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From: Vladimir G. <vla...@du...> - 2010-03-24 01:18:00
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It's only possible to delete the whole submission, not its individual parts, right? --VG Begin forwarded message: > From: "Elizabeth H. Zacharias via RT" <he...@tr...> > Date: March 23, 2010 7:26:29 PM EDT > To: undisclosed-recipients: ; > Subject: [[treebase-help] #7630] TreeBASE Submission S10318 > Reply-To: he...@tr... > > > Tue Mar 23 19:26:28 2010: Request 7630 was acted upon. > Transaction: Ticket created by eza...@oe... > Queue: Treebase-help > Subject: TreeBASE Submission S10318 > Owner: Nobody > Requestors: eza...@oe... > Status: new > Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7630 > > > > Hello, > I am trying to delete my matrix to upload the corrected one but I > can't seem to delete it. Would you help me? > Thank you, > Elizabeth Zacharias > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Elizabeth H. Zacharias, Ph.D. > Harvard University Herbaria | 22 Divinity Avenue | Cambridge, MA > 02138 | U.S.A. > Tel. 1-617-496-8514 (direct) | Fax. 1-617-495-9484 | www.huh.harvard.edu > > > > > > > > > |
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From: William P. <wil...@ya...> - 2010-03-24 01:37:34
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Youjun is working on solving the deleting-matrix problem. I don't think that deleting submissions work either. I'm suggesting to her that she rename her matrices "don't use" and simply not include them in any analysis. By the way, how do I get access to the help ticketing system? bp On Mar 23, 2010, at 9:17 PM, Vladimir Gapeyev wrote: > It's only possible to delete the whole submission, not its individual parts, right? > --VG > > Begin forwarded message: > >> From: "Elizabeth H. Zacharias via RT" <he...@tr...> >> Date: March 23, 2010 7:26:29 PM EDT >> To: undisclosed-recipients: ; >> Subject: [[treebase-help] #7630] TreeBASE Submission S10318 >> Reply-To: he...@tr... >> >> >> Tue Mar 23 19:26:28 2010: Request 7630 was acted upon. >> Transaction: Ticket created by eza...@oe... >> Queue: Treebase-help >> Subject: TreeBASE Submission S10318 >> Owner: Nobody >> Requestors: eza...@oe... >> Status: new >> Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7630 > >> >> >> Hello, >> I am trying to delete my matrix to upload the corrected one but I >> can't seem to delete it. Would you help me? >> Thank you, >> Elizabeth Zacharias >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Elizabeth H. Zacharias, Ph.D. >> Harvard University Herbaria | 22 Divinity Avenue | Cambridge, MA >> 02138 | U.S.A. >> Tel. 1-617-496-8514 (direct) | Fax. 1-617-495-9484 | www.huh.harvard.edu >> |
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From: Hilmar L. <hl...@ne...> - 2010-03-24 02:01:16
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On Mar 23, 2010, at 9:30 PM, William Piel wrote: > By the way, how do I get access to the help ticketing system? Go to https://help.nescent.org/ . Your username is wil...@ya.... There should be a button to have the system send you a new password if you don't know it anymore. You should have full permissions to the treebase-bugs and treebase- help queue. Who will be triaging the bugs so that those that are real and can't be addressed immediately get transferred to the Sf.net tracker? Let me know if that's Youjun and I'll add him to the queue watchers. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-03-24 01:41:43
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In theory it should be possible to delete a matrix from the matrixList page, but in practice clearing out all the matrix elements takes so long it hampers userfriendliness, no? On Wednesday, March 24, 2010, Vladimir Gapeyev <vla...@du...> wrote: > It's only possible to delete the whole submission, not its individual parts, right? --VG > > Begin forwarded message: > From: "Elizabeth H. Zacharias via RT" <he...@tr...>Date: March 23, 2010 7:26:29 PM EDTTo: undisclosed-recipients: ;Subject: [[treebase-help] #7630] TreeBASE Submission S10318Reply-To: he...@tr... > > Tue Mar 23 19:26:28 2010: Request 7630 was acted upon. > Transaction: Ticket created by eza...@oe... > Queue: Treebase-help > Subject: TreeBASE Submission S10318 > Owner: Nobody > Requestors: eza...@oe... > Status: new > Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7630 > > > > Hello, > I am trying to delete my matrix to upload the corrected one but I > can't seem to delete it. Would you help me? > Thank you, > Elizabeth Zacharias > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Elizabeth H. Zacharias, Ph.D. > Harvard University Herbaria | 22 Divinity Avenue | Cambridge, MA > 02138 | U.S.A. > Tel. 1-617-496-8514 (direct) | Fax. 1-617-495-9484 | www.huh.harvard.edu > > > > > > > > > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2010-03-24 02:43:56
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On Mar 23, 2010, at 9:41 PM, Rutger Vos wrote: > In theory it should be possible to delete a matrix from the matrixList > page, but in practice clearing out all the matrix elements takes so > long it hampers userfriendliness, no? Currently deleting even small matrices cause a proxy time-out. We're working of fixing this. The other thing that was never implemented in the original code is that taxon labels belonging to a deleted matrix or tree do not get deleted themselves, even if they are not used by anything else. Hence garbage builds up -- and it's confusing to the submitter to still find taxon labels there after deleting all matrices and trees. So we're also working to fix this. Youjun will try to implement this in the usual java-hibernate way, but if that proves too slow, other solutions like a Postgresql stored procedure might need to be used. bp |
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From: youjun g. <you...@ya...> - 2010-03-24 13:16:39
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The current code for deleting a matrix is a hybrid of hibernate operations and sql queries, I am going to make it 100% of sql queries. See if it will solve the problem. YOujun On Tue, Mar 23, 2010 at 10:43 PM, William Piel <wil...@ya...>wrote: > > On Mar 23, 2010, at 9:41 PM, Rutger Vos wrote: > > > In theory it should be possible to delete a matrix from the matrixList > > page, but in practice clearing out all the matrix elements takes so > > long it hampers userfriendliness, no? > > Currently deleting even small matrices cause a proxy time-out. We're > working of fixing this. > > The other thing that was never implemented in the original code is that > taxon labels belonging to a deleted matrix or tree do not get deleted > themselves, even if they are not used by anything else. Hence garbage builds > up -- and it's confusing to the submitter to still find taxon labels there > after deleting all matrices and trees. So we're also working to fix this. > > Youjun will try to implement this in the usual java-hibernate way, but if > that proves too slow, other solutions like a Postgresql stored procedure > might need to be used. > > bp > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > |
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From: Hilmar L. <hl...@ne...> - 2010-03-24 13:20:59
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On Mar 24, 2010, at 9:16 AM, youjun guo wrote: > The current code for deleting a matrix is a hybrid of hibernate > operations and sql queries, I am going to make it 100% of sql > queries. See if it will solve the problem. In theory making it 100% Hibernate should solve the problem, and should also make it consistent with the Hibernate ORM tier for data access. The more straight SQL we have in there, the more maintenance problems or risks we have down the road. Why does a pure Hibernate solution not work here? Hibernate is perfectly capable of orchestrating cascading deletes. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: youjun g. <you...@ya...> - 2010-03-24 14:28:00
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> > In theory making it 100% Hibernate should solve the problem, and should > also make it consistent with the Hibernate ORM tier for data access. The > more straight SQL we have in there, the more maintenance problems or risks > we have down the road. Why does a pure Hibernate solution not work here? > Hibernate is perfectly capable of orchestrating cascading deletes. > > -hilmar > > > Based on the information I get from Bill, the historic reason why Jin Ruan bring in SQL here is because the performance issue of hibernate. I think the sql created by hibernate is not as efficient when a task involved too many tables and too many cascade deletions. To delete a matrix we need to delete all related record from study, submission, matrix, sub_matrix matrixrow, rowsegment matrixcolumn, MATRIXCOLUMN_ITEMDEFINITION matrixelemnt, STATEMODIFIER ITEMVALUE Compound_element taxonlabelset taxonlabelset_taxonlabel taxonlabel and also need to check a group of tables to see make sure a taxonlabel is not refered by some other matrices or trees. While listing of the steps above I think our database schema may need a optimizing some how. Youjun |
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From: youjun g. <you...@ya...> - 2010-03-25 23:29:16
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Bill traversed all TB tables and finally found out to delete a matrix record, we will need to cascade delete related data from more than 50 other tables. Surprisingly the bottle neck that halt the deletion actually come from a piece of sql. So we may not need to bring in any new sql query, instead I will do some test and see if we can solve the problem with Hibernate only. Youjun On Wed, Mar 24, 2010 at 10:27 AM, youjun guo <you...@ya...> wrote: > In theory making it 100% Hibernate should solve the problem, and should >> also make it consistent with the Hibernate ORM tier for data access. The >> more straight SQL we have in there, the more maintenance problems or risks >> we have down the road. Why does a pure Hibernate solution not work here? >> Hibernate is perfectly capable of orchestrating cascading deletes. > > >> >> -hilmar >> >> >> > |
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