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From: <owl...@go...> - 2015-03-12 19:29:49
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Updates: Status: Fixed Comment #9 on issue 111 by cmu...@gm...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 Closing this as we are done, hurrah. Thanks Shahim, massively appreciate all your help here. https://github.com/owlcollab/owltools Some additional notes for anyone following in our footsteps: * GH has a max 50MB limit on any individual file * It can be a pain tying all committers to email addresses but it's worth it to preserve history -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: Chris M. <cjm...@lb...> - 2015-02-02 21:17:02
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The move is now complete. Many thanks to Shahim for doing this. Repo: https://github.com/owlcollab/owltools Contact me if you want to be on the dev team and are not already (some of you should have invites) Issues: https://github.com/owlcollab/owltools/issues Note that existing issues are moved across. Awesome! Wiki: https://github.com/owlcollab/owltools/wiki a few quirks here, easy to fix I will take care of adding redirects to the gcode site On Mon, Jan 5, 2015 at 9:58 PM, Shahim Essaid <es...@oh...> wrote: > What I need is a name and an email address, not your GitHub user name. > Both will be used in the Git commits that are generated from the SVN > commits. > > The name can be anything you like. The email (not your GitHub user name) > will help link your SVN commit to your GitHub account as long as you also > have that email listed in your GitHub profile. > > This is an example of how a SVN ID of "svnuser" would be mapped to a Git > commit author of "Joe User <us...@ex...>": > > svnuser (this is the SVN ID) = Joe User <us...@ex...> (this is the > Git ID) > > Thanks, > Shahim > > > -----Original Message----- > > From: Chris Mungall [mailto:cjm...@lb...] > > Sent: Monday, January 05, 2015 9:37 PM > > To: obo...@li... > > Cc: Shahim Essaid; Seth Carbon; Mark Wilkinson; Nicole Washington; > Frederic > > Bastian > > Subject: Re: Moving the repo to github > > > > If you have made any commits to owltools and would like the history to be > > migrated to your google code account, can you email your github ID and an > > email address you have registered with github to Shahim (cc'd). > > Thanks! > > > > On 5 Jan 2015, at 16:24, Chris Mungall wrote: > > > > > We'd like to move owltools from google code to github, the ticket is > > > here: > > > > > > https://code.google.com/p/owltools/issues/detail?id=111 > > > > > > I'd like to do this some time next week. Let me know if this causes > > > any inconvenience or you'd prefer a different timing. > |
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From: <owl...@go...> - 2015-02-02 17:15:46
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Comment #8 on issue 111 by sh...@es...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 I did a new import to make sure the commit SHAs are all good and to update the authors. The finished migration is at: https://github.com/ShahimEssaid/owltools Chris can move and rename as needed in GitHub. Heiko, the email I used for your commits appears not be be listed in your GitHub account. You can add it to your secondary emails in GitHub and the commits will be linked to your GitHub profile. -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2015-01-23 00:25:37
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Comment #7 on issue 111 by HD...@lb...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 I just removed all the big go.owl files from the test resources and replaced it smaller modules for the relevant tests. See r2446 for changes. Does this mean you need to import the SVN again? Or is it just possible to pull the changes from SVN (even with the deleted go.owl files)? -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2015-01-21 19:09:54
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Comment #6 on issue 111 by cmu...@gm...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 I just committed a few odds and ends to gcode. We're ready to switch assuming this passes: http://build.berkeleybop.org/job/owltools/1160/ cjm AT berkeleybop.org I think Heiko's will be hdietze AT lbl.gov -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2015-01-21 17:20:31
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Comment #5 on issue 111 by sh...@es...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 Should we go ahead with this or not yet? Chris, I need the GitHub emails for you and Keiko (not the GitHub login/name) before running the final Git import. Can you please send them to me when we are ready for the move? -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2015-01-20 22:35:20
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Comment #4 on issue 111 by cmu...@gm...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 After done, update GO FAQ and other links. Eg http://geneontology.org/faq/how-do-i-map-set-annotations-high-level-go-terms-go-slim -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2015-01-20 22:11:06
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Status: New Owner: ---- Labels: Type-Defect Priority-Medium New issue 112 by rlw...@gm...: Add feature for converting license statements between OBO and OWL https://code.google.com/p/owltools/issues/detail?id=112 The wording for OBO Foundry Principle 1 has been revised to (we hope) make it clearer and easier to implement (https://docs.google.com/document/d/1nCCO88uOWgWp3z5AwyapcTP0T_C2ZmdPi7cWiO9_aDM/edit#). The new wording specifies that OWL ontologies must include a dc:license statement plus a comment on ontology reuse conditions for OWL ontologies. For OBO format ontologies, the ontology must contain a license statement and a seperate comment for any re-use conditions. Is it possible to add a feature to OORT, so that during the conversion process, these annotations are properly converted? Thanks, Ramona -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2015-01-06 17:10:20
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Comment #3 on issue 111 by cmu...@gm...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 What about the generated apidocs? gh-pages? -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: Shahim E. <es...@oh...> - 2015-01-06 05:58:20
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What I need is a name and an email address, not your GitHub user name. Both will be used in the Git commits that are generated from the SVN commits. The name can be anything you like. The email (not your GitHub user name) will help link your SVN commit to your GitHub account as long as you also have that email listed in your GitHub profile. This is an example of how a SVN ID of "svnuser" would be mapped to a Git commit author of "Joe User <us...@ex...>": svnuser (this is the SVN ID) = Joe User <us...@ex...> (this is the Git ID) Thanks, Shahim > -----Original Message----- > From: Chris Mungall [mailto:cjm...@lb...] > Sent: Monday, January 05, 2015 9:37 PM > To: obo...@li... > Cc: Shahim Essaid; Seth Carbon; Mark Wilkinson; Nicole Washington; Frederic > Bastian > Subject: Re: Moving the repo to github > > If you have made any commits to owltools and would like the history to be > migrated to your google code account, can you email your github ID and an > email address you have registered with github to Shahim (cc'd). > Thanks! > > On 5 Jan 2015, at 16:24, Chris Mungall wrote: > > > We'd like to move owltools from google code to github, the ticket is > > here: > > > > https://code.google.com/p/owltools/issues/detail?id=111 > > > > I'd like to do this some time next week. Let me know if this causes > > any inconvenience or you'd prefer a different timing. |
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From: <owl...@go...> - 2015-01-06 05:41:52
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Comment #2 on issue 111 by cmu...@gm...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 Fantastic. This would be a good time to refactor tests that involve enormous files -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: Chris M. <cjm...@lb...> - 2015-01-06 05:37:24
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If you have made any commits to owltools and would like the history to be migrated to your google code account, can you email your github ID and an email address you have registered with github to Shahim (cc'd). Thanks! On 5 Jan 2015, at 16:24, Chris Mungall wrote: > We'd like to move owltools from google code to github, the ticket is > here: > > https://code.google.com/p/owltools/issues/detail?id=111 > > I'd like to do this some time next week. Let me know if this causes > any inconvenience or you'd prefer a different timing. |
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From: <owl...@go...> - 2015-01-06 04:17:25
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Comment #1 on issue 111 by sh...@es...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 Here is an example migration: https://github.com/ShahimEssaid/owltools I used git svn: git svn clone --prefix=origin/ --authors-file=../authors --authors-prog=../authors-default -s http://owltools.googlecode.com/svn . I had to remove large files from the history because GitHub doesn't like > 50mb and refuses > 100mb files: remote: error: GH001: Large files detected. remote: error: Trace: 415df2b385d9bf1f9c72fa5a226558c6 remote: error: See http://git.io/iEPt8g for more information. remote: error: File OWLTools-Annotation/src/test/resources/rules/ontology/go.owl is 129.98 MB; this exceeds GitHub's file size limit of 100 MB remote: error: File OWLTools-Core/src/test/resources/go.owl is 116.81 MB; this exceeds GitHub's file size limit of 100 MB remote: error: File OWLTools-Annotation/src/test/resources/rules/ontology/go.owl is 129.54 MB; this exceeds GitHub's file size limit of 100 MB remote: error: File OWLTools-Annotation/src/test/resources/rules/ontology/go.owl is 125.45 MB; this exceeds GitHub's file size limit of 100 MB Ran the following to clear the history from these files: git filter-branch --prune-empty -d /dev/shm/owltools \ --index-filter "git rm --cached -f --ignore-unmatch OWLTools-Annotation/src/test/resources/rules/ontology/go.owl" \ --tag-name-filter cat -- --all git filter-branch --prune-empty -d /dev/shm/owltools \ --index-filter "git rm --cached -f --ignore-unmatch OWLTools-Core/src/test/resources/go.owl" \ --tag-name-filter cat -- --all Maybe these files can be downloaded from somewhere else when tests are ran. Finally: git checkout -t -b hmc-clinic git remote add origin gi...@gi...:ShahimEssaid/owltools.git git push -u origin master hmc-clinic The current commits don't have proper user names but I can fix this once I have the correct user names and email addresses to use for the commits. For the issues, I used: https://github.com/arthur-debert/google-code-issues-migrator For the wiki: https://github.com/trentm/googlecode2github -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: Nicole W. <nlw...@lb...> - 2015-01-06 00:53:26
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ok for me Nicole L. Washington, Ph.D. Research Scientist Genomics Division Lawrence Berkeley National Laboratory Berkeley, CA USA NLW...@lb... ORCID:0000-0001-8936-9143 On Jan 5, 2015, at 4:24 PM, Chris Mungall <cjm...@lb...> wrote: > We'd like to move owltools from google code to github, the ticket is here: > > https://code.google.com/p/owltools/issues/detail?id=111 > > I'd like to do this some time next week. Let me know if this causes any inconvenience or you'd prefer a different timing. |
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From: Chris M. <cjm...@lb...> - 2015-01-06 00:24:22
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We'd like to move owltools from google code to github, the ticket is here: https://code.google.com/p/owltools/issues/detail?id=111 I'd like to do this some time next week. Let me know if this causes any inconvenience or you'd prefer a different timing. |
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From: <owl...@go...> - 2015-01-05 23:17:16
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Status: Accepted Owner: cmu...@gm... Labels: Type-Defect Priority-Medium New issue 111 by cmu...@gm...: Move repo to github https://code.google.com/p/owltools/issues/detail?id=111 ## SVN History This should be straightforward to move over; Ignazio managed this for oboformat easily. We would move everything across at first, but then may decide to split things up ## Modularization Lego stuff should go to a separate repo. We should move OWLTools-Sim, but this will gradually be abandoned as owlsim-v3 (already a separate github repo) comes into play. ## Issue Tracker We will not attempt to migrate; we will start afresh with the gh tracker. We will leave the gcode one up and running and may manually migrate a select few items. ## Wiki There is a lot of good material on the wiki - will probably have to be manually moved, with links from old to new added. -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2014-12-09 21:53:40
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Updates: Summary: Make taxon check a workable long-term service Comment #1 on issue 109 by HD...@lb...: Make taxon check a workable long-term service https://code.google.com/p/owltools/issues/detail?id=109 (No comment was entered for this change.) -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2014-12-09 21:52:30
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Status: New Owner: HD...@lb... CC: cmu...@gm... Labels: Type-Enhancement Priority-Medium New issue 110 by HD...@lb...: GAF validation - More descriptive reporting for unsatisfiable classes https://code.google.com/p/owltools/issues/detail?id=110 For normal annotators, the general error report of unsatisfiable classes is too generic. The most common reasons for unsatisfiable classes are: * taxon constraints * domain or range for properties In both case a short explanation would be better. At the moment we generate a module for the unsatisfiable classes, which is good for advanced users and debugging in Protege. The general solution of always generating explanation (similar to Protege) may prove to be too resource intensive. -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2014-12-09 21:49:16
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Status: Accepted Owner: sjc...@lb... Labels: Type-Defect Priority-Medium New issue 109 by sjc...@lb...: Make taxon check a worable long-term service https://code.google.com/p/owltools/issues/detail?id=109 The taxon-check tools is located at a strange URL and is hard to monitor. A possible solution would be to: * Add a CNAME to a proxy server to give it a more standard location * Add a /status route so that it can be easily monitored remotely -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2014-12-04 21:57:11
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Updates: Status: Done Comment #5 on issue 106 by HD...@lb...: Internal error: null when using "Create Ontology From Query" https://code.google.com/p/owltools/issues/detail?id=106 As no further input from the original requester is available, assume the problem has been resolved with the provided work-around. -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2014-12-04 21:55:59
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Updates: Status: Fixed Comment #3 on issue 107 by HD...@lb...: owltools maven build failure https://code.google.com/p/owltools/issues/detail?id=107 (No comment was entered for this change.) -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2014-11-28 13:49:45
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Comment #4 on issue 45 by fre...@gm...: Provide graph view over GCIs https://code.google.com/p/owltools/issues/detail?id=45 Solution 2 has been implemented, see issue #102. OWLGraphEdge now has gci_relation and gci_filler attributes. OWLGraphWrapperEdgesExtended implements many methods reproducing behavior of OWLGraphWrapperEdges methods, but taking into account GCI relations. The ticket might be closed. -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2014-11-27 13:15:40
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Status: New Owner: ---- Labels: Type-Defect Priority-Medium New issue 108 by lee...@gm...: Citing OWL Tools https://code.google.com/p/owltools/issues/detail?id=108 What steps will reproduce the problem? 1. I would like to cite OWL Tools in a scientific paper. What is the expected output? What do you see instead? It would be great to find information on how to cite OWL Tools in the Wiki, either a reference to a paper, technical report, or, if none of these apply, a web citation. -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2014-11-24 14:18:34
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Comment #2 on issue 107 by mid...@gm...: owltools maven build failure https://code.google.com/p/owltools/issues/detail?id=107 Thanks -- I had to delete owltools and do a fresh svn checkout (svn update didn't do the trick), and then the build succeeded. m -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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From: <owl...@go...> - 2014-11-21 19:07:18
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Comment #4 on issue 105 by HD...@lb...: Error in building of topology graph in solr loading https://code.google.com/p/owltools/issues/detail?id=105 A failing integration test related to GAF Solr loading revealed some issues on the memory requirements (and unnecessary computations) for the setup of the ExpressionMaterializingReasoner. The strategy is now to only create expressions for a requested subset of properties. -- You received this message because this project is configured to send all issue notifications to this address. You may adjust your notification preferences at: https://code.google.com/hosting/settings |
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