[galaxy-dev] Data library not properly showing up
Hi all, The data library I have created is only showing up partially. I have made a data libray, via het Admin menu, with one folder in it. I changed permissions, because I wanted it only to be visible to me. That worked fine. Next I created plenty more folders in that data library. Now, the folders created afterwards are not visible in the data library, when accessed via 'Shared data'. I have played a lot with changing permissions of those libraries, but to no avail. Cheers, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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/
Re: [galaxy-dev] Data library and symbolic links
Thanks for your answer!!! Cyril On 12/14/2012 04:17 PM, Nate Coraor wrote: Hi Cyril, Jen's response includes the correct information about how symlinks are handled, and why. Changing the symlink underlying a dataset is not a great idea since it will cause the dataset's metadata to be incorrect and break Galaxy's concept of reproducibility. I would suggest that you utilize the library dataset versioning features to accomplish what you're trying to do. Hope this helps, --nate On Dec 14, 2012, at 10:07 AM, Jennifer Jackson wrote: Hello, The original question/reply is posted here: http://lists.bx.psu.edu/pipermail/galaxy-user/2012-December/005665.html But the dev community is welcomed to add in additional comments/advice to this re-post! Thanks, Jen Galaxy team On 12/14/12 6:49 AM, MONJEAUD wrote: Hi all, I created data libraries using options "Upload files from filesystem paths" and "Link to files without copying into Galaxy". It worked but I use symbolic links because my data are frequently updated The problem is that Galaxy takes the real link (inside "external_filename" column in "dataset" table) and doesn't find the files when it is deleted. For example, I uploaded a dataset for a data library without copying : /databank/uniprot/current/fasta/all.fasta -> /databank/uniprot/01_12_2012/fasta/all.fasta The real path is put in the database and it's a problem when it is deleted. Is there a way for galaxy to take the symbolic link directly in the database instead of the real path. Thanks in advance! Cheers, -- Cyril Monjeaud Equipe Symbiose / Plate-forme GenOuest Bureau D156 IRISA-INRIA, Campus de Beaulieu 35042 Rennes cedex, France Tél: +33 (0) 2 99 84 74 17 ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/ -- Cyril Monjeaud Equipe Symbiose / Plate-forme GenOuest Bureau D156 IRISA-INRIA, Campus de Beaulieu 35042 Rennes cedex, France Tél: +33 (0) 2 99 84 74 17 ___ 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/
Re: [galaxy-dev] Data library and symbolic links
Hi Cyril, Jen's response includes the correct information about how symlinks are handled, and why. Changing the symlink underlying a dataset is not a great idea since it will cause the dataset's metadata to be incorrect and break Galaxy's concept of reproducibility. I would suggest that you utilize the library dataset versioning features to accomplish what you're trying to do. Hope this helps, --nate On Dec 14, 2012, at 10:07 AM, Jennifer Jackson wrote: > Hello, > > The original question/reply is posted here: > http://lists.bx.psu.edu/pipermail/galaxy-user/2012-December/005665.html > > But the dev community is welcomed to add in additional comments/advice to > this re-post! > > Thanks, > > Jen > Galaxy team > > On 12/14/12 6:49 AM, MONJEAUD wrote: >> Hi all, >> >> I created data libraries using options "Upload files from filesystem paths" >> and "Link to files without copying into Galaxy". >> It worked but I use symbolic links because my data are frequently updated >> >> The problem is that Galaxy takes the real link (inside "external_filename" >> column in "dataset" table) and doesn't find the >> files when it is deleted. >> >> For example, I uploaded a dataset for a data library without copying : >> /databank/uniprot/current/fasta/all.fasta -> >> /databank/uniprot/01_12_2012/fasta/all.fasta >> The real path is put in the database and it's a problem when it is deleted. >> >> Is there a way for galaxy to take the symbolic link directly in the database >> instead of the real path. >> >> Thanks in advance! >> Cheers, >> -- >> >> Cyril Monjeaud >> Equipe Symbiose / Plate-forme GenOuest >> Bureau D156 >> IRISA-INRIA, Campus de Beaulieu >> 35042 Rennes cedex, France >> Tél: +33 (0) 2 99 84 74 17 >> >> >> >> ___ >> 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/ > > -- > Jennifer Jackson > > http://galaxyproject.org > ___ > 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/ ___ 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/
Re: [galaxy-dev] Data library and symbolic links
Hello, The original question/reply is posted here: http://lists.bx.psu.edu/pipermail/galaxy-user/2012-December/005665.html But the dev community is welcomed to add in additional comments/advice to this re-post! Thanks, Jen Galaxy team On 12/14/12 6:49 AM, MONJEAUD wrote: Hi all, I created data libraries using options "Upload files from filesystem paths" and "_Link to files without copying into Galaxy_". It worked but I use symbolic links because my data are frequently updated The problem is that Galaxy takes the real link (inside "external_filename" column in "dataset" table) and doesn't find the files when it is deleted. For example, I uploaded a dataset for a data library without copying : /databank/uniprot/current/fasta/all.fasta -> /databank/uniprot/01_12_2012/fasta/all.fasta The real path is put in the database and it's a problem when it is deleted. Is there a way for galaxy to take the symbolic link directly in the database instead of the real path. Thanks in advance! Cheers, -- Cyril Monjeaud Equipe Symbiose / Plate-forme GenOuest Bureau D156 IRISA-INRIA, Campus de Beaulieu 35042 Rennes cedex, France Tél: +33 (0) 2 99 84 74 17 ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
[galaxy-dev] Data library and symbolic links
Hi all, I created data libraries using options "Upload files from filesystem paths" and "_Link to files without copying into Galaxy_". It worked but I use symbolic links because my data are frequently updated The problem is that Galaxy takes the real link (inside "external_filename" column in "dataset" table) and doesn't find the files when it is deleted. For example, I uploaded a dataset for a data library without copying : /databank/uniprot/current/fasta/all.fasta -> /databank/uniprot/01_12_2012/fasta/all.fasta The real path is put in the database and it's a problem when it is deleted. Is there a way for galaxy to take the symbolic link directly in the database instead of the real path. Thanks in advance! Cheers, -- Cyril Monjeaud Equipe Symbiose / Plate-forme GenOuest Bureau D156 IRISA-INRIA, Campus de Beaulieu 35042 Rennes cedex, France Tél: +33 (0) 2 99 84 74 17 ___ 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/
[galaxy-dev] Data library displays "(OperationError) no such column" error
Hi all, After updating my galaxy-dist to the latest release (23/Oct) I get the following error message when I try to access one of my data libraries. Error attempting to display contents of library (testlibrary): (OperationalError) no such column: True u'SELECT dataset_permissions.id AS dataset_permissions_id, dataset_permissions.create_time AS dataset_permissions_create_time, dataset_permissions.update_time AS dataset_permissions_update_time, dataset_permissions.action AS dataset_permissions_action, dataset_permissions.dataset_id AS dataset_permissions_dataset_id, dataset_permissions.role_id AS dataset_permissions_role_id XnFROM dataset_permissions XnWHERE True AND dataset_permissions.action = ?' ['access']. I was getting the same error message as the previous post (http://gmod.827538.n3.nabble.com/quot-No-module-named-controllers-library-common-quot-error-on-fresh-Galaxy-install-from-4-Oct-2012-td4025537.html) before the update and it’s now replaced with the above. I’ve also tried cloning a fresh galaxy-dist but I’m still receiving the same error message. The library exists and files are present because I can see them when I go to http://localhost:8080/api/libraries/X ... I just cannot access it via the web interface. Has anyone experienced a similar situation, or have any ideas? Many Thanks, Xin-Yi ___ 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/
[galaxy-dev] Data library
Hi, I have installed the local galaxy. And I have tried to use the data library to upload some CEL datasets. However, it occurred an error when I use data library to add datasets. It showed: Miscellaneous information: The uploaded binary file contains inappropriate content error Do you know how to fix it ? Best, This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ 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/
Re: [galaxy-dev] Data library fails to display contents
W. Augustine Dunn III wrote: > I am starting to really get the hang of customizing my new galaxy instance, > and please just let me THANK YOU GUYS! > > However, I am also running into a problem. I am trying to link genome fasta > files that i obtained through metazoa.ensembl.org. I created a library > called "Genome Sequences" with sub-folders to house them. Everything was > going fine until I tried to change the info on a couple so that they were > fasta not so other randomly autoassigned type. > > Now I get this error msg when ever i try to browse ANY of the "Genome Seq" > Library: > > Error attempting to display contents of library (Genome Sequences): > 'NoneType' object has no attribute 'dataset'. > > I am running this instance using a postgresql backend but the default paste > web-server since its mostly gonna me me and one or two other lab-mates using > it. > > I can NOT figure out whats up. Hi Gus, Sorry for the delay in response. If you're still experiencing this problem, I have a couple ideas. It looks like somehow you've gotten a LibraryDataset or LibraryDatasetDatasetAssociation that is not properly associated, possibly due to an unhandled exception when you were populating the library. If this is the case, it's certainly a bug, but may be difficult to track down. Could you check the contents of your database for the following: select * from library_dataset_dataset_association where library_dataset_id is null; select * from library_dataset where library_dataset_dataset_association_id is null; Thanks, --nate > > Relevant excerpt of Server log follows: > xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:03 -0700] "GET / HTTP/1.1" 200 - > "http://xxx.xxx.xxx.xxx/library"; "Mozilla/5.0 (X11; Linux x86_64) > AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" > xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /root/tool_menu > HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/"; "Mozilla/5.0 (X11; Linux x86_64) > AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" > xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /history HTTP/1.1" 200 > - "http://xxx.xxx.xxx.xxx/"; "Mozilla/5.0 (X11; Linux x86_64) > AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" > xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET /admin HTTP/1.1" 200 - > "http://vlad.bio.uci.edu:8081/"; "Mozilla/5.0 (X11; Linux x86_64) > AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" > xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET > /admin/center?webapp=galaxy HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin"; > "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) > Chrome/12.0.742.112 Safari/534.30" > xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:10 -0700] "GET > /library_admin/browse_libraries HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin"; > "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) > Chrome/12.0.742.112 Safari/534.30" > xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET > /library_admin/browse_libraries?f-deleted=False&f-name=All&f-description=All&sort=name&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=browse&id=9a8774fee61dd122& > HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries"; > "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) > Chrome/12.0.742.112 Safari/534.30" > xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET > /library_common/browse_library?sort=name&operation=browse&f-description=All&f-name=All&f-deleted=False&cntrller=library_admin&async=false&show_item_checkboxes=false&webapp=galaxy&id=9a8774fee61dd122&page=1 > HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries"; > "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) > Chrome/12.0.742.112 Safari/534.30" > xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET > /library_admin/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%28Genome+Sequences%29%3A+__sq__NoneType__sq__+object+has+no+attribute+__sq__dataset__sq__. > HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries"; > "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) > Chrome/12.0.742.112 Safari/534.30" > > > Thanks in advance! And thanks for this priceless tool! > > Gus > > -- > In science, "fact" can only mean "confirmed to such a degree that it would > be perverse to withhold provisional assent." I suppose that apples might > start to rise tomorrow, but the possibility does not merit equal time in > physics classrooms. > *-Stephen Jay Gould* > ___ > 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/
[galaxy-dev] Data library fails to display contents
I am starting to really get the hang of customizing my new galaxy instance, and please just let me THANK YOU GUYS! However, I am also running into a problem. I am trying to link genome fasta files that i obtained through metazoa.ensembl.org. I created a library called "Genome Sequences" with sub-folders to house them. Everything was going fine until I tried to change the info on a couple so that they were fasta not so other randomly autoassigned type. Now I get this error msg when ever i try to browse ANY of the "Genome Seq" Library: Error attempting to display contents of library (Genome Sequences): 'NoneType' object has no attribute 'dataset'. I am running this instance using a postgresql backend but the default paste web-server since its mostly gonna me me and one or two other lab-mates using it. I can NOT figure out whats up. Relevant excerpt of Server log follows: xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:03 -0700] "GET / HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/library"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /root/tool_menu HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /history HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET /admin HTTP/1.1" 200 - "http://vlad.bio.uci.edu:8081/"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET /admin/center?webapp=galaxy HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:10 -0700] "GET /library_admin/browse_libraries HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET /library_admin/browse_libraries?f-deleted=False&f-name=All&f-description=All&sort=name&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=browse&id=9a8774fee61dd122& HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET /library_common/browse_library?sort=name&operation=browse&f-description=All&f-name=All&f-deleted=False&cntrller=library_admin&async=false&show_item_checkboxes=false&webapp=galaxy&id=9a8774fee61dd122&page=1 HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET /library_admin/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%28Genome+Sequences%29%3A+__sq__NoneType__sq__+object+has+no+attribute+__sq__dataset__sq__. HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries"; "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30" Thanks in advance! And thanks for this priceless tool! Gus -- In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. *-Stephen Jay Gould* ___ 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/
Re: [galaxy-dev] Data Library Upload Issues
With the latest change set, non-admin users are not able to import files from file system paths. On Feb 15, 2011, at 5:35 AM, SHAUN WEBB wrote: > > Thanks Greg. > >>> 1. Non-admin users with add permissions on a library are offered the option >>> to upload from file systems path. Should this be restricted to admin users >>> only? >> > > Has this also been fixed in the latest change-set or do I have to manually > set an option to make this exclusive to admin users? I want to give users the > ability to add data to their libraries but I'm not willing to do that until > this option is removed. > > Shaun > Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Data Library Upload Issues
Thanks Greg. 1. Non-admin users with add permissions on a library are offered the option to upload from file systems path. Should this be restricted to admin users only? Yes, this should be restricted to admin users only as access to the file system for all users could result in undesired security problems or other issues. Has this also been fixed in the latest change-set or do I have to manually set an option to make this exclusive to admin users? I want to give users the ability to add data to their libraries but I'm not willing to do that until this option is removed. Shaun Quoting Greg Von Kuster : Hello Shaun, Thanks for your message. On Feb 11, 2011, at 6:54 AM, SHAUN WEBB wrote: Hi, I have notice a few problems which may or may not have been fixed in the latest distribution (I am yet to update) but wanted to make you aware. 1. Non-admin users with add permissions on a library are offered the option to upload from file systems path. Should this be restricted to admin users only? Yes, this should be restricted to admin users only as access to the file system for all users could result in undesired security problems or other issues. 2. If a user chooses the option "upload a directory of files" but does not have a folder with their username in the library upload directory they get a server error. Would be nicer to get a help message that says they are not set up for this method and to contact the Galaxy admin. This issue was corrected in change set 4999. 3. If files are being uploaded to a library and I click on the manage jobs tab in the admin section I get a server error. This persists until the server is restarted. I am not able to reproduce this behavior in the latest change set, which is 5053. This change set should be available in the distribution within a few weeks, or if you want to run the latest code you could pull directly from our development repo at: https://@bitbucket.org/galaxy/galaxy-central Keep in mind that the development repo is less stable than the distribution. Thanks for your help! Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Data Library Upload Issues
Hello Shaun, Thanks for your message. On Feb 11, 2011, at 6:54 AM, SHAUN WEBB wrote: > > Hi, I have notice a few problems which may or may not have been fixed in the > latest distribution (I am yet to update) but wanted to make you aware. > > 1. Non-admin users with add permissions on a library are offered the option > to upload from file systems path. Should this be restricted to admin users > only? Yes, this should be restricted to admin users only as access to the file system for all users could result in undesired security problems or other issues. > > 2. If a user chooses the option "upload a directory of files" but does not > have a folder with their username in the library upload directory they get a > server error. Would be nicer to get a help message that says they are not set > up for this method and to contact the Galaxy admin. This issue was corrected in change set 4999. > > 3. If files are being uploaded to a library and I click on the manage jobs > tab in the admin section I get a server error. This persists until the server > is restarted. I am not able to reproduce this behavior in the latest change set, which is 5053. This change set should be available in the distribution within a few weeks, or if you want to run the latest code you could pull directly from our development repo at: https://@bitbucket.org/galaxy/galaxy-central Keep in mind that the development repo is less stable than the distribution. > > > Thanks for your help! > > Shaun > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > ___ > galaxy-dev mailing list > galaxy-dev@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Data Library Upload Issues
Hi, I have notice a few problems which may or may not have been fixed in the latest distribution (I am yet to update) but wanted to make you aware. 1. Non-admin users with add permissions on a library are offered the option to upload from file systems path. Should this be restricted to admin users only? 2. If a user chooses the option "upload a directory of files" but does not have a folder with their username in the library upload directory they get a server error. Would be nicer to get a help message that says they are not set up for this method and to contact the Galaxy admin. 3. If files are being uploaded to a library and I click on the manage jobs tab in the admin section I get a server error. This persists until the server is restarted. Thanks for your help! Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] Data Library - upload files from filesystem paths
Hi Greg As an admin I have created a data library on our local instance of galaxy, created folders in that library and added datasets using 'upload files from filesystem paths' option, choosing not to copy the data into Galaxy, which then loads all the files in the given directory into the data library. Is there a way to refresh this list automatically? so that if a new file is added into that directory it will appear in the data library? or do I have to add new files in that directory manually, giving the path to the new file? You could write a script that polls the desired directory and uses Galaxy's API to upload new files. See / scripts/api/README for some information. The distribution includes a script in this same directory to upload library datasets ( library_upload_from_import_dir.py ). I have had a quick look at this script and I'm not sure this will do what we want. I see it says I should " browse to that user's preferences and generate a new API Key" - will it need to be done for each user? Any user that uses the API will need an API key. They'll need to go to User -> Preferences -> Manage your API keys to generate one if it is not set for them. The API key only needs to be set once. thanks, I will try this and see if this will do what we require and let you know. What we would like is to initially upload a directory path for each user, and then the user can refresh this "library list" (or it happen automatically say, every 10 secs) I notice that under the 'admin-manage data libraries' there is an 'Upload a new version of this dataset' option which replaces existing datasets - how easy would it be to create something similar for a directory? an "Upload a new version of this file system directory" and could the user be able to do that themselves? The best approach for doing this would be to upload each new directory "version" to a different folder or data library. When you upload a directory of files, whether copying files into the Galaxy files location or using file system paths, Galaxy creates pointers to those files, enabling the dataset objects associated with them to be versioned. Versions of local subdirectories cannot be done in Galaxy data libraries because the structure of the data library hierarchy is "data library / folder / datasets", and subdirectories themselves ( or information about them ) are not stored. I am also having a problem with creating sub folders - I choose to create sub folder from the drop down list and it reports that the sub folder has been created but I cant see it, and I cant click on the blue triangles to the left of the folders either. Does anyone else have this problem? Assuming you are adding sub-folders from the Shared Data -> Data Libraries view ( and not the Admin - Manage data libraries view ), this may be a result of permissions that have been placed on the library or parent folder in which you are adding sub-folders. The behavior you see could be a bug, but if so, I'll need some help tracking it down. Can you confirm from what view you are adding hte sub-folders, and what the permissions are on the parent folder and library? I was creating sub folders from the Admin - Manage data libraries view. I click on the arrow next the folder name, choose Add sub- folder, give it a name and get "The new folder named 'xxx' has been added to the data library." but I cant see it What browser are you using? Safari, chrome or firefox are recommended as IE tends to have many more behavioral problems like this. I was using Camino - I have just tried with Firefox and I can see all the sub folders now. Thanks for your help! Nicki ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] Data Library - upload files from filesystem paths
On Feb 1, 2011, at 12:04 PM, Nicki Gray wrote: > Hi Greg > thanks for your response, I have some questions about your reply. > > On 1 Feb 2011, at 16:14, Greg Von Kuster wrote: >> Hello Nicki, >> On Jan 28, 2011, at 1:13 PM, Nicki Gray wrote: >> >>> Hi >>> >>> As an admin I have created a data library on our local instance of galaxy, >>> created folders in that library and added datasets using >>> 'upload files from filesystem paths' option, choosing not to copy the data >>> into Galaxy, which then loads all the files in the given directory into the >>> data library. >>> >>> Is there a way to refresh this list automatically? so that if a new file is >>> added into that directory it will appear in the data library? >>> or do I have to add new files in that directory manually, giving the path >>> to the new file? >> >> You could write a script that polls the desired directory and uses Galaxy's >> API to upload new files. See /scripts/api/README for >> some information. The distribution includes a script in this same directory >> to upload library datasets ( library_upload_from_import_dir.py ). > > I have had a quick look at this script and I'm not sure this will do what we > want. I see it says I should " browse to that user's preferences and generate > a new API Key" - will it need to be done for each user? Any user that uses the API will need an API key. They'll need to go to User -> Preferences -> Manage your API keys to generate one if it is not set for them. The API key only needs to be set once. > > What we would like is to initially upload a directory path for each user, and > then the user can refresh this "library list" (or it happen automatically > say, every 10 secs) > > I notice that under the 'admin-manage data libraries' there is an 'Upload a > new version of this dataset' option which replaces existing datasets - how > easy would it be to create something similar for a directory? an "Upload a > new version of this file system directory" and could the user be able to do > that themselves? The best approach for doing this would be to upload each new directory "version" to a different folder or data library. When you upload a directory of files, whether copying files into the Galaxy files location or using file system paths, Galaxy creates pointers to those files, enabling the dataset objects associated with them to be versioned. Versions of local subdirectories cannot be done in Galaxy data libraries because the structure of the data library hierarchy is "data library / folder / datasets", and subdirectories themselves ( or information about them ) are not stored. > >>> I am also having a problem with creating sub folders - I choose to create >>> sub folder from the drop down list and it reports that the sub folder has >>> been created but I cant see it, and I cant click on the blue triangles to >>> the left of the folders either. Does anyone else have this problem? >> >> Assuming you are adding sub-folders from the Shared Data -> Data Libraries >> view ( and not the Admin - Manage data libraries view ), this may be a >> result of permissions that have been placed on the library or parent folder >> in which you are adding sub-folders. The behavior you see could be a bug, >> but if so, I'll need some help tracking it down. Can you confirm from what >> view you are adding hte sub-folders, and what the permissions are on the >> parent folder and library? > > I was creating sub folders from the Admin - Manage data libraries view. I > click on the arrow next the folder name, choose Add sub-folder, give it a > name and get > "The new folder named 'xxx' has been added to the data library." > but I cant see it What browser are you using? Safari, chrome or firefox are recommended as IE tends to have many more behavioral problems like this. > > Thanks for your help, > Nicki > > >> >> Thanks! >> >> Greg Von Kuster >> >>> >>> Any help would be appreciated, >>> Thanks, Nicki >>> >>> - >>> Nicki Gray >>> MRC Molecular Haematology Unit >>> 01865 222434 >>> >>> ___ >>> galaxy-dev mailing list >>> galaxy-dev@lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> Greg Von Kuster >> Galaxy Development Team >> g...@bx.psu.edu >> >> >> > > ___ > galaxy-dev mailing list > galaxy-dev@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] Data Library - upload files from filesystem paths
Hi Greg thanks for your response, I have some questions about your reply. On 1 Feb 2011, at 16:14, Greg Von Kuster wrote: Hello Nicki, On Jan 28, 2011, at 1:13 PM, Nicki Gray wrote: Hi As an admin I have created a data library on our local instance of galaxy, created folders in that library and added datasets using 'upload files from filesystem paths' option, choosing not to copy the data into Galaxy, which then loads all the files in the given directory into the data library. Is there a way to refresh this list automatically? so that if a new file is added into that directory it will appear in the data library? or do I have to add new files in that directory manually, giving the path to the new file? You could write a script that polls the desired directory and uses Galaxy's API to upload new files. See /scripts/ api/README for some information. The distribution includes a script in this same directory to upload library datasets ( library_upload_from_import_dir.py ). I have had a quick look at this script and I'm not sure this will do what we want. I see it says I should " browse to that user's preferences and generate a new API Key" - will it need to be done for each user? What we would like is to initially upload a directory path for each user, and then the user can refresh this "library list" (or it happen automatically say, every 10 secs) I notice that under the 'admin-manage data libraries' there is an 'Upload a new version of this dataset' option which replaces existing datasets - how easy would it be to create something similar for a directory? an "Upload a new version of this file system directory" and could the user be able to do that themselves? I am also having a problem with creating sub folders - I choose to create sub folder from the drop down list and it reports that the sub folder has been created but I cant see it, and I cant click on the blue triangles to the left of the folders either. Does anyone else have this problem? Assuming you are adding sub-folders from the Shared Data -> Data Libraries view ( and not the Admin - Manage data libraries view ), this may be a result of permissions that have been placed on the library or parent folder in which you are adding sub-folders. The behavior you see could be a bug, but if so, I'll need some help tracking it down. Can you confirm from what view you are adding hte sub-folders, and what the permissions are on the parent folder and library? I was creating sub folders from the Admin - Manage data libraries view. I click on the arrow next the folder name, choose Add sub- folder, give it a name and get "The new folder named 'xxx' has been added to the data library." but I cant see it Thanks for your help, Nicki Thanks! Greg Von Kuster Any help would be appreciated, Thanks, Nicki - Nicki Gray MRC Molecular Haematology Unit 01865 222434 ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Re: [galaxy-dev] Data Library - upload files from filesystem paths
Hello Nicki, On Jan 28, 2011, at 1:13 PM, Nicki Gray wrote: > Hi > > As an admin I have created a data library on our local instance of galaxy, > created folders in that library and added datasets using > 'upload files from filesystem paths' option, choosing not to copy the data > into Galaxy, which then loads all the files in the given directory into the > data library. > > Is there a way to refresh this list automatically? so that if a new file is > added into that directory it will appear in the data library? > or do I have to add new files in that directory manually, giving the path to > the new file? You could write a script that polls the desired directory and uses Galaxy's API to upload new files. See /scripts/api/README for some information. The distribution includes a script in this same directory to upload library datasets ( library_upload_from_import_dir.py ). > > I am also having a problem with creating sub folders - I choose to create sub > folder from the drop down list and it reports that the sub folder has been > created but I cant see it, and I cant click on the blue triangles to the left > of the folders either. Does anyone else have this problem? Assuming you are adding sub-folders from the Shared Data -> Data Libraries view ( and not the Admin - Manage data libraries view ), this may be a result of permissions that have been placed on the library or parent folder in which you are adding sub-folders. The behavior you see could be a bug, but if so, I'll need some help tracking it down. Can you confirm from what view you are adding hte sub-folders, and what the permissions are on the parent folder and library? Thanks! Greg Von Kuster > > Any help would be appreciated, > Thanks, Nicki > > - > Nicki Gray > MRC Molecular Haematology Unit > 01865 222434 > > ___ > galaxy-dev mailing list > galaxy-dev@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
[galaxy-dev] Data Library - upload files from filesystem paths
Hi As an admin I have created a data library on our local instance of galaxy, created folders in that library and added datasets using 'upload files from filesystem paths' option, choosing not to copy the data into Galaxy, which then loads all the files in the given directory into the data library. Is there a way to refresh this list automatically? so that if a new file is added into that directory it will appear in the data library? or do I have to add new files in that directory manually, giving the path to the new file? I am also having a problem with creating sub folders - I choose to create sub folder from the drop down list and it reports that the sub folder has been created but I cant see it, and I cant click on the blue triangles to the left of the folders either. Does anyone else have this problem? Any help would be appreciated, Thanks, Nicki - Nicki Gray MRC Molecular Haematology Unit 01865 222434 ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
