming. Are there places where we > can make use of Darwin Core terms rather than defining new terms? DWC has a > datasetID as well as a whole pile of Taxon-related terms. Good idea, haven't looked at that yet. Thanks for your comments - let's keep this discussion going! Rutger > On Jun 12, 2009, at 4:45 PM, rut...@gm... wrote: > >> >> Hi, >> >> I'm sharing a google docs spreadsheet with you. It contains candidate >> search predicates we would like to expose through a TreeBASE web service >> interface. In addition, it contains the subjects they may apply to, the >> value space of the objects, where/how they would be expressed and >> retrieved >> in nexml and a short description of the application of each of these >> predicates. >> >> All implementation details aside, we imagine one should be able to search >> for example on dc.title='foo' and get a result set where the study titles >> match 'foo'. The list of predicates is a combination of dublin core/prism >> (for publication metadata) and a tb (TreeBASE) prefix. >> >> As a request for team CDAO, are any of the tb predicates in the >> spreadsheet >> concepts in CDAO? Could they be? >> >> To everyone else, please comment on the naming scheme. For example, it >> seems redundant to have taxonID and taxaID and treeID (etc.), on the other >> hand, it disambiguates the subject of the query. Should things be renamed? >> Does it make sense as is? >> >> Thanks, >> >> Rutger >> >> TreeBASE search predicates >> http://spreadsheets.google.com/ccc?key=rL--O7pyhR8FcnnG5-ofAlw >> >> --~--~---------~--~----~------------~-------~--~----~ >> You received this message because you are subscribed to the Google Groups >> "PhyloWS" group. >> To post to this group, send email to ph...@go... >> To unsubscribe from this group, send email to >> phy...@go... >> For more options, visit this group at >> http://groups.google.com/group/phylows?hl=en >> -~----------~----~----~----~------~----~------~--~--- >> > > -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
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From: Rutger V. <rut...@gm...> - 2009-06-13 01:15:33
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Hi, On Fri, Jun 12, 2009 at 5:23 PM, William Piel<wil...@ya...> wrote: > Thanks Rutger. This is really useful. > > Some questions: > > -- Regarding the "prism.startingPage" and "prism.endingPage", I think our > model stores these in one field (i.e. "123-132") -- I guess that means > splitting the field with some sort of regular expression -- e.g. > /^(\d+)[\s-\.]+(\d*)$/ -- unless prism also offers a combined "pages" > option. There is a pageRange property, which I've added. > -- In instances where an LSID exists (e.g. all taxonNamebankIDs have LSIDs), > would it be better to offer that, or stick with CDAO? W.r.t. the identifiers I'm the least pleased with what I'm suggesting. Now the identifiers are treated as TreeBASE specific (e.g. tb:taxonID). It's possible that these can be moved into CDAO, or, if objects have IDs doesn't seem to fit in with CDAO's mission of representing the core knowledge of phylogenetics (and IDs are more of an implementation detail) maybe they should be moved into a PhyloWS vocabulary? And should different classes of IDs have different syntax, e.g. a special predicate for LSIDs, versus namespaced IDs for other authorities (say, "TreeBASE:Tr1231", "Dryad:2324" etc.)? > -- I was, in a way, chagrined to see that a new "superset" of taxa is > available -- the GNI (http://globalnames.org/). They've essentially grabbed > all of uBio's data and added Species2000 and ZooBank to become a source of > names for EOL and GBIF, together with a names architecture > (http://gnapartnership.org/gna/wiki) that is under development. Given (a) > the similarity with uBio's mission, and (b) the fact that big money players > are involved while uBio seems to be languishing, it may be that this marks > the beginning of the end for uBio. And that may mean that some day a lot of > our taxon intel work will need to be rewritten. I only mention this in case > a bit of foresight, while designing our API terms, might help us adapt to a > future changing name informatics landscape. > -- I take it that separate dc.creator elements are created for each author: > is there a way to communicate author order? Actually, this is treated inconsistently in practice: I've seen multiple dc:creator annotations with one author each and I've seen them all concatenated within a single dc:creator annotation. I would like us to be as granular as possible so I'd favour the former. Alternatively, authors could be annotated using FOAF, so we can break it down in first/last/middle name, and add other contact info (email). > -- Is there a dc. or prism. for author email, abstract, or keywords? There is a prism.keyword (used as a set of atomic annotations) and dc.subject (best practice dictates this would be a comma-separated list of terms from a controlled vocab.). If we want to make available more about authors/editors perhaps we might use FOAF? > [Actually, I just realized that I was think about all this vocabulary > largely in terms of decorating returned NeXML with metadata rather than as > PhyloWS search terms. Of course people don't need to search on "email" > (etc)] Mmmm... maybe they do need to search on "email", I don't want to presume to know that :) Rutger > On Jun 12, 2009, at 7:45 PM, rut...@gm... wrote: > >> Hi, >> >> I'm sharing a google docs spreadsheet with you. It contains candidate >> search predicates we would like to expose through a TreeBASE web service >> interface. In addition, it contains the subjects they may apply to, the >> value space of the objects, where/how they would be expressed and retrieved >> in nexml and a short description of the application of each of these >> predicates. >> >> All implementation details aside, we imagine one should be able to search >> for example on dc.title='foo' and get a result set where the study titles >> match 'foo'. The list of predicates is a combination of dublin core/prism >> (for publication metadata) and a tb (TreeBASE) prefix. >> >> As a request for team CDAO, are any of the tb predicates in the >> spreadsheet concepts in CDAO? Could they be? >> >> To everyone else, please comment on the naming scheme. For example, it >> seems redundant to have taxonID and taxaID and treeID (etc.), on the other >> hand, it disambiguates the subject of the query. Should things be renamed? >> Does it make sense as is? >> >> Thanks, >> >> Rutger >> >> TreeBASE search predicates >> http://spreadsheets.google.com/ccc?key=rL--O7pyhR8FcnnG5-ofAlw > > > > > -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
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From: <rut...@gm...> - 2009-06-13 00:11:38
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Hi, I'm sharing a google docs spreadsheet with you. It contains candidate search predicates we would like to expose through a TreeBASE web service interface. In addition, it contains the subjects they may apply to, the value space of the objects, where/how they would be expressed and retrieved in nexml and a short description of the application of each of these predicates. All implementation details aside, we imagine one should be able to search for example on dc.title='foo' and get a result set where the study titles match 'foo'. The list of predicates is a combination of dublin core/prism (for publication metadata) and a tb (TreeBASE) prefix. As a request for team CDAO, are any of the tb predicates in the spreadsheet concepts in CDAO? Could they be? To everyone else, please comment on the naming scheme. For example, it seems redundant to have taxonID and taxaID and treeID (etc.), on the other hand, it disambiguates the subject of the query. Should things be renamed? Does it make sense as is? Thanks, Rutger TreeBASE search predicates http://spreadsheets.google.com/ccc?key=rL--O7pyhR8FcnnG5-ofAlw |
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From: William P. <wil...@ya...> - 2009-06-12 20:33:50
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On Jun 12, 2009, at 4:11 PM, Rutger Vos wrote: > I've never come across those optimizations, so I'm not sure. Raw HQL, > yes, but SQL, haven't seen it. I might be missing something though; > Mark, do you know what Val is talking about? I seem to remember that the inserting of character records (after parsing a nexus file) was a big choke point, and that Jin had to "bypass" Hibernate to increase speed. I don't know whether this means "raw HQL" or passing SQL via JDBC... bp |
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From: Rutger V. <rut...@gm...> - 2009-06-12 20:11:58
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I've never come across those optimizations, so I'm not sure. Raw HQL, yes, but SQL, haven't seen it. I might be missing something though; Mark, do you know what Val is talking about? On Fri, Jun 12, 2009 at 8:09 AM, Val Tannen<va...@ci...> wrote: >> > > Rutger writes: > >> annotations) need to be changed. The treebase code is pretty >> well-behaved (no raw sql) > > Are you sure about this? I was under the impression that Jin > had added some optimizations that use SQL directly. > Val > > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
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From: Val T. <va...@ci...> - 2009-06-12 15:09:24
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> Rutger writes: > annotations) need to be changed. The treebase code is pretty > well-behaved (no raw sql) Are you sure about this? I was under the impression that Jin had added some optimizations that use SQL directly. Val |
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From: Mark D. <mj...@ge...> - 2009-06-12 13:30:54
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Rutger Vos wrote: > Hence, one action item is to ask Mark Miller > if we can temporarily get some more space to dump these archives (if I > recall correctly he promised that would be possible). I requested this on 8 June, and sent a followup yesterday. If I don't hear back by midday Monday I will get Mark Miller involved. > > Assuming we can serve it up at SDSC the next step is to get it to > NESCent, and this may entail a download of dozens of gigabytes. Unlikely. The whole thing is only 27GB uncompressed, and it seems to compress at better than 90%. |
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From: Rutger V. <rut...@gm...> - 2009-06-12 11:04:51
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Hi, we are nearly at the point of being able to make gzip-compressed archives of insert statements for all tables available for download from SDSC (i.e. data dumps). Mark and I have been working on some scripts that fetch all the data for all tables, reformat it to inserts and pipe it into gzip. I ran some tests on a local pg install and the data imports correctly. However, I haven't been able to test this for all tables because I couldn't run the dumper to completion on gigahertz.sdsc.edu - because of disk quota overruns. Hence, one action item is to ask Mark Miller if we can temporarily get some more space to dump these archives (if I recall correctly he promised that would be possible). Assuming we can serve it up at SDSC the next step is to get it to NESCent, and this may entail a download of dozens of gigabytes. Not an impossibility, but maybe we want to serve up checksum files (md5) as well so we can check whether everything arrived correctly. The second thing that needs to happen is to port the schema from db2's version of SQL to postgresql's. Attached is a script that does that: the lines prefixed with --'s are the commands to create a db2 instance, the uncommented lines next to the equivalent blocks do the same for pg. I've had to make some choices: * pg likes lower case, so all table names and column names have become lower case (whereas they are all upper on DB2) * USER (or user) is a reserved word for pg, so it always has to be quoted "user" (same for "type", "version", "name", "input", "value", "nchar" and "password") * DOUBLE is called DOUBLE PRECISION on pg * CLOBs are mapped onto TEXT * the big integers that are used for identifiers are created as follows on db2: "BIGINT GENERATED BY DEFAULT AS IDENTITY (START WITH 1, INCREMENT BY 1, CACHE 20) NOT NULL," ...but in the pg version they are simply BIGINT NOT NULL (I'm sure we can improve on this.). Other than these issues pg quite happily accepted the same SQL for creating indices, primary and foreign keys as needed for db2 instances. The third thing that needs to happen is to test the treebase hibernate code against pg. Given the case changes (table and column names have gone from uppercase to lowercase), maybe some of the mappings (java annotations) need to be changed. The treebase code is pretty well-behaved (no raw sql) so beyond those annotations there's probably not that much work to do inside the java code. Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
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From: Rutger V. <rut...@gm...> - 2009-06-10 21:50:05
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Hi Kasia, you don't want to have the properties file listed in your classpaths.xml. All you need in there is the path to the root of the compiled nexml classes, i.e. <classpath>../../nexmltest/java/bin</classpath> or wherever the root of the folder structure is that contains org/nexml/model/Annotatable.class (and all other core nexml classes) and mesquite/nexml/InterpretNEXML/HyperlinkHandler.class (and all other mesquite/nexml classes). Under a clean mesquite install that path is all you need to have in your classpaths.xml, you don't need to point to the nexml source, or the mesquite source, or your Mesquite_Folder, or your properties file. The properties file needs to be in the jvm classpath (NOT in the classpaths.xml) such that it can be read from within InterpretNEXML.class. Please have a look at the code for java/src/mesquite/nexml/InterpretNEXML/InterpretNEXML.java for where that properties file is read (lines 65 and 81) and try to figure out why it's not working - reading a properties file is pretty standard so I'm a little bit at the end of my wits as to why this isn't working. Once you think you have it figured out, try loading the attached file and send me the mesquite log. The first log you sent me you were basically there except that the properties file couldn't be found. Rutger On Wed, Jun 10, 2009 at 2:07 PM, Hayden, Katherine M.<KH...@be...> wrote: > Hi Rutger, > > Thanks for spending all this time working through this! > > When I've used the url > https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java for > checkout, rather than > https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/ I don't have > the Examples folder that the hyperlink.xml file is in, so I can't read that. > > But about using the first url, I now have the problem that when I try to > export in Nexml I no longer get the default hyperlink.xml that treated > hyperlink as a predicate; instead it crashes, with the log file reproduced > below. What's odd is that for Mesquite to even load nexml now, > predicateHandlerMapping.properties must be commented out. > > So, two log files. The fist is where the .properties file is commented out > in my classpaths.xml file and thus Mesquite loads the nexml module, provides > exporting as NeXml as an option, but crashes when I try to export. The > second is when the .properties file isn't commented out in my classpaths.xml > file, but not you don't see that Mesquite loads nexml in the log. > > Error message when I try to export with nexml. Log: > > > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/dom4j-1.6.1.jar > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/JSci.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/pal.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/Jama-1.0.1.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/iText.jar > Mesquite version 2.6+ (build 499) > Copyright (c) 1997-2009 W. Maddison and D. Maddison > The basic Mesquite package (class library and basic modules) is free > software; you can redistribute it and/or modify it under the terms of the > GNU Lesser General Public License. Mesquite is distributed in the hope > that it will be useful, but WITHOUT ANY WARRANTY. For details on license > and lack of warranty see the GNU Lesser General Public License by selecting > "Display License" from the Window menu or at www.gnu.org > > Principal Authors: Wayne Maddison & David Maddison > Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver > Development Team Alumnus: Danny Mandel > > > Wed Jun 10 16:25:01 EDT 2009 > Running under Java 1.6.0_13; virtual machine by Sun Microsystems Inc. on > Linux 2.6.28-13-generic (architecture: i386) > User: kasia > > Incorporated from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/ > dom4j-1.6.1.jar JSci.zip pal.zip Jama-1.0.1.zip iText.jar > > > Mesquite directory: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/ > Log file located in: /home/kasia/Mesquite_Support_Files > Prefs directory: /home/kasia/Mesquite_Support_Files/Mesquite_Prefs > > Modules loading from directory /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/mesquite/ > > ancstates basic categ charMatrices charts cont genesis io lists minimal > parsimony stochchar trees align assoc batchArch coalesce consensus correl > distance diverse dmanager mb meristic molec ornamental pairwise rhetenor > search tol treefarm iText jama jsci pal trunk > > Additional modules loaded from > /home/kasia/workspace/MesquiteGSoC/Mesquite_Folder > > > Additional modules loaded from /home/kasia/workspace/nexmltest/java/bin > nexml > > 687 modules installed. > 1 prerelease substantive modules installed. > > Mesquite makes use of BrowserLauncher by Eric Albert, corejava.Format by > Horstmann & Cornell, and iText by Lowagie & Soares > > ------------------------------ > > > > > THIS IS A PRERELEASE (BETA) VERSION: Please do not publish results from this > version without permission of authors. > > Loading manual for searching..... manual ready. > Mesquite > openGeneral "Open_URL" > Opening external > at Wed Jun 10 16:25:13 EDT 2009 > Dialog box shown. Title: Open URL > > For console choice use component numbers > 1 <blank> > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a editable text, enter > both number of component and the text within it > (e.g. if you want to specify the text for component 1 to be "100.0", > enter "1 100.0" > > (Open URL) # > (Mesquite) # Dialog closed > Location: > http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex > > Reading NEXUS file hyperlink.nex > Reading block: TAXA > Reading block: TREES > Reading block: NOTES > Reading block: MESQUITE > File reading complete (file hyperlink.nex) > Basic File Coordinator > export > Dialog box shown. Title: Export format > > For console choice use component numbers > Export part or all of the information as a file of the following > format > -------------- > 1 List > 1 *Export NEXUS Tree File > 2 Export NEXUS Tree File from Tree Source > 3 Phylip (trees) > 4 Export Taxa Distance Matrix > 5 NeXML (taxa, matrices, trees and annotations) > -------------- > Exports NEXUS file with a tree block, and optionally a taxa block. > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a list or choice menu, enter > both number of component and number of item within it to choose > (e.g. if a list is component 1, and you want to select its item 2, enter "1 > 2" > > > (Export format) # > (Mesquite) # Dialog closed > (Following stack trace from object of class: class > mesquite.lib.PendingCommand) > java.lang.NullPointerException > at java.util.Properties$LineReader.readLine(Properties.java:418) > at java.util.Properties.load0(Properties.java:337) > at java.util.Properties.load(Properties.java:325) > at mesquite.nexml.InterpretNEXML.InterpretNEXML.exportFile(Unknown > Source) > at > mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator.export(BasicFileCoordinator.java:1003) > at > mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator.doCommand(BasicFileCoordinator.java:1488) > at mesquite.lib.PendingCommand.go(PendingCommand.java:205) > at mesquite.lib.MainThread.run(MainThread.java:116) > > Dialog box shown. Title: Crash > > For console choice use component numbers > A command could not be completed because an exception occurred (i.e. a > crash; class java.lang.NullPointerException ). WARNING: there is a chance > this crash could have corrupted your data. Please check your data > carefully. If you save any files, you might best use Save As... in case > file saving doesn't work properly. > > Please send a report of this crash to the Mesquite server, to help us debug > it and improve Mesquite. None of your data will be sent, but your log file > up to this point will be sent. > 1 (Close without sending) > 2 (OK, Send and Force Quit) > 3 (OK, Send Report and Continue) > Enter number of component to select. > > (Crash) # > (Mesquite) # Dialog closed > > > > > - Curiously, when I change my classpaths.xml file so that > predicateHandlerMapping isn't commented out, the nexml module doesn't even > load and exporting as NeXml isn't an option. classpaths.xml: > > <?xml version="1.0"?> > <mesquite> > <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath> > <classpath>predicateHandlerMapping.properties</classpath> > <!-- classpath>../../nexml/java</classpath--> > <!--classpath>../..nexml/java/src</classpath--> > > <!--classpath>../../teest/java/bin</classpath> < The test that > worked to bring up nexml option again, but crashed. Only needed this > classpath. --> > <!--classpath>../../nexmltest3/nexml/java/bin</classpath--> > <classpath>../../nexmltest/java/bin</classpath> > > </mesquite> > > > Log: > > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/dom4j-1.6.1.jar > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/JSci.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/pal.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/Jama-1.0.1.zip > Jar file added to classpath: /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/jars/iText.jar > Mesquite version 2.6+ (build 499) > Copyright (c) 1997-2009 W. Maddison and D. Maddison > The basic Mesquite package (class library and basic modules) is free > software; you can redistribute it and/or modify it under the terms of the > GNU Lesser General Public License. Mesquite is distributed in the hope > that it will be useful, but WITHOUT ANY WARRANTY. For details on license > and lack of warranty see the GNU Lesser General Public License by selecting > "Display License" from the Window menu or at www.gnu.org > > Principal Authors: Wayne Maddison & David Maddison > Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver > Development Team Alumnus: Danny Mandel > > > Wed Jun 10 16:30:03 EDT 2009 > Running under Java 1.6.0_13; virtual machine by Sun Microsystems Inc. on > Linux 2.6.28-13-generic (architecture: i386) > User: kasia > > Incorporated from /home/kasia/workspace/Mesquite Project/Mesquite_Folder/ > dom4j-1.6.1.jar JSci.zip pal.zip Jama-1.0.1.zip iText.jar > > > Mesquite directory: /home/kasia/workspace/Mesquite Project/Mesquite_Folder/ > Log file located in: /home/kasia/Mesquite_Support_Files > Prefs directory: /home/kasia/Mesquite_Support_Files/Mesquite_Prefs > > Modules loading from directory /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/mesquite/ > > ancstates basic categ charMatrices charts cont genesis io lists minimal > parsimony stochchar trees align assoc batchArch coalesce consensus correl > distance diverse dmanager mb meristic molec ornamental pairwise rhetenor > search tol treefarm iText jama jsci pal trunk > > Additional modules loaded from > /home/kasia/workspace/MesquiteGSoC/Mesquite_Folder > > > Additional modules loaded from /home/kasia/workspace/Mesquite > Project/Mesquite_Folder/predicateHandlerMapping.properties > > > 686 modules installed. > 1 prerelease substantive modules installed. > > Mesquite makes use of BrowserLauncher by Eric Albert, corejava.Format by > Horstmann & Cornell, and iText by Lowagie & Soares > > --------------------- > > > THIS IS A PRERELEASE (BETA) VERSION: Please do not publish results from this > version without permission of authors. > > Loading manual for searching..... manual ready. > Mesquite > openGeneral "Open_URL" > Opening external > at Wed Jun 10 16:31:08 EDT 2009 > Dialog box shown. Title: Open URL > > For console choice use component numbers > 1 <blank> > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a editable text, enter > both number of component and the text within it > (e.g. if you want to specify the text for component 1 to be "100.0", > enter "1 100.0" > > (Open URL) # > (Mesquite) # Dialog closed > Mesquite > openGeneral "Open_URL" > Opening external > at Wed Jun 10 16:31:25 EDT 2009 > Dialog box shown. Title: Open URL > > For console choice use component numbers > 1 <blank> > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a editable text, enter > both number of component and the text within it > (e.g. if you want to specify the text for component 1 to be "100.0", > enter "1 100.0" > > (Open URL) # > (Mesquite) # Dialog closed > Location: > http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex > > Reading NEXUS file hyperlink.nex > Reading block: TAXA > Reading block: TREES > Reading block: NOTES > Reading block: MESQUITE > File reading complete (file hyperlink.nex) > Basic File Coordinator > export > Dialog box shown. Title: Export format > > For console choice use component numbers > Export part or all of the information as a file of the following > format > -------------- > 1 List > 1 *Export NEXUS Tree File > 2 Export NEXUS Tree File from Tree Source > 3 Phylip (trees) > 4 Export Taxa Distance Matrix > -------------- > Exports NEXUS file with a tree block, and optionally a taxa block. > 2 (Cancel) > 3 (OK) > Enter number of component to select. > If component is a list or choice menu, enter > both number of component and number of item within it to choose > (e.g. if a list is component 1, and you want to select its item 2, enter "1 > 2" > > > (Export format) # > (Mesquite) # Dialog closed > > > Kasia > > > > Katherine "Kasia" Hayden > Bennington College, Class of 2011 > 312.576.8175 > kh...@be... > > > > -----Original Message----- > From: Rutger Vos [mailto:rut...@gm...] > Sent: Wed 6/10/2009 3:52 PM > To: Hayden, Katherine M. > Cc: Wayne Maddison; TreeBASE Developers; Enrico Pontelli; ju...@ig...; > nex...@li...; ph...@go... > Subject: Re: [Nexml-discuss] CDAO term inclusion community process > > Ok, so now that you have nexml as an export option, could you send the > log for when you're reading the hyperlink.xml file? > > On Wed, Jun 10, 2009 at 8:41 AM, Hayden, Katherine > M.<KH...@be...> wrote: >> Hi Rutger, >> >> I couldn't get NeXml as an export option with these new instructions, but >> when I made a test directory and used the old checkout url >> (https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java) the >> option to export as NeXml was back. Still trying to figure out the >> difference. >> >> Kasia >> >> >> >> Katherine "Kasia" Hayden >> Bennington College, Class of 2011 >> 312.576.8175 >> kh...@be... >> >> >> >> -----Original Message----- >> From: Rutger Vos [mailto:rut...@gm...] >> Sent: Wed 6/10/2009 7:07 AM >> To: Wayne Maddison >> Cc: Hayden, Katherine M.; TreeBASE Developers; Enrico Pontelli; >> ju...@ig...; nex...@li...; >> ph...@go... >> Subject: Re: [Nexml-discuss] CDAO term inclusion community process >> >> Hi, >> >> Wayne, thanks for chiming in - I changed the way the properties file >> is loaded a little bit (sorry I left the absolute paths in >> previously!). Kasia, could you try the following, >> >> - assuming $NEXMLTRUNK is your local equivalent for >> https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/ >> - assuming $MESQUITE_FOLDER is your local equivalent for >> >> http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/Mesquite%20Project/Mesquite_Folder/ >> >> * cd $NEXMLTRUNK/java >> * export CLASSPATH=$CLASSPATH:"$MESQUITE_FOLDER" >> * ant mesquite >> * pico "$MESQUITE_FOLDER/classpaths.xml" >> * add an entry in classpaths.xml: >> <classpath>$NEXMLTRUNK/java/bin/</classpath>, where $NEXMLTRUNK must >> be substituted for the real path (either relative or absolute) to the >> bin folder in which ant placed the compiled classes. Attached is how I >> have it, which works when you check the mesquite trunk and the full >> nexml code (trunk and branches) in the same folder (for me that's >> ~/Documents/workspace but it shouldn't matter) >> >> Now, when Mesquite starts up, could you copy and paste what happens in >> the log window when you read the local version of this file: >> $NEXMLTRUNK/examples/translations/hyperlink.xml >> >> Hope this helps! >> >> Rutger -- Dr. Rutger A. Vos Department of zoology University of British Columbia http://www.nexml.org http://rutgervos.blogspot.com |
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