Dataset Display

From p.j.a.cock@googlemail.com Wed Oct 2 12:37:46 2013 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] Tabular data not displaying in main panel Date: Wed, 02 Oct 2013 17:37:08 +0100 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============0858381384059669766==" --===============0858381384059669766== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi all, Multiple users of our internal Galaxy server have reported with multiple browsers that tabular data is not displayed in the main central panel. The preview in the history works, but clicking on the "eye" icon gives a blank page. I can confirm this in Firefox 24.0 and Safari 6.0.5, the HTML for the central frame looks blank but is actually a script when viewed via the frame source. The tabular file data is there in the script's first_data_chunk entry - but does not get shown. An except is shown below. Has anyone else noticed this problem? I believe it began when I last updated this Galaxy instance, but was not noticed immediately. Thanks, Peter ----------------------- I believe we are running the current stable release, or at least the latest commit on the default branch from galaxy-dist $ hg pull warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) real URL is https://bitbucket.org/galaxy/galaxy-dist pulling from http://bitbucket.org/galaxy/galaxy-dist searching for changes no changes found $ hg update 0 files updated, 0 files merged, 0 files removed, 0 files unresolved $ hg branch default [galaxy(a)ppserver galaxy-dist]$ hg log -b default | head changeset: 10411:c42567f43aa7 user: greg date: Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. changeset: 10410:e9ee9c5d30ae user: Dave Bouvier date: Mon Aug 19 13:08:45 2013 -0400 summary: Remove duplicate method from the install and test's functional_tests.py. ... ----------------------- Dataset Display -- --===============0858381384059669766==-- From bjoern.gruening@pharmazie.uni-freiburg.de Wed Oct 2 14:48:42 2013 From: =?utf-8?q?Bj=C3=B6rn_Gr=C3=BCning?= To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Wed, 02 Oct 2013 20:48:07 +0200 Message-ID: <1380739687.27109.25.camel@threonin> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3959173834680197243==" --===============3959173834680197243== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Peter, we can confirm. Latest Galaxy stable version and its occurring randomly. I was not able to reproduce it by myself. Cheers, Bjoern=20 > Hi all, >=20 > Multiple users of our internal Galaxy server have reported with > multiple browsers that tabular data is not displayed in the main > central panel. The preview in the history works, but clicking on > the "eye" icon gives a blank page. >=20 > I can confirm this in Firefox 24.0 and Safari 6.0.5, the HTML > for the central frame looks blank but is actually a script when > viewed via the frame source. The tabular file data is there in > the script's first_data_chunk entry - but does not get shown. > An except is shown below. >=20 > Has anyone else noticed this problem? I believe it began > when I last updated this Galaxy instance, but was not > noticed immediately. >=20 > Thanks, >=20 > Peter >=20 > ----------------------- >=20 > I believe we are running the current stable release, or at least > the latest commit on the default branch from galaxy-dist >=20 > $ hg pull > warning: bitbucket.org certificate with fingerprint > 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not > verified (check hostfingerprints or web.cacerts config setting) > real URL is https://bitbucket.org/galaxy/galaxy-dist > pulling from http://bitbucket.org/galaxy/galaxy-dist > searching for changes > no changes found >=20 > $ hg update > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved >=20 > $ hg branch > default >=20 > [galaxy(a)ppserver galaxy-dist]$ hg log -b default | head > changeset: 10411:c42567f43aa7 > user: greg > date: Mon Aug 19 13:19:56 2013 -0400 > summary: Filter invalid objects when generating the list of > repository_dependencies objects that are associated with a tool shed > repository installed into Galaxy. >=20 > changeset: 10410:e9ee9c5d30ae > user: Dave Bouvier > date: Mon Aug 19 13:08:45 2013 -0400 > summary: Remove duplicate method from the install and test's > functional_tests.py. > ... >=20 >=20 > ----------------------- >=20 > > > > > Dataset Display > >=20 > media=3D"screen" rel=3D"Stylesheet" type=3D"text/css" /> >=20 > > > > > > > > > >=20 > >=20 > >=20 > >=20 >=20 >=20 > > >=20 > >=20 > > >=20 > > >=20 > -- > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ >=20 > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ --===============3959173834680197243==-- From aysam.guerler@gmail.com Wed Oct 2 14:56:50 2013 From: sam guerler To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Wed, 02 Oct 2013 14:56:11 -0400 Message-ID: In-Reply-To: <1380739687.27109.25.camel@threonin> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============7581291633295053208==" --===============7581291633295053208== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Peter, Does the Javascript console of the browser show any error messages? Thanks, Sam On Wed, Oct 2, 2013 at 2:48 PM, Bj=C3=B6rn Gr=C3=BCning < bjoern.gruening(a)pharmazie.uni-freiburg.de> wrote: > Hi Peter, > > we can confirm. Latest Galaxy stable version and its occurring randomly. > I was not able to reproduce it by myself. > > Cheers, > Bjoern > > > Hi all, > > > > Multiple users of our internal Galaxy server have reported with > > multiple browsers that tabular data is not displayed in the main > > central panel. The preview in the history works, but clicking on > > the "eye" icon gives a blank page. > > > > I can confirm this in Firefox 24.0 and Safari 6.0.5, the HTML > > for the central frame looks blank but is actually a script when > > viewed via the frame source. The tabular file data is there in > > the script's first_data_chunk entry - but does not get shown. > > An except is shown below. > > > > Has anyone else noticed this problem? I believe it began > > when I last updated this Galaxy instance, but was not > > noticed immediately. > > > > Thanks, > > > > Peter > > > > ----------------------- > > > > I believe we are running the current stable release, or at least > > the latest commit on the default branch from galaxy-dist > > > > $ hg pull > > warning: bitbucket.org certificate with fingerprint > > 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not > > verified (check hostfingerprints or web.cacerts config setting) > > real URL is https://bitbucket.org/galaxy/galaxy-dist > > pulling from http://bitbucket.org/galaxy/galaxy-dist > > searching for changes > > no changes found > > > > $ hg update > > 0 files updated, 0 files merged, 0 files removed, 0 files unresolved > > > > $ hg branch > > default > > > > [galaxy(a)ppserver galaxy-dist]$ hg log -b default | head > > changeset: 10411:c42567f43aa7 > > user: greg > > date: Mon Aug 19 13:19:56 2013 -0400 > > summary: Filter invalid objects when generating the list of > > repository_dependencies objects that are associated with a tool shed > > repository installed into Galaxy. > > > > changeset: 10410:e9ee9c5d30ae > > user: Dave Bouvier > > date: Mon Aug 19 13:08:45 2013 -0400 > > summary: Remove duplicate method from the install and test's > > functional_tests.py. > > ... > > > > > > ----------------------- > > > > > > > > > > > > Dataset Display > > charset=3Dutf-8" /> > > > > > media=3D"screen" rel=3D"Stylesheet" type=3D"text/css" /> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > --===============7581291633295053208== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGRpdiBkaXI9Imx0ciI+SGkgUGV0ZXIsPGRpdj48YnI+PC9kaXY+PGRpdj5Eb2VzIHRoZSBKYXZh c2NyaXB0IGNvbnNvbGUgb2YgdGhlIGJyb3dzZXIgc2hvdyBhbnkgZXJyb3IgbWVzc2FnZXM/PC9k aXY+PGRpdj48YnI+PC9kaXY+PGRpdj5UaGFua3MsPC9kaXY+PGRpdj5TYW08L2Rpdj48L2Rpdj48 ZGl2IGNsYXNzPSJnbWFpbF9leHRyYSI+PGJyPjxicj48ZGl2IGNsYXNzPSJnbWFpbF9xdW90ZSI+ Ck9uIFdlZCwgT2N0IDIsIDIwMTMgYXQgMjo0OCBQTSwgQmr2cm4gR3L8bmluZyA8c3BhbiBkaXI9 Imx0ciI+Jmx0OzxhIGhyZWY9Im1haWx0bzpiam9lcm4uZ3J1ZW5pbmdAcGhhcm1hemllLnVuaS1m cmVpYnVyZy5kZSIgdGFyZ2V0PSJfYmxhbmsiPmJqb2Vybi5ncnVlbmluZ0BwaGFybWF6aWUudW5p 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The problem has disappeared now. At the time I had the suspicion, it only happened to browser sessions=20 which were already open before the upgrade, Hence, closing the browser,=20 and starting again helped. But this was just a guess. Regards, Hans-Rudolf On 10/02/2013 08:48 PM, Bj=C3=B6rn Gr=C3=BCning wrote: > Hi Peter, > > we can confirm. Latest Galaxy stable version and its occurring randomly. > I was not able to reproduce it by myself. > > Cheers, > Bjoern > >> Hi all, >> >> Multiple users of our internal Galaxy server have reported with >> multiple browsers that tabular data is not displayed in the main >> central panel. The preview in the history works, but clicking on >> the "eye" icon gives a blank page. >> >> I can confirm this in Firefox 24.0 and Safari 6.0.5, the HTML >> for the central frame looks blank but is actually a script when >> viewed via the frame source. The tabular file data is there in >> the script's first_data_chunk entry - but does not get shown. >> An except is shown below. >> >> Has anyone else noticed this problem? I believe it began >> when I last updated this Galaxy instance, but was not >> noticed immediately. >> >> Thanks, >> >> Peter >> >> ----------------------- >> >> I believe we are running the current stable release, or at least >> the latest commit on the default branch from galaxy-dist >> >> $ hg pull >> warning: bitbucket.org certificate with fingerprint >> 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not >> verified (check hostfingerprints or web.cacerts config setting) >> real URL is https://bitbucket.org/galaxy/galaxy-dist >> pulling from http://bitbucket.org/galaxy/galaxy-dist >> searching for changes >> no changes found >> >> $ hg update >> 0 files updated, 0 files merged, 0 files removed, 0 files unresolved >> >> $ hg branch >> default >> >> [galaxy(a)ppserver galaxy-dist]$ hg log -b default | head >> changeset: 10411:c42567f43aa7 >> user: greg >> date: Mon Aug 19 13:19:56 2013 -0400 >> summary: Filter invalid objects when generating the list of >> repository_dependencies objects that are associated with a tool shed >> repository installed into Galaxy. >> >> changeset: 10410:e9ee9c5d30ae >> user: Dave Bouvier >> date: Mon Aug 19 13:08:45 2013 -0400 >> summary: Remove duplicate method from the install and test's >> functional_tests.py. >> ... >> >> >> ----------------------- >> >> >> >> >> >> Dataset Display >> >> >> > media=3D"screen" rel=3D"Stylesheet" type=3D"text/css" /> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > --===============3946941177770929237==-- From p.j.a.cock@googlemail.com Thu Oct 3 05:09:48 2013 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Thu, 03 Oct 2013 10:09:40 +0100 Message-ID: In-Reply-To: <524D1677.4000508@fmi.ch> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============7551378243405733699==" --===============7551378243405733699== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit On Thu, Oct 3, 2013 at 8:02 AM, Hans-Rudolf Hotz wrote: > Hi Peter and Bjoern > > we had similar problems in August, when we upgraded to 'release_2013.06.03'. > The problem has disappeared now. > > At the time I had the suspicion, it only happened to browser sessions which > were already open before the upgrade, Hence, closing the browser, and > starting again helped. But this was just a guess. > > > Regards, Hans-Rudolf Thanks Hans, On my machine restarting the browser made no difference. Also (within Galaxy) logging out and logging in made no difference. On Wed, Oct 2, 2013 at 7:56 PM, sam guerler wrote: > Hi Peter, > > Does the Javascript console of the browser show any error messages? > > Thanks, > Sam Under Firefox, there are lots of (what I assume are harmless) CSS warnings. Also: [10:05:12.293] TypeError: j is undefined @ http://xxx/galaxy/static/scripts/mvc/data.js:1 [10:05:12.291] "TabularButtonTrackster : Chromosome column undefined." Peter --===============7551378243405733699==-- From aysam.guerler@gmail.com Thu Oct 3 09:47:51 2013 From: sam guerler To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Thu, 03 Oct 2013 09:47:44 -0400 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============0822418899835414169==" --===============0822418899835414169== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit Hi Peter, I cannot reproduce the type error you are observing, but that one might be critical. The second message is rather an information than an error message. Is it possible that data.js is modified in your local galaxy version? You could apply an hg diff on data.js or maybe send the first few code lines in order verify this? Thanks, Sam On Thu, Oct 3, 2013 at 5:09 AM, Peter Cock wrote: > On Thu, Oct 3, 2013 at 8:02 AM, Hans-Rudolf Hotz wrote: > > Hi Peter and Bjoern > > > > we had similar problems in August, when we upgraded to > 'release_2013.06.03'. > > The problem has disappeared now. > > > > At the time I had the suspicion, it only happened to browser sessions > which > > were already open before the upgrade, Hence, closing the browser, and > > starting again helped. But this was just a guess. > > > > > > Regards, Hans-Rudolf > > Thanks Hans, > > On my machine restarting the browser made no difference. > > Also (within Galaxy) logging out and logging in made no difference. > > On Wed, Oct 2, 2013 at 7:56 PM, sam guerler > wrote: > > Hi Peter, > > > > Does the Javascript console of the browser show any error messages? > > > > Thanks, > > Sam > > Under Firefox, there are lots of (what I assume are harmless) CSS warnings. > Also: > > [10:05:12.293] TypeError: j is undefined @ > http://xxx/galaxy/static/scripts/mvc/data.js:1 > [10:05:12.291] "TabularButtonTrackster : Chromosome column undefined." > > Peter > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > --===============0822418899835414169== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.htm" MIME-Version: 1.0 PGRpdiBkaXI9Imx0ciI+SGkgUGV0ZXIsPGRpdj48YnI+PC9kaXY+PGRpdiBzdHlsZT5JIGNhbm5v dCByZXByb2R1Y2UgdGhlIHR5cGUgZXJyb3IgeW91IGFyZSBvYnNlcnZpbmcsIGJ1dCB0aGF0IG9u ZSBtaWdodCBiZSBjcml0aWNhbC4gVGhlIHNlY29uZCBtZXNzYWdlIGlzIHJhdGhlciBhbiBpbmZv cm1hdGlvbiB0aGFuIGFuIGVycm9yIG1lc3NhZ2UuIElzIGl0IHBvc3NpYmxlIHRoYXQgZGF0YS5q cyBpcyBtb2RpZmllZCBpbiB5b3VyIGxvY2FsIGdhbGF4eSB2ZXJzaW9uPyBZb3UgY291bGQgYXBw bHkgYW4gaGcgZGlmZiBvbiBkYXRhLmpzIG9yIG1heWJlIHNlbmQgdGhlIGZpcnN0IGZldyBjb2Rl IGxpbmVzIGluIG9yZGVyIHZlcmlmeSB0aGlzPzwvZGl2Pgo8ZGl2IHN0eWxlPjxicj48L2Rpdj48 ZGl2IHN0eWxlPlRoYW5rcyw8L2Rpdj48ZGl2IHN0eWxlPlNhbTwvZGl2PjwvZGl2PjxkaXYgY2xh c3M9ImdtYWlsX2V4dHJhIj48YnI+PGJyPjxkaXYgY2xhc3M9ImdtYWlsX3F1b3RlIj5PbiBUaHUs IE9jdCAzLCAyMDEzIGF0IDU6MDkgQU0sIFBldGVyIENvY2sgPHNwYW4gZGlyPSJsdHIiPiZsdDs8 YSBocmVmPSJtYWlsdG86cC5qLmEuY29ja0Bnb29nbGVtYWlsLmNvbSIgdGFyZ2V0PSJfYmxhbmsi PnAuai5hLmNvY2tAZ29vZ2xlbWFpbC5jb208L2E+Jmd0Ozwvc3Bhbj4gd3JvdGU6PGJyPgo8Ymxv Y2txdW90ZSBjbGFzcz0iZ21haWxfcXVvdGUiIHN0eWxlPSJtYXJnaW46MCAwIDAgLjhleDtib3Jk ZXItbGVmdDoxcHggI2NjYyBzb2xpZDtwYWRkaW5nLWxlZnQ6MWV4Ij48ZGl2IGNsYXNzPSJpbSI+ T24gVGh1LCBPY3QgMywgMjAxMyBhdCA4OjAyIEFNLCBIYW5zLVJ1ZG9sZiBIb3R6ICZsdDs8YSBo cmVmPSJtYWlsdG86aHJoQGZtaS5jaCI+aHJoQGZtaS5jaDwvYT4mZ3Q7IHdyb3RlOjxicj4KCiZn dDsgSGkgUGV0ZXIgYW5kIEJqb2Vybjxicj4KJmd0Ozxicj4KJmd0OyB3ZSBoYWQgc2ltaWxhciBw cm9ibGVtcyBpbiBBdWd1c3QsIHdoZW4gd2UgdXBncmFkZWQgdG8gJiMzOTtyZWxlYXNlXzIwMTMu MDYuMDMmIzM5Oy48YnI+CiZndDsgVGhlIHByb2JsZW0gaGFzIGRpc2FwcGVhcmVkIG5vdy48YnI+ CiZndDs8YnI+CiZndDsgQXQgdGhlIHRpbWUgSSBoYWQgdGhlIHN1c3BpY2lvbiwgaXQgb25seSBo YXBwZW5lZCB0byBicm93c2VyIHNlc3Npb25zIHdoaWNoPGJyPgomZ3Q7IHdlcmUgYWxyZWFkeSBv cGVuIGJlZm9yZSB0aGUgdXBncmFkZSwgSGVuY2UsIGNsb3NpbmcgdGhlIGJyb3dzZXIsIGFuZDxi cj4KJmd0OyBzdGFydGluZyBhZ2FpbiBoZWxwZWQuIEJ1dCB0aGlzIHdhcyBqdXN0IGEgZ3Vlc3Mu PGJyPgomZ3Q7PGJyPgomZ3Q7PGJyPgomZ3Q7IFJlZ2FyZHMsIEhhbnMtUnVkb2xmPGJyPgo8YnI+ CjwvZGl2PlRoYW5rcyBIYW5zLDxicj4KPGJyPgpPbiBteSBtYWNoaW5lIHJlc3RhcnRpbmcgdGhl IGJyb3dzZXIgbWFkZSBubyBkaWZmZXJlbmNlLjxicj4KPGJyPgpBbHNvICh3aXRoaW4gR2FsYXh5 KSBsb2dnaW5nIG91dCBhbmQgbG9nZ2luZyBpbiBtYWRlIG5vIGRpZmZlcmVuY2UuPGJyPgo8ZGl2 IGNsYXNzPSJpbSI+PGJyPgpPbiBXZWQsIE9jdCAyLCAyMDEzIGF0IDc6NTYgUE0sIHNhbSBndWVy bGVyICZsdDs8YSBocmVmPSJtYWlsdG86YXlzYW0uZ3VlcmxlckBnbWFpbC5jb20iPmF5c2FtLmd1 ZXJsZXJAZ21haWwuY29tPC9hPiZndDsgd3JvdGU6PGJyPgomZ3Q7IEhpIFBldGVyLDxicj4KJmd0 Ozxicj4KJmd0OyBEb2VzIHRoZSBKYXZhc2NyaXB0IGNvbnNvbGUgb2YgdGhlIGJyb3dzZXIgc2hv dyBhbnkgZXJyb3IgbWVzc2FnZXM/PGJyPgomZ3Q7PGJyPgomZ3Q7IFRoYW5rcyw8YnI+CiZndDsg U2FtPGJyPgo8YnI+CjwvZGl2PlVuZGVyIEZpcmVmb3gsIHRoZXJlIGFyZSBsb3RzIG9mICh3aGF0 IEkgYXNzdW1lIGFyZSBoYXJtbGVzcykgQ1NTIHdhcm5pbmdzLjxicj4KQWxzbzo8YnI+Cjxicj4K WzEwOjA1OjEyLjI5M10gVHlwZUVycm9yOiBqIGlzIHVuZGVmaW5lZCBAPGJyPgo8YSBocmVmPSJo dHRwOi8veHh4L2dhbGF4eS9zdGF0aWMvc2NyaXB0cy9tdmMvZGF0YS5qczoxIiB0YXJnZXQ9Il9i bGFuayI+aHR0cDovL3h4eC9nYWxheHkvc3RhdGljL3NjcmlwdHMvbXZjL2RhdGEuanM6MTwvYT48 YnI+ClsxMDowNToxMi4yOTFdICZxdW90O1RhYnVsYXJCdXR0b25UcmFja3N0ZXIgOiBDaHJvbW9z b21lIGNvbHVtbiB1bmRlZmluZWQuJnF1b3Q7PGJyPgo8c3BhbiBjbGFzcz0iSE9FblpiIj48Zm9u dCBjb2xvcj0iIzg4ODg4OCI+PGJyPgpQZXRlcjxicj4KPC9mb250Pjwvc3Bhbj48ZGl2IGNsYXNz PSJIT0VuWmIiPjxkaXYgY2xhc3M9Img1Ij5fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fXzxicj4KUGxlYXNlIGtlZXAgYWxsIHJlcGxpZXMg b24gdGhlIGxpc3QgYnkgdXNpbmcgJnF1b3Q7cmVwbHkgYWxsJnF1b3Q7PGJyPgppbiB5b3VyIG1h aWwgY2xpZW50LiCgVG8gbWFuYWdlIHlvdXIgc3Vic2NyaXB0aW9ucyB0byB0aGlzPGJyPgphbmQg b3RoZXIgR2FsYXh5IGxpc3RzLCBwbGVhc2UgdXNlIHRoZSBpbnRlcmZhY2UgYXQ6PGJyPgqgIDxh IGhyZWY9Imh0dHA6Ly9saXN0cy5ieC5wc3UuZWR1LyIgdGFyZ2V0PSJfYmxhbmsiPmh0dHA6Ly9s aXN0cy5ieC5wc3UuZWR1LzwvYT48YnI+Cjxicj4KVG8gc2VhcmNoIEdhbGF4eSBtYWlsaW5nIGxp c3RzIHVzZSB0aGUgdW5pZmllZCBzZWFyY2ggYXQ6PGJyPgqgIDxhIGhyZWY9Imh0dHA6Ly9nYWxh eHlwcm9qZWN0Lm9yZy9zZWFyY2gvbWFpbGluZ2xpc3RzLyIgdGFyZ2V0PSJfYmxhbmsiPmh0dHA6 Ly9nYWxheHlwcm9qZWN0Lm9yZy9zZWFyY2gvbWFpbGluZ2xpc3RzLzwvYT48YnI+CjwvZGl2Pjwv ZGl2PjwvYmxvY2txdW90ZT48L2Rpdj48YnI+PC9kaXY+Cg== --===============0822418899835414169==-- From p.j.a.cock@googlemail.com Thu Oct 3 10:13:29 2013 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Thu, 03 Oct 2013 15:12:51 +0100 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============2788899582677939096==" --===============2788899582677939096== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable On Thu, Oct 3, 2013 at 2:47 PM, sam guerler wrote: > Hi Peter, > > I cannot reproduce the type error you are observing, but that one might be > critical. The second message is rather an information than an error message. > Is it possible that data.js is modified in your local galaxy version? You > could apply an hg diff on data.js or maybe send the first few code lines in > order verify this? > > Thanks, > Sam Thanks Sam, Unfortunately my data.js seems to match galaxy-dist perfectly: $ wget https://bitbucket.org/galaxy/galaxy-dist/raw/c42567f43aa762a45f7eb7fc0= 917260edcaa5636/static/scripts/mvc/data.js ... $ diff data.js /mnt/galaxy/galaxy-dist/static/scripts/mvc/data.js (no difference) I wonder if part of the issue is which tool created the tabular file, and if it uses some of the special column names like chromosome etc. The tools I've noticed this with do not use column name metadata (but do tend to have a #comment line with column names as the first line). Peter --===============2788899582677939096==-- From p.j.a.cock@googlemail.com Thu Oct 3 11:44:44 2013 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Thu, 03 Oct 2013 16:44:07 +0100 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============8823581079070411446==" --===============8823581079070411446== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable The good news is that running the default branch from galaxy-central seems to work, so at some point the fix/change/regression should reach the stable releases on galaxy-dist as well. Peter On Thu, Oct 3, 2013 at 3:12 PM, Peter Cock wrot= e: > On Thu, Oct 3, 2013 at 2:47 PM, sam guerler wro= te: >> Hi Peter, >> >> I cannot reproduce the type error you are observing, but that one might be >> critical. The second message is rather an information than an error messag= e. >> Is it possible that data.js is modified in your local galaxy version? You >> could apply an hg diff on data.js or maybe send the first few code lines in >> order verify this? >> >> Thanks, >> Sam > > Thanks Sam, > > Unfortunately my data.js seems to match galaxy-dist perfectly: > > $ wget https://bitbucket.org/galaxy/galaxy-dist/raw/c42567f43aa762a45f7eb7f= c0917260edcaa5636/static/scripts/mvc/data.js > ... > $ diff data.js /mnt/galaxy/galaxy-dist/static/scripts/mvc/data.js > (no difference) > > I wonder if part of the issue is which tool created the tabular file, and > if it uses some of the special column names like chromosome etc. > The tools I've noticed this with do not use column name metadata > (but do tend to have a #comment line with column names as the > first line). > > Peter --===============8823581079070411446==-- From rasche.eric@yandex.ru Thu Oct 3 12:15:16 2013 From: Eric Rasche To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Thu, 03 Oct 2013 11:14:54 -0500 Message-ID: <524D97FE.9080608@yandex.ru> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============1413361093699348225==" --===============1413361093699348225== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I see the same issue, repeatedly on my galaxy instance. Running unmodified from the galaxy-dist/default branch. Since I'm running the uncompressed data.js, I get a bit more information from my errors than Peter's > [10:05:12.293] TypeError: j is undefined @ > http://xxx/galaxy/static/scripts/mvc/data.js:1 > [10:05:12.291] "TabularButtonTrackster : Chromosome column > undefined." Mine points to line 188 in data.js, specifically the "else if" in this function. _renderCell: function(cell_contents, index, colspan) { var column_types =3D this.model.get_metadata('column_types'); if (colspan !=3D=3D undefined) { return $('').attr('colspan', colspan).addClass('stringalign').text(cell_contents); } else if (column_types[index] =3D=3D=3D 'str' || column_types =3D=3D= =3D 'list') { /* Left align all str columns, right align the rest */ return $('').addClass('stringalign').text(cell_contents); } else { return $('').text(cell_contents); } }, I get an error: "Uncaught TypeError: Cannot read property '0' of undefined", indicating that upon attempting to read index 0 of "column_types" it determines that column_types is null. I commented out the else-if block and found that everything else was working, it just rendered as right aligned. Hope this helps! Eric Rasche On 10/03/2013 10:44 AM, Peter Cock wrote: > The good news is that running the default branch from galaxy-central > seems to work, so at some point the fix/change/regression should > reach the stable releases on galaxy-dist as well. >=20 > Peter >=20 >=20 > On Thu, Oct 3, 2013 at 3:12 PM, Peter Cock wr= ote: >> On Thu, Oct 3, 2013 at 2:47 PM, sam guerler wr= ote: >>> Hi Peter, >>> >>> I cannot reproduce the type error you are observing, but that one might be >>> critical. The second message is rather an information than an error messa= ge. >>> Is it possible that data.js is modified in your local galaxy version? You >>> could apply an hg diff on data.js or maybe send the first few code lines = in >>> order verify this? >>> >>> Thanks, >>> Sam >> >> Thanks Sam, >> >> Unfortunately my data.js seems to match galaxy-dist perfectly: >> >> $ wget https://bitbucket.org/galaxy/galaxy-dist/raw/c42567f43aa762a45f7eb7= fc0917260edcaa5636/static/scripts/mvc/data.js >> ... >> $ diff data.js /mnt/galaxy/galaxy-dist/static/scripts/mvc/data.js >> (no difference) >> >> I wonder if part of the issue is which tool created the tabular file, and >> if it uses some of the special column names like chromosome etc. >> The tools I've noticed this with do not use column name metadata >> (but do tend to have a #comment line with column names as the >> first line). >> >> Peter > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ >=20 > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >=20 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.19 (GNU/Linux) iQIcBAEBAgAGBQJSTZf+AAoJEMqDXdrsMcpVUI8P/2MhPwHy7+YeLuK+5isq1rDl zEqAxRXXRc28IkHkJnvUm5CpRAdhGZse+ICUHU0CMDWXOrIy9+1eGQzGSeNmeWzD rUIil6PSdR6lMQOXhJ2cgeQYrz5ACu9XIlYjE9ZRD/cAT0I+M4llpCK+iZH1ZIbq ZGi7tBTANNuRoP9qP6iv0o2SaXHw/ly4Gs06yxOG536IaHfns51LQXXUr3055aR/ hj3fq2IfpCOr1GQyMvZUnwMqhLjk/eUhG9mXs2UJlfnLD3YXimCpwju7GBmh4/Sd T+GZUPZs9V2qG23zCCnr3kGZWWt8K3v9SUnxY1in/cTjaSZidh8PrdROBVw2KtI2 fSvSAGAVm0zm7yHIkyMLjNPLATRE12Qq2uqBnD+mNTYM71xyiidsfC+7X/g/widM +yeiWZrDayFhhDoe4bHYqDH4lNztorTcFioHMESLTv2OirPBERIv/TT7kqn56Czl 7BoPGV6mMvcGjt/ULX+nDfbuymcbzDctn1UzfKqvVkhWQK3JOHz2lJbEvHf11dZe t8Bv6Sq/6gRrk3z49qoBgMp7aoA4c2ZoS7Tm/NkJCf3lreVtkz6tA2GKMEmrJLqY ZqfE+7NwG+MorG+OvgQbj/VKjzowDKaeZgkAShIRjLC51oRA7t2MtwzyM3H4Ur7x Lk5qkZHn+yRNcDRqYXJh =3DVoDi -----END PGP SIGNATURE----- --===============1413361093699348225==-- From aysam.guerler@gmail.com Thu Oct 3 13:30:50 2013 From: sam guerler To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Thu, 03 Oct 2013 13:30:11 -0400 Message-ID: In-Reply-To: <524D97FE.9080608@yandex.ru> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3099537018496994510==" --===============3099537018496994510== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Thanks Eric. I updated the data.js file in an attempt to catch this error. On Thu, Oct 3, 2013 at 12:14 PM, Eric Rasche wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > I see the same issue, repeatedly on my galaxy instance. Running > unmodified from the galaxy-dist/default branch. > > Since I'm running the uncompressed data.js, I get a bit more information > from my errors than Peter's > > > [10:05:12.293] TypeError: j is undefined @ > > http://xxx/galaxy/static/scripts/mvc/data.js:1 > > [10:05:12.291] "TabularButtonTrackster : Chromosome column > > undefined." > > Mine points to line 188 in data.js, specifically the "else if" in this > function. > > _renderCell: function(cell_contents, index, colspan) { > var column_types =3D this.model.get_metadata('column_types'); > if (colspan !=3D=3D undefined) { > return $('').attr('colspan', > colspan).addClass('stringalign').text(cell_contents); > } > else if (column_types[index] =3D=3D=3D 'str' || column_types =3D=3D= =3D 'list') > { > /* Left align all str columns, right align the rest */ > return $('').addClass('stringalign').text(cell_contents); > } > else { > return $('').text(cell_contents); > } > }, > > I get an error: > > "Uncaught TypeError: Cannot read property '0' of undefined", indicating > that upon attempting to read index 0 of "column_types" it determines > that column_types is null. > > I commented out the else-if block and found that everything else was > working, it just rendered as right aligned. > > Hope this helps! > > Eric Rasche > > On 10/03/2013 10:44 AM, Peter Cock wrote: > > The good news is that running the default branch from galaxy-central > > seems to work, so at some point the fix/change/regression should > > reach the stable releases on galaxy-dist as well. > > > > Peter > > > > > > On Thu, Oct 3, 2013 at 3:12 PM, Peter Cock > wrote: > >> On Thu, Oct 3, 2013 at 2:47 PM, sam guerler > wrote: > >>> Hi Peter, > >>> > >>> I cannot reproduce the type error you are observing, but that one > might be > >>> critical. The second message is rather an information than an error > message. > >>> Is it possible that data.js is modified in your local galaxy version? > You > >>> could apply an hg diff on data.js or maybe send the first few code > lines in > >>> order verify this? > >>> > >>> Thanks, > >>> Sam > >> > >> Thanks Sam, > >> > >> Unfortunately my data.js seems to match galaxy-dist perfectly: > >> > >> $ wget > https://bitbucket.org/galaxy/galaxy-dist/raw/c42567f43aa762a45f7eb7fc091726= 0edcaa5636/static/scripts/mvc/data.js > >> ... > >> $ diff data.js /mnt/galaxy/galaxy-dist/static/scripts/mvc/data.js > >> (no difference) > >> > >> I wonder if part of the issue is which tool created the tabular file, > and > >> if it uses some of the special column names like chromosome etc. > >> The tools I've noticed this with do not use column name metadata > >> (but do tend to have a #comment line with column names as the > >> first line). > >> > >> Peter > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v2.0.19 (GNU/Linux) > > iQIcBAEBAgAGBQJSTZf+AAoJEMqDXdrsMcpVUI8P/2MhPwHy7+YeLuK+5isq1rDl > zEqAxRXXRc28IkHkJnvUm5CpRAdhGZse+ICUHU0CMDWXOrIy9+1eGQzGSeNmeWzD > rUIil6PSdR6lMQOXhJ2cgeQYrz5ACu9XIlYjE9ZRD/cAT0I+M4llpCK+iZH1ZIbq > ZGi7tBTANNuRoP9qP6iv0o2SaXHw/ly4Gs06yxOG536IaHfns51LQXXUr3055aR/ > hj3fq2IfpCOr1GQyMvZUnwMqhLjk/eUhG9mXs2UJlfnLD3YXimCpwju7GBmh4/Sd > T+GZUPZs9V2qG23zCCnr3kGZWWt8K3v9SUnxY1in/cTjaSZidh8PrdROBVw2KtI2 > fSvSAGAVm0zm7yHIkyMLjNPLATRE12Qq2uqBnD+mNTYM71xyiidsfC+7X/g/widM > +yeiWZrDayFhhDoe4bHYqDH4lNztorTcFioHMESLTv2OirPBERIv/TT7kqn56Czl > 7BoPGV6mMvcGjt/ULX+nDfbuymcbzDctn1UzfKqvVkhWQK3JOHz2lJbEvHf11dZe > t8Bv6Sq/6gRrk3z49qoBgMp7aoA4c2ZoS7Tm/NkJCf3lreVtkz6tA2GKMEmrJLqY > 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Thanks! Bjoern > Thanks Eric. I updated the data.js file in an attempt to catch this > error. >=20 >=20 > On Thu, Oct 3, 2013 at 12:14 PM, Eric Rasche > wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > =20 > I see the same issue, repeatedly on my galaxy instance. > Running > unmodified from the galaxy-dist/default branch. > =20 > Since I'm running the uncompressed data.js, I get a bit more > information > from my errors than Peter's > =20 > > [10:05:12.293] TypeError: j is undefined @ > > http://xxx/galaxy/static/scripts/mvc/data.js:1 > > [10:05:12.291] "TabularButtonTrackster : Chromosome column > > undefined." > =20 > =20 > Mine points to line 188 in data.js, specifically the "else if" > in this > function. > =20 > _renderCell: function(cell_contents, index, colspan) { > var column_types =3D > this.model.get_metadata('column_types'); > if (colspan !=3D=3D undefined) { > return $('').attr('colspan', > colspan).addClass('stringalign').text(cell_contents); > } > else if (column_types[index] =3D=3D=3D 'str' || column_types > =3D=3D=3D 'list') { > /* Left align all str columns, right align the > rest */ > return > $('').addClass('stringalign').text(cell_contents); > } > else { > return $('').text(cell_contents); > } > }, > =20 > I get an error: > =20 > "Uncaught TypeError: Cannot read property '0' of undefined", > indicating > that upon attempting to read index 0 of "column_types" it > determines > that column_types is null. > =20 > I commented out the else-if block and found that everything > else was > working, it just rendered as right aligned. > =20 > Hope this helps! > =20 > Eric Rasche > =20 > On 10/03/2013 10:44 AM, Peter Cock wrote: > > The good news is that running the default branch from > galaxy-central > > seems to work, so at some point the fix/change/regression > should > > reach the stable releases on galaxy-dist as well. > > > > Peter > > > > > > On Thu, Oct 3, 2013 at 3:12 PM, Peter Cock > wrote: > >> On Thu, Oct 3, 2013 at 2:47 PM, sam guerler > wrote: > >>> Hi Peter, > >>> > >>> I cannot reproduce the type error you are observing, but > that one might be > >>> critical. The second message is rather an information than > an error message. > >>> Is it possible that data.js is modified in your local > galaxy version? You > >>> could apply an hg diff on data.js or maybe send the first > few code lines in > >>> order verify this? > >>> > >>> Thanks, > >>> Sam > >> > >> Thanks Sam, > >> > >> Unfortunately my data.js seems to match galaxy-dist > perfectly: > >> > >> $ wget > https://bitbucket.org/galaxy/galaxy-dist/raw/c42567f43aa762a45f7eb7= fc0917260edcaa5636/static/scripts/mvc/data.js > >> ... > >> $ diff > data.js /mnt/galaxy/galaxy-dist/static/scripts/mvc/data.js > >> (no difference) > >> > >> I wonder if part of the issue is which tool created the > tabular file, and > >> if it uses some of the special column names like chromosome > etc. > >> The tools I've noticed this with do not use column name > metadata > >> (but do tend to have a #comment line with column names as > the > >> first line). > >> > >> Peter > =20 > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > =20 > =20 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v2.0.19 (GNU/Linux) > =20 > iQIcBAEBAgAGBQJSTZf+AAoJEMqDXdrsMcpVUI8P/2MhPwHy7+YeLuK > +5isq1rDl > zEqAxRXXRc28IkHkJnvUm5CpRAdhGZse+ICUHU0CMDWXOrIy9 > +1eGQzGSeNmeWzD > rUIil6PSdR6lMQOXhJ2cgeQYrz5ACu9XIlYjE9ZRD/cAT0I+M4llpCK > +iZH1ZIbq > ZGi7tBTANNuRoP9qP6iv0o2SaXHw/ly4Gs06yxOG536IaHfns51LQXXUr3055aR/ > hj3fq2IfpCOr1GQyMvZUnwMqhLjk/eUhG9mXs2UJlfnLD3YXimCpwju7GBmh4/Sd > T > +GZUPZs9V2qG23zCCnr3kGZWWt8K3v9SUnxY1in/cTjaSZidh8PrdROBVw2KtI2 > fSvSAGAVm0zm7yHIkyMLjNPLATRE12Qq2uqBnD+mNTYM71xyiidsfC > +7X/g/widM > +yeiWZrDayFhhDoe4bHYqDH4lNztorTcFioHMESLTv2OirPBERIv/TT7kqn56Czl > 7BoPGV6mMvcGjt/ULX > +nDfbuymcbzDctn1UzfKqvVkhWQK3JOHz2lJbEvHf11dZe > t8Bv6Sq/6gRrk3z49qoBgMp7aoA4c2ZoS7Tm/NkJCf3lreVtkz6tA2GKMEmrJLqY > ZqfE+7NwG+MorG > +OvgQbj/VKjzowDKaeZgkAShIRjLC51oRA7t2MtwzyM3H4Ur7x > Lk5qkZHn+yRNcDRqYXJh > =3DVoDi > -----END PGP SIGNATURE----- >=20 >=20 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ >=20 > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ --===============8344602273222438084==-- From p.j.a.cock@googlemail.com Fri Oct 4 04:53:22 2013 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Fri, 04 Oct 2013 09:52:44 +0100 Message-ID: In-Reply-To: <1380821652.3349.37.camel@threonin> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6374432652509095503==" --===============6374432652509095503== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable On Thu, Oct 3, 2013 at 6:34 PM, Bj=C3=B6rn Gr=C3=BCning wrote: > Hi Sam, > > any chance to commit that fix to Galaxy-stable? > > Thanks! > Bjoern The error Sam and Eric reported is different to mine, and so this doesn't solve the display issue on my machine: $ hg diff static/scripts/mvc/data.js diff -r c42567f43aa7 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js Mon Aug 19 13:19:56 2013 -0400 +++ b/static/scripts/mvc/data.js Fri Oct 04 09:44:39 2013 +0100 @@ -185,10 +185,10 @@ if (colspan !=3D=3D undefined) { return $('').attr('colspan', colspan).addClass('stringalign').text(cell_contents); } - else if (column_types[index] =3D=3D=3D 'str' || column_types =3D=3D= =3D 'list') { - /* Left align all str columns, right align the rest */ - return $('').addClass('stringalign').text(cell_contents); - } + //else if (column_types[index] =3D=3D=3D 'str' || column_types =3D= =3D=3D 'list') { + // /* Left align all str columns, right align the rest */ + // return $('').addClass('stringalign').text(cell_contents); + //} else { return $('').text(cell_contents); } This bit code hasn't changed on the galaxy-central, so whatever is breaking the column_types on Eric's machine seems to be coming from elsewhere. The workaround looks like it would have the downside of right align string columns, which is undesirable. Eric, is there a simple trick to get data.js into the browser with multiple lines? Right now Firefox tells me the 'j' error is on line one because the entire file is one long line :( [09:47:34.057] TypeError: j is undefined @ http://xxx/galaxy/static/scripts/mvc/data.js:1 Presumably I need Galaxy to serve data.js uncompressed? Thanks, Peter --===============6374432652509095503==-- From rasche.eric@yandex.ru Fri Oct 4 09:16:43 2013 From: Eric Rasche To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Fri, 04 Oct 2013 08:09:58 -0500 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============1957394895297946122==" --===============1957394895297946122== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Yes, the code is definitely broken somewhere else, not in this function, but = this fix ensures that data is at least visible. However, data is right aligne= d as you mentioned, which is definitely undesirable.=20 As for getting the script onto multiple lines, you are correct, you'd need to= serve the uncompressed version. Then again, I believe you're experiencing th= e same issue as me, because the compressed version of data.js uses column_typ= es as 'j' and index as 'i'.=20 Cheers, Eric Peter Cock schrieb: >On Thu, Oct 3, 2013 at 6:34 PM, Bj=C3=B6rn Gr=C3=BCning > wrote: >> Hi Sam, >> >> any chance to commit that fix to Galaxy-stable? >> >> Thanks! >> Bjoern > >The error Sam and Eric reported is different to mine, and so this >doesn't solve the display issue on my machine: > >$ hg diff static/scripts/mvc/data.js >diff -r c42567f43aa7 static/scripts/mvc/data.js >--- a/static/scripts/mvc/data.js Mon Aug 19 13:19:56 2013 -0400 >+++ b/static/scripts/mvc/data.js Fri Oct 04 09:44:39 2013 +0100 >@@ -185,10 +185,10 @@ > if (colspan !=3D=3D undefined) { > return $('').attr('colspan', >colspan).addClass('stringalign').text(cell_contents); > } >- else if (column_types[index] =3D=3D=3D 'str' || column_types =3D=3D= =3D >'list') { >- /* Left align all str columns, right align the rest */ >- return >$('').addClass('stringalign').text(cell_contents); >- } >+ //else if (column_types[index] =3D=3D=3D 'str' || column_types =3D= =3D=3D >'list') { >+ // /* Left align all str columns, right align the rest */ >+ // return >$('').addClass('stringalign').text(cell_contents); >+ //} > else { > return $('').text(cell_contents); > } > >This bit code hasn't changed on the galaxy-central, so >whatever is breaking the column_types on Eric's machine >seems to be coming from elsewhere. The workaround >looks like it would have the downside of right align string >columns, which is undesirable. > >Eric, is there a simple trick to get data.js into the browser >with multiple lines? Right now Firefox tells me the 'j' error >is on line one because the entire file is one long line :( > >[09:47:34.057] TypeError: j is undefined @ >http://xxx/galaxy/static/scripts/mvc/data.js:1 > >Presumably I need Galaxy to serve data.js uncompressed? > >Thanks, > >Peter > >___________________________________________________________ >Please keep all replies on the list by using "reply all" >in your mail client. To manage your subscriptions to this >and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > >To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ --=20 Sent from my Android phone with K-9 Mail. 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b2R5PjwvaHRtbD4= --===============1957394895297946122==-- From p.j.a.cock@googlemail.com Fri Oct 4 09:25:02 2013 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Fri, 04 Oct 2013 14:24:54 +0100 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============4346512374082602177==" --===============4346512374082602177== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit On Fri, Oct 4, 2013 at 2:09 PM, Eric Rasche wrote: > Yes, the code is definitely broken somewhere else, not in this function, but > this fix ensures that data is at least visible. However, data is right > aligned as you mentioned, which is definitely undesirable. I would find this an improvement in the short term. > As for getting the script onto multiple lines, you are correct, you'd need > to serve the uncompressed version. How do I do this? > Then again, I believe you're experiencing > the same issue as me, because the compressed version of data.js uses > column_types as 'j' and index as 'i'. I tried the fix by editing data.js but there was no change. If this is the same bug, then maybe a cached (compressed?) copy of data.js must still be in use. Thanks, Peter --===============4346512374082602177==-- From p.j.a.cock@googlemail.com Thu Oct 17 08:59:01 2013 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Thu, 17 Oct 2013 13:58:52 +0100 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============4967774626800417847==" --===============4967774626800417847== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable On Fri, Oct 4, 2013 at 2:24 PM, Peter Cock wrot= e: > On Fri, Oct 4, 2013 at 2:09 PM, Eric Rasche wrote: >> Yes, the code is definitely broken somewhere else, not in this function, b= ut >> this fix ensures that data is at least visible. However, data is right >> aligned as you mentioned, which is definitely undesirable. > > I would find this an improvement in the short term. > >> As for getting the script onto multiple lines, you are correct, you'd need >> to serve the uncompressed version. > > How do I do this? > >> Then again, I believe you're experiencing >> the same issue as me, because the compressed version of data.js uses >> column_types as 'j' and index as 'i'. > > I tried the fix by editing data.js but there was no change. If this > is the same bug, then maybe a cached (compressed?) copy of > data.js must still be in use. In the meantime to help ensure this does get fixed in the next stable release, I filed an issue on Trello: https://trello.com/c/it0oXXeT/1190-tabular-data-not-displaying-in-main-panel-= data-js-error Peter --===============4967774626800417847==-- From rasche.eric@yandex.ru Thu Oct 17 11:05:48 2013 From: Eric Rasche To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Thu, 17 Oct 2013 10:05:36 -0500 Message-ID: <525FFCC0.4040000@yandex.ru> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============7184767556621285697==" --===============7184767556621285697== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Peter, On 10/17/2013 07:58 AM, Peter Cock wrote: > On Fri, Oct 4, 2013 at 2:24 PM, Peter Cock wr= ote: >> On Fri, Oct 4, 2013 at 2:09 PM, Eric Rasche wrot= e: >>> Yes, the code is definitely broken somewhere else, not in this function, = but >>> this fix ensures that data is at least visible. However, data is right >>> aligned as you mentioned, which is definitely undesirable. >> >> I would find this an improvement in the short term. >> >>> As for getting the script onto multiple lines, you are correct, you'd need >>> to serve the uncompressed version. >> >> How do I do this? >> >>> Then again, I believe you're experiencing >>> the same issue as me, because the compressed version of data.js uses >>> column_types as 'j' and index as 'i'. >> >> I tried the fix by editing data.js but there was no change. If this >> is the same bug, then maybe a cached (compressed?) copy of >> data.js must still be in use. >=20 > In the meantime to help ensure this does get fixed in the next > stable release, I filed an issue on Trello: >=20 > https://trello.com/c/it0oXXeT/1190-tabular-data-not-displaying-in-main-pane= l-data-js-error >=20 > Peter >=20 Wonderful! However, in upgrading to the latest galaxy-dist release (Oct. 12), I saw my issue go away. Formatting is back and working. Is it the same for you? Regards, Eric - --=20 Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJSX/zAAAoJEMqDXdrsMcpV1KkQAIlZFZQt7N33zhWC/ydAsSWv yg+TLrTVABbDjzCATS3WYlj2zJXou4PxDjr4uFIlJT/oZ88t15Rmywep+cnm7ZL2 kqrPTeP4H6edtvr8iOakBfgSN6+wh/mwPTE3BeqEFi1vA4iTuW2r4Ze5mQaQ6+Wi B4Zd+lkElMClKO7UJ2wGFQrqFy90c629C3gHYDOO/igtkiqU6N0+GxS48pucF4Za oWObXdfg3OLHaooiW7gyR72/UJIF5O0XFaNZaQGD8OBN6/+epQQrMKZSJqMbXAzO 9yZhQ6/mz9PSh6hDzEF7/pi0KbF1g2aYWLCOD4h+rdQ2ULoMl2EpQF9qVT5RQbkS KiaTay36d8Jf243hU6WCd9wBmkP1Dn4JXW2DLLqpz5P42nVucatHdwZI8wumgXk3 uoOUZmGvZF6dnG8h45WwT0o5cXav9kwTcZmeDnCsTM0YQOrD5a5Nla+wOqgJdp+I Hg9xREo/SLu9nsUKAX9ZBijyaQt8JM+EqsR+iok4OanSmeiW5VvurPbrxYVnqQYB o6MZDkr/yLNhGSsLK2pPHfp395lZP0jkBVH49FJBs/upBz2L1d00fbxP8L5UZxYN pHKpMbeYnjDptu4OSXQBbjuVlou8PkUztofIiIvQVfrXs8XcHcpio47pXzUeqJfk +bKRTrbGslFsZSKqQfUZ =3Ds/4f -----END PGP SIGNATURE----- --===============7184767556621285697==-- From p.j.a.cock@googlemail.com Thu Oct 17 11:28:47 2013 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Thu, 17 Oct 2013 16:28:38 +0100 Message-ID: In-Reply-To: <525FFCC0.4040000@yandex.ru> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6166108260120311171==" --===============6166108260120311171== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable On Thu, Oct 17, 2013 at 4:05 PM, Eric Rasche wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Peter, > > On 10/17/2013 07:58 AM, Peter Cock wrote: >> On Fri, Oct 4, 2013 at 2:24 PM, Peter Cock w= rote: >>> On Fri, Oct 4, 2013 at 2:09 PM, Eric Rasche wro= te: >>>> Yes, the code is definitely broken somewhere else, not in this function,= but >>>> this fix ensures that data is at least visible. However, data is right >>>> aligned as you mentioned, which is definitely undesirable. >>> >>> I would find this an improvement in the short term. >>> >>>> As for getting the script onto multiple lines, you are correct, you'd ne= ed >>>> to serve the uncompressed version. >>> >>> How do I do this? >>> >>>> Then again, I believe you're experiencing >>>> the same issue as me, because the compressed version of data.js uses >>>> column_types as 'j' and index as 'i'. >>> >>> I tried the fix by editing data.js but there was no change. If this >>> is the same bug, then maybe a cached (compressed?) copy of >>> data.js must still be in use. >> >> In the meantime to help ensure this does get fixed in the next >> stable release, I filed an issue on Trello: >> >> https://trello.com/c/it0oXXeT/1190-tabular-data-not-displaying-in-main-pan= el-data-js-error >> >> Peter >> > Wonderful! However, in upgrading to the latest galaxy-dist release (Oct. > 12), I saw my issue go away. Formatting is back and working. Is it the > same for you? > > Regards, > Eric > Hi Eric, Its still broken on our production instance, which is running what I thought was the galaxy-dist current release Aug 12, 2013 Galaxy Distribution http://wiki.galaxyproject.org/DevNewsBriefs $ hg head changeset: 10421:a477486bf18e branch: stable tag: tip user: Nate Coraor date: Thu Sep 26 11:02:58 2013 -0400 summary: Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased. changeset: 10411:c42567f43aa7 user: greg date: Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. [galaxy(a)ppserver galaxy-dist]$ hg branch default Looking at https://bitbucket.org/galaxy/galaxy-dist/commits/all the latest commits are in September, so where did your Oct 12 release you are running come from? (I know this has been fixed on galaxy-central although I don't know which commit was important or when it happened.) Peter --===============6166108260120311171==-- From p.j.a.cock@googlemail.com Wed Oct 30 07:43:12 2013 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Date: Wed, 30 Oct 2013 11:43:03 +0000 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6750329593614301843==" --===============6750329593614301843== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable On Thu, Oct 17, 2013 at 4:28 PM, Peter Cock wro= te: > On Thu, Oct 17, 2013 at 4:05 PM, Eric Rasche wrot= e: >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Peter, >> >> On 10/17/2013 07:58 AM, Peter Cock wrote: >>> On Fri, Oct 4, 2013 at 2:24 PM, Peter Cock = wrote: >>>> On Fri, Oct 4, 2013 at 2:09 PM, Eric Rasche wr= ote: >>>>> Yes, the code is definitely broken somewhere else, not in this function= , but >>>>> this fix ensures that data is at least visible. However, data is right >>>>> aligned as you mentioned, which is definitely undesirable. >>>> >>>> I would find this an improvement in the short term. >>>> >>>>> As for getting the script onto multiple lines, you are correct, you'd n= eed >>>>> to serve the uncompressed version. >>>> >>>> How do I do this? >>>> >>>>> Then again, I believe you're experiencing >>>>> the same issue as me, because the compressed version of data.js uses >>>>> column_types as 'j' and index as 'i'. >>>> >>>> I tried the fix by editing data.js but there was no change. If this >>>> is the same bug, then maybe a cached (compressed?) copy of >>>> data.js must still be in use. >>> >>> In the meantime to help ensure this does get fixed in the next >>> stable release, I filed an issue on Trello: >>> >>> https://trello.com/c/it0oXXeT/1190-tabular-data-not-displaying-in-main-pa= nel-data-js-error >>> >>> Peter >>> >> Wonderful! However, in upgrading to the latest galaxy-dist release (Oct. >> 12), I saw my issue go away. Formatting is back and working. Is it the >> same for you? >> >> Regards, >> Eric >> > > Hi Eric, > > Its still broken on our production instance, which is running what I thought > was the galaxy-dist current release Aug 12, 2013 Galaxy Distribution > http://wiki.galaxyproject.org/DevNewsBriefs > > $ hg head > changeset: 10421:a477486bf18e > branch: stable > tag: tip > user: Nate Coraor > date: Thu Sep 26 11:02:58 2013 -0400 > summary: Bugfix for tool-to-destination mapping, tool ids are > lowercased but the mapping id was not lowercased. > > changeset: 10411:c42567f43aa7 > user: greg > date: Mon Aug 19 13:19:56 2013 -0400 > summary: Filter invalid objects when generating the list of > repository_dependencies objects that are associated with a tool shed > repository installed into Galaxy. > > [galaxy(a)ppserver galaxy-dist]$ hg branch > default > > Looking at https://bitbucket.org/galaxy/galaxy-dist/commits/all the > latest commits are in September, so where did your Oct 12 > release you are running come from? > > (I know this has been fixed on galaxy-central although I don't > know which commit was important or when it happened.) > > Peter Has anyone else tried this on the current next-stable branch? It seems to be working, $ hg branch next-stable $ hg head | more ... changeset: 12215:232ef8122d54 branch: next-stable parent: 12209:a00d08d23543 user: Bjoern Gruening date: Wed Oct 23 14:39:49 2013 +0200 summary: cleanup & bugfix for R environment ... Regards, Peter --===============6750329593614301843==--