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From: SourceForge.net <no...@so...> - 2009-05-07 09:24:58
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Bugs item #2666103, was opened at 2009-03-05 20:12 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2666103&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Priority: 3 Private: No Submitted By: Mark Dominus (mjdominus) >Assigned to: Rutger Vos (rvos) Summary: Column sorting on taxon search results is done per-group Initial Comment: Suppose I do a taxon search and get 60 results. This is broken up and displayed as 3 groups of 20 each, in an essentially random order. Now I would like to read through these in alphabetical order by taxon label. I click the "taxon label" column heading and it displays, not the alphabetically-first 20 taxa, but the random first group in alphabetical order. For example, suppose the random order dictates that the item "Aardwolf aarhusi" happens to appear in the second group. Then it will still appear in the second group (albiet at the top of that group, in the 21st position overall) even after I request that the items be sorted by taxonlabel. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-05-07 09:24 Message: As of rev. 6453, taxon search results are no longer displayed as paged groups, so this issue is now moot. ---------------------------------------------------------------------- Comment By: Mark Dominus (mjdominus) Date: 2009-03-11 19:17 Message: BP says: Minor bug. Not required for beta, but will will get complaints. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2666103&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-07 09:16:59
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Bugs item #2785703, was opened at 2009-05-02 17:32 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2785703&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: None Status: Open Priority: 5 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Mark Dominus (mjdominus) Summary: CHARSTATELABELS missing in continuous data Initial Comment: Uploading a continuous dataset that has CHARSTATELABELS fails to store the CHARSTATELABELS and fails to reconstruct them in the downloaded/reconstructed file. Continuous characters do not have state labels, but they have the names/title of characters. Compare the attached data-in vs the data-out to see what has failed to be captured. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-05-07 09:16 Message: Shouldn't we be using CHARLABELS, not CHARSTATELABELS, for continuous matrices? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2785703&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-07 09:14:33
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Bugs item #2683609, was opened at 2009-03-11 19:01 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2683609&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: piel >Status: Closed Priority: 4 Private: No Submitted By: Mark Dominus (mjdominus) Assigned to: Rutger Vos (rvos) Summary: Expose more citation information in study summary page Initial Comment: BP says: Also, other citation information should at least be exposed in the Summary page. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-05-07 09:14 Message: As of rev. 6453, the citation summary page now lists: * legacy id * full reference * authors (+ email addresses) * abstract * keywords * bibtex reference * ris reference ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2683609&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-07 09:05:25
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Bugs item #2683246, was opened at 2009-03-11 16:48 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2683246&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. >Category: ui Group: tannen >Status: Closed Priority: 4 Private: No Submitted By: Mark Dominus (mjdominus) >Assigned to: Rutger Vos (rvos) Summary: tree<->Matrix conversions don't work Initial Comment: They lost the search results entirely. This has low priority because the tree-matrix conversion is not required for beta testing. change #2683245 is acceptable instead. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-05-07 09:05 Message: As of rev. 6453, tree<->Matrix conversions *do* work. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2683246&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-07 09:02:49
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Bugs item #2712101, was opened at 2009-03-25 16:21 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2712101&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: piel >Status: Closed Priority: 4 Private: No Submitted By: Mark Dominus (mjdominus) >Assigned to: Rutger Vos (rvos) Summary: Taxon search results page length is not configurable Initial Comment: > > - the Taxa tab (which still has the ORDER BY bug) would be more useful > if there was a pop-up list to specify how many rows to display per page. > (e.g.: 20, 50, 100, 1000, and >1000). ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-05-07 09:02 Message: As of rev. 6453, the taxon search results are displayed as one list, not as paged results. This bug report is moot. ---------------------------------------------------------------------- Comment By: Mark Dominus (mjdominus) Date: 2009-03-25 16:21 Message: (Report above is from BP.) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2712101&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-07 09:01:00
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Bugs item #2712100, was opened at 2009-03-25 16:20 Message generated for change (Settings changed) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2712100&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: piel >Status: Closed Priority: 4 Private: No Submitted By: Mark Dominus (mjdominus) >Assigned to: Rutger Vos (rvos) Summary: Study summary displays incomplete citation Initial Comment: > - we need to expose other study metadata to the user. For example, when > the user looks here > <http://8ball.sdsc.edu:6666/treebase-web/search/study/summary.html?id=1975>, > he doesn't see the full citation, including volume and pages: > > Dikow T. 2009. Phylogeny of Asilidae inferred from morphological > characters of imagines (Insecta: Diptera: Brachycera: Asiloidea). > Bulletin of the American Museum of Natural History, 319: 1-175. > > (incidentally, we must already have some classes for creating this full > citation because this is presented to the submitting author in a summary > section). > ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-05-07 09:00 Message: As of rev. 6453 the full citation is displayed. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2712100&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-07 08:59:21
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Bugs item #2787978, was opened at 2009-05-06 17:31 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787978&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: easy >Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Rutger Vos (rvos) Summary: Trees don't always display in PhyloWidget Initial Comment: Search on study 1902 (Ranwez V., Berry V., Criscuolo A., Fabre P., Guillemot S., Scornavacca C., & Douzery E. 2007. PhySIC: a veto supertree method with desirable properties. Systematic Biology); get a list of trees; try to view on of the trees in PhyloWidget -- does not show up. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-05-07 08:59 Message: Fixed as of rev. 6453. The controller class now writes a default newick string as a parameter for phylowidget. This newick string is displayed, not the 'Homo sapiens' placeholder. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787978&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-07 08:54:09
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Bugs item #2683271, was opened at 2009-03-11 16:56 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2683271&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: tannen >Status: Closed Priority: 2 Private: No Submitted By: Mark Dominus (mjdominus) Assigned to: Rutger Vos (rvos) Summary: heisenbug in phylowidget popup window Initial Comment: Start with a fresh session. Go to matrix search. Search by TITLE for "M679". One matrix will come up. Go into its detail page. Return to the matrix's study. View the list of the study's trees. The magnifying-glass link javascript looks okay, but the window that it pops up SOMETIMES is missing the tree and has only a trivial "homo sapiens" tree instead. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-05-07 08:54 Message: Fixed as of revision 6453: a default tree is now written into phylowidget by the controller, so the "homo sapiens" node now never shows. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-03-19 06:19 Message: Still trying to figure this out. Looks like the failure is associated with a PrivilegedActionException/InvocationTargetException ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2683271&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-07 02:55:12
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Bugs item #2783189, was opened at 2009-04-28 20:28 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2783189&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: Mark Dominus (mjdominus) Assigned to: Rutger Vos (rvos) Summary: Icon missing from icon legend Initial Comment: http://8ball.sdsc.edu:6666/treebase-web/user/treeList.html contains an icon http://8ball.sdsc.edu:6666/treebase-web/images/icons/exclamation.png which is not mentioned in the legend at http://8ball.sdsc.edu:6666/treebase-web/help/iconLegend.jsp ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-05-07 02:55 Message: Fixed as of revision 6448. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2783189&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-06 17:57:06
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Bugs item #2787987, was opened at 2009-05-06 13:57 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787987&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: piel Status: Open Priority: 3 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Discard All button in tree topologies takes you to trees tab Initial Comment: Clicking the "Discard All Results" button in the "Tree Topologies" tab takes the user to the "Trees" tab when it should stay in the same tab. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787987&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-06 17:44:26
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Bugs item #2787981, was opened at 2009-05-06 13:39 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787981&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: piel Status: Open Priority: 3 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Quicklinks in phylowidget page open to new window Initial Comment: It would be better if the quicklinks in the phylowidget page returned results into the same window, rather than into a new window. ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2009-05-06 13:44 Message: Whoops... after trying this again a few times, it seems to be working. I'm not sure how I got to the point where the quicklinks were opening new windows.. requires more research ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787981&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-06 17:39:31
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Bugs item #2787981, was opened at 2009-05-06 13:39 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787981&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: piel Status: Open Priority: 3 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Quicklinks in phylowidget page open to new window Initial Comment: It would be better if the quicklinks in the phylowidget page returned results into the same window, rather than into a new window. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787981&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-06 17:31:54
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Bugs item #2787978, was opened at 2009-05-06 13:31 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787978&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: easy Status: Open Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Trees don't always display in PhyloWidget Initial Comment: Search on study 1902 (Ranwez V., Berry V., Criscuolo A., Fabre P., Guillemot S., Scornavacca C., & Douzery E. 2007. PhySIC: a veto supertree method with desirable properties. Systematic Biology); get a list of trees; try to view on of the trees in PhyloWidget -- does not show up. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2787978&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-02 17:32:42
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Bugs item #2785703, was opened at 2009-05-02 13:32 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2785703&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: None Status: Open Priority: 5 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Mark Dominus (mjdominus) Summary: CHARSTATELABELS missing in continuous data Initial Comment: Uploading a continuous dataset that has CHARSTATELABELS fails to store the CHARSTATELABELS and fails to reconstruct them in the downloaded/reconstructed file. Continuous characters do not have state labels, but they have the names/title of characters. Compare the attached data-in vs the data-out to see what has failed to be captured. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2785703&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-05-02 17:20:40
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Bugs item #2785695, was opened at 2009-05-02 13:20 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2785695&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: None Status: Open Priority: 5 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Mark Dominus (mjdominus) Summary: NCHAR=NULL in morphological downloaded datasets Initial Comment: In test matrix M4232 and submission id S2424, the reconstructed matrices have "NCHAR=NULL" when they should have a real number, e.g. "NCHAR=98" ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2785695&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-29 19:08:49
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Bugs item #2712107, was opened at 2009-03-25 16:23 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2712107&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 4 Private: No Submitted By: Mark Dominus (mjdominus) >Assigned to: Rutger Vos (rvos) Summary: Remove "View Taxa" links from matrix results page Initial Comment: BP says: > - I'm thinking that maybe we don't need the "View Taxa" link under the > Matrix Tab. This seems redundant with just clicking on the Taxa tab, and > if you do follow the "View Taxa" link, you just get a simple list of > taxon_labels (without ubio and ncbi links), and from there it's > impossible to return to the tabbed display without clicking your > browser's backup button. Doesn't seem like something people would > benefit from. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-04-29 19:08 Message: Fixed as of revision 6430 ---------------------------------------------------------------------- Comment By: Mark Dominus (mjdominus) Date: 2009-03-25 18:15 Message: Demote as per BP email: > it would be nice if it happened, but it should not hold up the beta release. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2712107&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-29 19:05:18
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Bugs item #2782687, was opened at 2009-04-28 08:41 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2782687&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: piel >Status: Closed Priority: 4 Private: No Submitted By: Rutger Vos (rvos) >Assigned to: Rutger Vos (rvos) Summary: confusing semantics for book sections vs. articles Initial Comment: > • When entering a book citation, the user is presented with a field for > "title of citation" and a field for "title of book". What's the difference? > When entering a book section citation, the user is presented with a field > for "title of citation", "book section", and "book title" -- again, "title > of citation" is redundant with "book section title", but at least in this > case entering in either box seems to fill the same field. My guess is that > the correct behavior should be the following: > Journal: > Citation Title -> title_field > Journal -> journal_field > Book: > Book Title -> title_field > Book Section: > Section Title -> title_field > Book Title -> secondary_title_field > In other words, we should not have redundant entry points for "title of > citation" and either ("book title" or "section title"). Also, in each case > the title_field gets filled, in one case the article title, another the book > title, and the third the section title. Do I have this field usage correct, > or am I mistaken? ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-04-29 19:05 Message: Fixed as per revision 6429 ---------------------------------------------------------------------- Comment By: Mark Dominus (mjdominus) Date: 2009-04-28 20:42 Message: Piel adds: think the rationale and data model are probably correct, it's just that two redundant input boxes are presented to the user when they both are writing to the same field in the database. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2782687&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-28 21:05:25
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Bugs item #2776454, was opened at 2009-04-20 12:35 Message generated for change (Settings changed) made by mjdominus You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2776454&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: None Status: Open >Priority: 7 Private: No Submitted By: Mark Dominus (mjdominus) Assigned to: Rutger Vos (rvos) Summary: Four unimported citations Initial Comment: MJD -> BP: There are four studies whose citations have not yet been imported. These are the citations for studies S9x6x96c10c10c17 S451 S801 S914 The reason is that the citation dump file you sent specifies citation types "Thesis", "Thesis", "Electronic Source", and "Conference Proceedings", respectively. But our data model has (at present) only citations of types "Journal Article", "Book", and "Book Section". Rutger quite properly had the citation data importer ignore citations of unknown types. ---------------------------------------------------------------------- Comment By: Mark Dominus (mjdominus) Date: 2009-04-20 14:36 Message: BP says: My sense is that "Thesis" and "Electronic Source" can be squeezed into "Book"; and "Conference Proceedings" can be squeezed into "Book Section" -- we can do that for now just to accommodate these cases. But a future "new feature" might be to expand the repertoire of our publication categories -- but definitely only for down the road. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2776454&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-28 21:04:52
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Bugs item #2776454, was opened at 2009-04-20 12:35 Message generated for change (Settings changed) made by mjdominus You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2776454&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: None Status: Open Priority: 4 Private: No Submitted By: Mark Dominus (mjdominus) >Assigned to: Rutger Vos (rvos) Summary: Four unimported citations Initial Comment: MJD -> BP: There are four studies whose citations have not yet been imported. These are the citations for studies S9x6x96c10c10c17 S451 S801 S914 The reason is that the citation dump file you sent specifies citation types "Thesis", "Thesis", "Electronic Source", and "Conference Proceedings", respectively. But our data model has (at present) only citations of types "Journal Article", "Book", and "Book Section". Rutger quite properly had the citation data importer ignore citations of unknown types. ---------------------------------------------------------------------- Comment By: Mark Dominus (mjdominus) Date: 2009-04-20 14:36 Message: BP says: My sense is that "Thesis" and "Electronic Source" can be squeezed into "Book"; and "Conference Proceedings" can be squeezed into "Book Section" -- we can do that for now just to accommodate these cases. But a future "new feature" might be to expand the repertoire of our publication categories -- but definitely only for down the road. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2776454&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-28 21:03:47
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Bugs item #2783200, was opened at 2009-04-28 16:59 Message generated for change (Comment added) made by mjdominus You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2783200&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Mark Dominus (mjdominus) Assigned to: Nobody/Anonymous (nobody) >Summary: Merge Algorithm classes and expand algorithm choices Initial Comment: Algorithm is an abstract class from which ParsimonyAlgorithm, DistanceAlgorithm, LikelihoodAlgorithm, and OtherAlgorithm are derived. ParsimonyAlgorithm uses three other classes (GapMode, UserType, and PolyTCount) that are not used anywhere else. These should be merged into a single class with a flag and some sort of associated string data; the GapMode, UserType, and PolyTCount tables should be eliminated. Regarding this design, Jin Ruan, the original designer, says: (04:48:42 PM) Jin Ruan: The algorithm design is not well reviewed. What is there was the first pass I had to model different algorithms into the system. The reason for different subclasses was to enable more interactions/relationships between generated trees with a particular algorithm. However we never actually design/ implment any use case to use that design in treebase2. That is why we have this first pass design but it is largely not used. Please feel free to redesign it. For example, as a starting point using a string instead of different subclasses. ---------------------------------------------------------------------- >Comment By: Mark Dominus (mjdominus) Date: 2009-04-28 17:03 Message: Bill also says that the UI for the algorithm for an analysis step should include the following items: • Under analysis step entry, the "algorithm" lists the following in to popup: maximum likelihood, parsimony, distance, and other. Please change it to the following: bayesian inference maximum likelihood minimum evolution neighbor joining parsimony UPGMA other ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2783200&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-28 21:01:23
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Bugs item #2782676, was opened at 2009-04-28 04:10 Message generated for change (Comment added) made by mjdominus You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2782676&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: piel >Status: Closed Priority: 4 Private: No Submitted By: Rutger Vos (rvos) Assigned to: Mark Dominus (mjdominus) Summary: few taxa validate for submission 2403 Initial Comment: BP writes: I've been trying to validate taxa for submission 2403. Few seem to be working, but that may be uBios fault. ---------------------------------------------------------------------- >Comment By: Mark Dominus (mjdominus) Date: 2009-04-28 17:01 Message: This was probably because uBio was down: BP says: It was not recognizing lots of names that I know are in uBIO. I just retried it now, and it worked. Probably has to do with the fact that the uBIO site says "Bio is currently undergoing a perestroika of its system architecture. If you encounter any problems, please report them to us." ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2782676&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-28 21:00:01
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Bugs item #2783200, was opened at 2009-04-28 16:59 Message generated for change (Tracker Item Submitted) made by mjdominus You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2783200&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Private: No Submitted By: Mark Dominus (mjdominus) Assigned to: Nobody/Anonymous (nobody) Summary: Merge Algorithm classes Initial Comment: Algorithm is an abstract class from which ParsimonyAlgorithm, DistanceAlgorithm, LikelihoodAlgorithm, and OtherAlgorithm are derived. ParsimonyAlgorithm uses three other classes (GapMode, UserType, and PolyTCount) that are not used anywhere else. These should be merged into a single class with a flag and some sort of associated string data; the GapMode, UserType, and PolyTCount tables should be eliminated. Regarding this design, Jin Ruan, the original designer, says: (04:48:42 PM) Jin Ruan: The algorithm design is not well reviewed. What is there was the first pass I had to model different algorithms into the system. The reason for different subclasses was to enable more interactions/relationships between generated trees with a particular algorithm. However we never actually design/ implment any use case to use that design in treebase2. That is why we have this first pass design but it is largely not used. Please feel free to redesign it. For example, as a starting point using a string instead of different subclasses. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2783200&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-28 20:42:51
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Bugs item #2782687, was opened at 2009-04-28 04:41 Message generated for change (Comment added) made by mjdominus You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2782687&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: piel Status: Open Priority: 4 Private: No Submitted By: Rutger Vos (rvos) Assigned to: Nobody/Anonymous (nobody) Summary: confusing semantics for book sections vs. articles Initial Comment: > • When entering a book citation, the user is presented with a field for > "title of citation" and a field for "title of book". What's the difference? > When entering a book section citation, the user is presented with a field > for "title of citation", "book section", and "book title" -- again, "title > of citation" is redundant with "book section title", but at least in this > case entering in either box seems to fill the same field. My guess is that > the correct behavior should be the following: > Journal: > Citation Title -> title_field > Journal -> journal_field > Book: > Book Title -> title_field > Book Section: > Section Title -> title_field > Book Title -> secondary_title_field > In other words, we should not have redundant entry points for "title of > citation" and either ("book title" or "section title"). Also, in each case > the title_field gets filled, in one case the article title, another the book > title, and the third the section title. Do I have this field usage correct, > or am I mistaken? ---------------------------------------------------------------------- >Comment By: Mark Dominus (mjdominus) Date: 2009-04-28 16:42 Message: Piel adds: think the rationale and data model are probably correct, it's just that two redundant input boxes are presented to the user when they both are writing to the same field in the database. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2782687&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-28 20:29:01
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Bugs item #2783189, was opened at 2009-04-28 16:28 Message generated for change (Tracker Item Submitted) made by mjdominus You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2783189&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: Mark Dominus (mjdominus) Assigned to: Rutger Vos (rvos) Summary: Icon missing from icon legend Initial Comment: http://8ball.sdsc.edu:6666/treebase-web/user/treeList.html contains an icon http://8ball.sdsc.edu:6666/treebase-web/images/icons/exclamation.png which is not mentioned in the legend at http://8ball.sdsc.edu:6666/treebase-web/help/iconLegend.jsp ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2783189&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-04-28 08:43:49
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Bugs item #2782689, was opened at 2009-04-28 08:43 Message generated for change (Tracker Item Submitted) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2782689&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: data Group: piel Status: Open Priority: 4 Private: No Submitted By: Rutger Vos (rvos) Assigned to: Mark Dominus (mjdominus) Summary: Data Access Failure when changing citation type Initial Comment: • The error (below) happened when I switched from a book section back to a book, and then tried to save it. Data Access Failure Object with id: null was not of the specified subclass: org.cipres.treebase.domain.study.BookCitation (class of the given object did not match class of persistent copy); nested exception is org.hibernate.WrongClassException: Object with id: null was not of the specified subclass: org.cipres.treebase.domain.study.BookCitation (class of the given object did not match class of persistent copy) org.springframework.orm.hibernate3.HibernateObjectRetrievalFailureException: Object with id: null was not of the specified subclass: org.cipres.treebase.domain.study.BookCitation (class of the given object did not match class of persistent copy); nested exception is org.hibernate.WrongClassException: Object with id: null was not of the specified subclass: org.cipres.treebase.domain.study.BookCitation (class of the given object did not match class of persistent copy) Caused by: org.hibernate.WrongClassException: Object with id: null was not of the specified subclass: org.cipres.treebase.domain.study.BookCitation (class of the given object did not match class of persistent copy) at org.hibernate.event.def.DefaultMergeEventListener.entityIsDetached(DefaultMergeEventListener.java:250) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:120) at org.hibernate.event.def.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:53) at org.hibernate.impl.SessionImpl.fireMerge(SessionImpl.java:677) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:661) at org.hibernate.impl.SessionImpl.merge(SessionImpl.java:665) at org.springframework.orm.hibernate3.HibernateTemplate$23.doInHibernate(HibernateTemplate.java:765) at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:372) at org.springframework.orm.hibernate3.HibernateTemplate.merge(HibernateTemplate.java:762) at org.cipres.treebase.dao.AbstractDAO.merge(AbstractDAO.java:168) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:198) at $Proxy59.merge(Unknown Source) at org.cipres.treebase.service.AbstractServiceImpl.update(AbstractServiceImpl.java:55) at org.cipres.treebase.service.study.CitationServiceImpl.replaceCitation(CitationServiceImpl.java:130) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy78.replaceCitation(Unknown Source) at org.cipres.treebase.web.controllers.CitationFormController.replaceCitation(CitationFormController.java:360) at org.cipres.treebase.web.controllers.CitationFormController.onSubmit(CitationFormController.java:316) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:710) at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:874) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:595) « Back ---------------------------------------------------------------------- You 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