Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)
I updated our wiki with this new build information. https://wiki.galaxyproject.org/Develop/JSA M. On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler aysam.guer...@gmail.com wrote: Hi Christophe, In order to apply the changes scripts have to be packed properly. Please follow these steps: 1. Go to the client/ directory and type 'npm install' 2. Now type 'grunt watch'. This will start a listener which captures code changes and repacks scripts automatically 3. Finally, make your changes to the code files in client/galaxy/scripts/mvc/upload and reload your browser Let me know if that works for you or if you have any other questions. Thanks, Sam On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Hi, As we have arranged an sftp upload system through ftp port for our Galaxy instance, we would need to customize the Upload File tool form, so that a few more line explain how-to-do in the FTP section of the form, in addition to the This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy credentials (email address and password). I dug into /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js and /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js but the changes I tried into these files do not show up in the tool form. If someone can indicate the right way to intercept this content and enrich it as mentioned above, I would be grateful ! Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.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/ 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/ ___ 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/
Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)
corrrect: /client is a directory within Galaxy root - it contains all the javascripts The build (grunt) process takes the /client directory and copies the scripts to /static/scripts directory within Galaxy root (and packs them and stuff) from where the files are served to the browser. If you want to make JS changes, make them in /client and propagate it via grunt. Make sure you have up to date version of Galaxy since the grunt building was added fairly recently. note: /scripts directory within Galaxy root has a different purpose, those are python scripts (API and stuff) M. On Wed, Nov 12, 2014 at 1:16 PM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Aysam and Martin, Thanks for your help. I am not familiar with JS development. To make client crystal clear : /client stands for the home directory where Galaxy-dist is installed ? and client/galaxy/scripts/mvc/upload stands for ~/galaxy-dist/scripts/mvc/upload (assuming that the galaxy code is installed in galaxy-dis) ? right ? Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.org 2014-11-12 16:42 GMT+01:00 Martin Čech mar...@bx.psu.edu: I updated our wiki with this new build information. https://wiki.galaxyproject.org/Develop/JSA M. On Wed, Nov 12, 2014 at 10:11 AM, Aysam Guerler aysam.guer...@gmail.com wrote: Hi Christophe, In order to apply the changes scripts have to be packed properly. Please follow these steps: 1. Go to the client/ directory and type 'npm install' 2. Now type 'grunt watch'. This will start a listener which captures code changes and repacks scripts automatically 3. Finally, make your changes to the code files in client/galaxy/scripts/mvc/upload and reload your browser Let me know if that works for you or if you have any other questions. Thanks, Sam On Wed, Nov 12, 2014 at 4:47 AM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Hi, As we have arranged an sftp upload system through ftp port for our Galaxy instance, we would need to customize the Upload File tool form, so that a few more line explain how-to-do in the FTP section of the form, in addition to the This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at 127.0.0.1 using your Galaxy credentials (email address and password). I dug into /home/galaxy/galaxy-dist/static/scripts/mvc/upload/upload-ftp.js and /home/galaxy/galaxy-dist/static/scripts/packed/mvc/upload/upload-ftp.js but the changes I tried into these files do not show up in the tool form. If someone can indicate the right way to intercept this content and enrich it as mentioned above, I would be grateful ! Cheers Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniew...@upmc.fr http://drosophile.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/ 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/ ___ 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/
Re: [galaxy-dev] Tool Shed Categories
The category Combinatorial Selections has been created on both Test and Main ToolShed. Thank you for your tool contributions Khalid. Martin On Mon, Oct 6, 2014 at 1:02 PM, Nicola Soranzo sora...@crs4.it wrote: Hi Khalid, I'd suggest you to open a Trello card for this: http://galaxyproject.org/trello/ Best, Nicola Il giorno ven, 03/10/2014 alle 17.30 +, Alam, Khalid K. (MU-Student) ha scritto: Hi; I’m getting ready to submit several (5) tools for processing data related to combinatorial selection technologies (aptamer and (deoxy)ribozyme selections, phage display, etc.) and would like to propose a new category for the Tool Shed entitled “Combinatorial Selections” where these repositories can be published. Khalid Kamal Alam University of Missouri Department of Biochemistry 415 Life Sciences Center 1201 Rollins St. Columbia, MO 65211 mailto:khalidka...@mail.missouri.eduKhalidKAlammailto: khalidka...@mail.missouri.edu@mail.missouri.edumailto: kka...@mail.missouri.edu @BiochemPhD ___ 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/ ___ 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/
Re: [galaxy-dev] no universe_wsgi.ini can't install tools from the standard toolshed because: Initializing repository installation failed
Hi Chris, (1) Galaxy configuration has been moved to /config/galaxy.ini ( https://bitbucket.org/galaxy/galaxy-dist/src/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/config/ ) (2) There might have been some changes to the conf syntax regarding the dependency directory etc. since the version of universe.wsgi.ini that you are using. So please make sure you are using the current galaxy.ini file and try installing a tool again. If it does not go well please include the log of errors. Let us know how it goes. Thanks Martin On Tue, Oct 7, 2014 at 3:50 PM, Chris Dagdigian d...@sonsorol.org wrote: Hi folks, Got a strange problem - it's hit me on all my self-install options today including using the Chef cookbook as well as the galaxy mecurial install method on Ubuntu 12.04 LTS I'm trying to build a local galaxy that supports a few common extra tools (things like samtools etc.) I can boot a fresh Ubuntu 12.04 LTS and follow the instructions at getgalaxy.org: hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hg update stable sh ./run.sh There are two strange things that don't quite match what I'm expecting to see from the docs ... (1) The file universe_wsgi.ini no longer gets created in galaxy-dist/ after running run.sh for the first time. This is strange because I remember it working days ago but now on fresh server and fresh checkout the file does not get created and I have to manually create one in oder to set host = 0.0.0.0 (2) I can't even install simple tools like samtools from the standard tool sheds. The status page gets stuck at installing dependencies and if I navigate away I get a browser javascript error (Initializing repository installation failed Any tips or tricks appreciated, thanks! Regards, Chris ___ 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/
Re: [galaxy-dev] Internal Server Error on metadata reset
Seems like missing import: from galaxy.model.orm import or_ I will check on it tomorrow as a whole. Thanks for reporting this. M. On Tue, Oct 7, 2014 at 7:03 PM, Saket Choudhary sake...@gmail.com wrote: I am trying to reset metadata on all my repositories at once using the Reset metadata on my repositories button on https://testtoolshed.g2.bx.psu.edu/ It fails with: Internal Server Error Galaxy was unable to successfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/repository/reset_metadata_on_my_writable_repositories_in_tool_shed Module galaxy.web.framework.middleware.error:149 in __call__ app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ environ, self.app) Module paste.wsgilib:543 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:2795 inreset_metadata_on_my_writable_repositories_in_tool_shed my_writable=True ) Module tool_shed.metadata.repository_metadata_manager:65 in build_repository_ids_select_field query = self.get_query_for_setting_metadata_on_repositories( my_writable=my_writable,order=True ) Module tool_shed.metadata.repository_metadata_manager:513 in get_query_for_setting_metadata_on_repositories .filter( or_( *clause_list ) ) NameError: global name 'or_' is not defined extra data ___ 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/
Re: [galaxy-dev] Main tool shed installation issues
somehow a space (escaped) got into your id this is the correct url: https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b5459666changeset_revisions=a54de7e658f7 I will look around why it got there. On Tue, Sep 16, 2014 at 4:41 PM, Yves Gagnon yves.gag...@dnalandmarks.ca wrote: Hello fellow Galaxy-Dev users, We are having an issue trying to install tools from the main tool shed. Trying to install bowtie2 (or any other tool for that matter) gives us the following error message : *Error Traceback:* ⇝ URLError: urlopen error [Errno -2] Name or service not known Looking further in the error traceback, the url not found in question is this one (in the case of bowtie2): https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b54596%2066changeset_revisions=a54de7e658f7 Indeed, copy pasting this URL into a browser gives me the Internal server error page. Anyone knows if this is a widespread issue? Thanks for your feedback! Yves ___ 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/
Re: [galaxy-dev] Main tool shed installation issues
I tried installing this exact repo and changeset on the latest -central galaxy code and encountered no problems. What version of Galaxy are you using. Did you modify it? Martin On Tue, Sep 16, 2014 at 4:44 PM, Martin Čech mar...@bx.psu.edu wrote: somehow a space (escaped) got into your id this is the correct url: https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b5459666changeset_revisions=a54de7e658f7 I will look around why it got there. On Tue, Sep 16, 2014 at 4:41 PM, Yves Gagnon yves.gag...@dnalandmarks.ca wrote: Hello fellow Galaxy-Dev users, We are having an issue trying to install tools from the main tool shed. Trying to install bowtie2 (or any other tool for that matter) gives us the following error message : *Error Traceback:* ⇝ URLError: urlopen error [Errno -2] Name or service not known Looking further in the error traceback, the url not found in question is this one (in the case of bowtie2): https://toolshed.g2.bx.psu.edu/repository/get_repository_information?repository_ids=126c0918b54596%2066changeset_revisions=a54de7e658f7 Indeed, copy pasting this URL into a browser gives me the Internal server error page. Anyone knows if this is a widespread issue? Thanks for your feedback! Yves ___ 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/
Re: [galaxy-dev] Serious start-up delay in next-stable
I just freshly cloned galaxy-central, switched to next-stable and did initial startup - no problems detected and Galaxy booted in under 2m. On Tue, Aug 5, 2014 at 2:54 PM, Langhorst, Brad langho...@neb.com wrote: I’ve noticed that startup is very slow. It’s about 15 minutes for me to stop and restart my 4 daemons. It was much faster with galaxy on local storage. brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 5, 2014, at 2:41 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi all, does anyone encountered a long start-up delay with the recent next-stable and starting a instance from scratch? For me its hanging at: tool_shed.galaxy_install.migrate.check DEBUG 2014-08-05 18:39:45,207 psycopg2 egg successfully loaded for postgres dialect for 3-5 minutes. Cheers, Bjoern ___ 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/ ___ 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/
Re: [galaxy-dev] Local deployments of galaxy
There is a list of the ones that reached back to us and are publicly accessible (~60): https://wiki.galaxyproject.org/PublicGalaxyServers As of private ones there is no good clue as Galaxy does not call home. M. On Thu, Jul 24, 2014 at 12:55 PM, Lapointe, David david.lapoi...@tufts.edu wrote: Not exactly a dev question, but I was asked recently how many sites are running galaxy. The wiki page listing deployments seems not to reflect the actual number, since may are most likely private. Is there an estimate? -- David Lapointe Ph.D. Sr. Bioinformatics Specialist Research and Geospatial Technology Services Tufts Technology Services (TTS) 16 Dearborn Road Somerville MA 02144 Phone: 617-627-5319 Fax: 617-627-3667 http://it.tufts.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/ 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/
Re: [galaxy-dev] getting API key from user/pass
file *api/authenticate.py* class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): @web.expose_api_anonymous def get_api_key( self, trans, **kwd ): def get_api_key( self, trans, **kwd ) * *GET /api/authenticate/baseauth* returns an API key for authenticated user based on BaseAuth headers :returns: api_key in json format :rtype: dict :raises: ObjectNotFound, HTTPBadRequest On Mon, Jul 21, 2014 at 10:06 AM, Eric Rasche rasche.e...@yandex.ru wrote: John, I'm looking to use blend4j, and I was wondering if there was a way to obtain the user's API key from a username/password pair? Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Texas AM Univesity College Station, TX 77843 Ph: 4046922048 http://tel:4046922048 ___ 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/
Re: [galaxy-dev] getting API key from user/pass
Done. On Mon, Jul 21, 2014 at 10:30 AM, Eric Rasche rasche.e...@yandex.ru wrote: Martin, Ah, good to have the API call needed. Could this possibly be added to the wiki, perhaps on Learn/API https://wiki.galaxyproject.org/Learn/API? That particular URL doesn't seem to be in blend4j so this answers that question as well, thanks! Cheers, Eric 21.07.2014, 15:13, Martin Čech mar...@bx.psu.edu: file api/authenticate.py class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): @web.expose_api_anonymous def get_api_key( self, trans, **kwd ): def get_api_key( self, trans, **kwd ) * GET /api/authenticate/baseauth returns an API key for authenticated user based on BaseAuth headers :returns: api_key in json format :rtype: dict :raises: ObjectNotFound, HTTPBadRequest On Mon, Jul 21, 2014 at 10:06 AM, Eric Rasche rasche.e...@yandex.ru wrote: John, I'm looking to use blend4j, and I was wondering if there was a way to obtain the user's API key from a username/password pair? Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Texas AM Univesity College Station, TX 77843 Ph: 4046922048 ___ 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/ -- Eric Rasche Programmer II Center for Phage Technology Texas AM Univesity College Station, TX 77843 Ph: 4046922048 ___ 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/
Re: [galaxy-dev] RE : Error with get data function
Hi Noémie, the special characters are probably in the file path, so some of your folders, or your file name or your computer user name may contain these and when our server gets that path he does not like it and throws an error. Like I said, it is a problem on our side but you can get around it by checking these. Martin On Tue, Apr 29, 2014 at 4:08 AM, DELRIEU Noemie noemie.delr...@gustaveroussy.fr wrote: Hello Martin, Thanks for your answer ! I have tried cleaning the browser cache and I have used another browser, but the problem persists... In fact, I clicked on get data and I chose one file in my computer to download. I didn't use the character é in my e mail adress but I take into account your advice ! Best regards, Noémie -- *De :* emulato...@gmail.com [emulato...@gmail.com] de la part de Martin Čech [mar...@bx.psu.edu] *Date d'envoi :* lundi 28 avril 2014 22:18 *À :* DELRIEU Noemie *Cc:* galaxy-dev@lists.bx.psu.edu *Objet :* Re: [galaxy-dev] Error with get data function Hello Noémie Delrieu, can you please describe the process in which the error happens? Do you only click on 'get data' or do you also select from the sublist? Also try cleaning the browser cache or using Galaxy with other browser to check on the issue. thanks Martin Galaxy Team On Sun, Apr 27, 2014 at 1:18 PM, DELRIEU Noemie noemie.delr...@gustaveroussy.fr wrote: Hello, I contact you because I need some help with my galaxy account. I can't use functionget data for 3 days. This number error appears : *GURU MEDITATION: #18e5fee395824913a0f27ff2063a0ead* The adress mail noemie.delr...@gustaveroussy.fr is used for log in on server. Thank you. Best regards *, * Noémie Delrieu ___ 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/
Re: [galaxy-dev] user account
Hi Jun, you can change any user's email through admin interface of Galaxy, no need for SQL. You may break consistency when using SQL for changing users, which might have happened to you. best Martin On Fri, Apr 25, 2014 at 7:49 PM, Jun Fan j@qmul.ac.uk wrote: Hi Martin, Thanks for the tip of changing email and username under SQL. I managed that (update galaxy_user set email=’h...@haha.com’, username=’haha’ where id = NNN) and tried to re-register with the same email. Then I got some error saying “Internal Server Error *Galaxy was unable to successfully complete your request* An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. *The error has been logged to our team.* “ Also the link in the verification email does not do the job. Anyway, I used the SQL again to bypass this issue (active=’t’, activation_token=’’) Problem solved. Many thanks for your help. Best regards! Jun *From:* emulato...@gmail.com [mailto:emulato...@gmail.com] *On Behalf Of *Martin Cech *Sent:* Friday, April 25, 2014 5:05 PM *To:* Jun Fan *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] user account Hi Jun, Galaxy does not really delete users. If you are trying to clear the user, just change its email as an admin and register the user again with the same address as before. Martin On Thu, Apr 24, 2014 at 8:56 PM, Jun Fan j@qmul.ac.uk wrote: Hi Martin, Thanks for the hint. After setting track_jobs_in_database to True, the status of the new upload is waiting to run, which should be the behavior expected. Luckily when I modified the setting in universal_wsgi.ini, I noticed that there is an option allow_user_deletion = True which enables the user deletion in UI. The problem is that even I deleted and purged one email, I still can re-register with that email. What is the solution to this? Direct SQL operation? Best regards! Jun *From:* emulato...@gmail.com [mailto:emulato...@gmail.com] *On Behalf Of *Martin Cech *Sent:* Thursday, April 24, 2014 9:50 PM *To:* Jun Fan *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] user account Hi Jun, the account activation is meant for multi-processor environments and these have to have the following option turned on in the configuration: track_jobs_in_database = True Please try to change it. thank you Martin On Thu, Apr 24, 2014 at 4:27 PM, Jun Fan j@qmul.ac.uk wrote: Hi Martin I am using Postgresql. Best regards! Jun *From:* emulato...@gmail.com [mailto:emulato...@gmail.com] *On Behalf Of *Martin Cech *Sent:* Thursday, April 24, 2014 5:21 PM *To:* Jun Fan *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] user account Hi Jun, what kind of database are you using? This feature might not be supported for SQLite (as no production Galaxy should run on it :)) best Martin Galaxy Team On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.uk wrote: Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for “operations.append” and “item.deleted” and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make “delete user” function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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
Re: [galaxy-dev] user account
Hi Jun, Galaxy does not really delete users. If you are trying to clear the user, just change its email as an admin and register the user again with the same address as before. Martin On Thu, Apr 24, 2014 at 8:56 PM, Jun Fan j@qmul.ac.uk wrote: Hi Martin, Thanks for the hint. After setting track_jobs_in_database to True, the status of the new upload is waiting to run, which should be the behavior expected. Luckily when I modified the setting in universal_wsgi.ini, I noticed that there is an option allow_user_deletion = True which enables the user deletion in UI. The problem is that even I deleted and purged one email, I still can re-register with that email. What is the solution to this? Direct SQL operation? Best regards! Jun *From:* emulato...@gmail.com [mailto:emulato...@gmail.com] *On Behalf Of *Martin Cech *Sent:* Thursday, April 24, 2014 9:50 PM *To:* Jun Fan *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] user account Hi Jun, the account activation is meant for multi-processor environments and these have to have the following option turned on in the configuration: track_jobs_in_database = True Please try to change it. thank you Martin On Thu, Apr 24, 2014 at 4:27 PM, Jun Fan j@qmul.ac.uk wrote: Hi Martin I am using Postgresql. Best regards! Jun *From:* emulato...@gmail.com [mailto:emulato...@gmail.com] *On Behalf Of *Martin Cech *Sent:* Thursday, April 24, 2014 5:21 PM *To:* Jun Fan *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] user account Hi Jun, what kind of database are you using? This feature might not be supported for SQLite (as no production Galaxy should run on it :)) best Martin Galaxy Team On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.uk wrote: Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for “operations.append” and “item.deleted” and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make “delete user” function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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/
Re: [galaxy-dev] Help Galaxy
Hi Moussa,
as Enis suggests please read the documentation and/or just call the API on
your local instance and see what it returns.
e.g. calling {{localhost}}/api/workflows?key={{API_key}} on my local
instance results in
https://gist.github.com/martenson/6b8e1d402fa193c914a5
Nice tool for calling API from browser is Postman http://www.getpostman.com/
M.
On Thu, Apr 24, 2014 at 10:49 AM, Enis Afgan afg...@gmail.com wrote:
Hello,
Galaxy workflow and history structure is stored in Galaxy's database vs.
flat files so you can't just find the representation of those on the file
system.
I actually don't know if there is any documentation about the JSON
structure for those artifacts - I've CC'd the -dev mailing list so someone
there might know (btw, emailing the -dev list is preferred with questions
like these because your question get more exposure). In the mean time, you
can explore the API documentation (available
herehttp://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.workflowsand
herehttps://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController)
because that's where JSON objects can be retrieved.
Hope this helps,
Enis
On Thu, Apr 24, 2014 at 3:33 PM, yattara Moussa
moussayatta...@yahoo.frwrote:
Hello,
I'm working at South Paris University (Université Paris-Sud) Computer
Science Research Laboratory (LRI), France.
I'm working on Galaxy.
I need to know about Galaxy syntax for worklfow internal structure
description with JSON, and Galaxy workflow history.
*if you have any technical document describing the JSON syntax used for
the storage of Galaxy workflow and Galaxy history, it will be very nice if
you can send it to me.
*I installed Galaxy on ubuntu, In which directory can I find workflow
histories files ?.
Thank you for your considération, I look forward to hearing from you.
Moussa YATTARA.
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Re: [galaxy-dev] user account
Hi Jun, what kind of database are you using? This feature might not be supported for SQLite (as no production Galaxy should run on it :)) best Martin Galaxy Team On Thu, Apr 24, 2014 at 11:42 AM, Jun Fan j@qmul.ac.uk wrote: Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for “operations.append” and “item.deleted” and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make “delete user” function available in the UI as Nate suggested. Any guidance? Best regards! Jun ___ 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/
Re: [galaxy-dev] User usage stats in local instance
Hi, the place to start is the Reports app that comes with Galaxy, please see the details here: https://wiki.galaxyproject.org/Admin/UsageReports Martin Galaxy Team On Thu, Apr 17, 2014 at 5:06 PM, Alejandro Barrera abarr...@biociphers.orgwrote: Hi, Apologizes if this is not the right place to ask this sort of questions, but I have been asked to report user usage in our lab’s instance of galaxy. In order to crunch the numbers by user (number of logins per month, number of jobs, memory usage, etc.), I thought that in principle, I could ask that info directly to the database (in our case, a MySQL instance). However, given the complex database schema, it looks like this is not the way to do it (at least, not the easy one...). Does anyone have experience retrieving this information? Many thanks in advance, Alex -- *Alejandro Barrera* Bioinformatics Developer University of Pennsylvania www.biociphers.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/ 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/
Re: [galaxy-dev] Download workflow from main Galaxy
Hello Xiaofei, it seems you don't have username set in usegalaxy.org and thus the links generated are wrong. Can you please set one (user/preferences/manage information) and try again? thanks Martin Galaxy team On Fri, Apr 4, 2014 at 12:07 PM, Wang, Xiaofei xfw...@ku.edu wrote: Dear there, I tried to download workflow and import it into another my local Galaxy instance. But, when I downloaded and exported it from main Galaxy by Download to File, it showed as below. Not Found The resource could not be found. No route for /u/w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json-download Then, I tried URL for Importing to Another Galaxy Use this URL to import the workflow directly into another Galaxy server: https://usegalaxy.org/u//w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json (Copy this URL into the box titled 'Workflow URL' in the Import Workflow page.) , it showed Failed to open URL: *https://usegalaxy.org/u//w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json https://usegalaxy.org/u//w/imported-cloudmap-ems-variant-density-mapping-workflow-takes-vcf-of-heterozygous-and-homozygous-variants-to-subtract/json* Exception: HTTP Error 404: Not Found What is the reason for this? Many thanks for helping me! Best, Xiaofei ___ 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/
Re: [galaxy-dev] [galaxy-bugs] Galaxy modules deployment
Hello, it is great you want to share tools with others through Galaxy, thank you! We call added software a 'Galaxy tool'. You can start by reading the tool basics in this page: https://wiki.galaxyproject.org/Admin/Tools and then you can browse through wiki where the vast of information about tool creation is available through tutorials. What you want is to 'wrap' your software for use within Galaxy with an XML file (sometimes called 'tool definition file' or 'wrapper') that will define the interactions of Galaxy and your software and the user interface of the tool page in Galaxy. You develop the tool first on your local Galaxy and then after it is working there you can submit your tool to the Tool Shed (Galaxy's appstore - https://wiki.galaxyproject.org/ToolShed). After your tool is in the Tool Shed it can be installed by any Galaxy worldwide. If you have any questions just ask in the dev-list mailing list (CCed in this conversation). Martin, Galaxy team On Thu, Apr 3, 2014 at 12:36 AM, ut...@bioinfo.sastra.edu wrote: Dear Sir/Mam, As a part of our project work, we have developed some Bioinformatics modules such as finding interactions for protein, displaying the contacts. We are interested in deploying our modules in your Galaxy platform. Is that possible? If so, what is the procedure? Can you guide us? Regards, M. Udayakumar, Dept. of Bioinformatics, SASTRA University, Thanjavur,Tamil Nadu, INDIA. ___ 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
Hi Huayan, these tools should mostly be available from the Tool Shed (Galaxy's appstore). You can install them easily into any Galaxy that you are an admin of. Please see more information here: https://wiki.galaxyproject.org/Admin/Tools Martin, galaxy team On Thu, Mar 20, 2014 at 1:57 AM, Huayan Gao huayan...@gmail.com wrote: Hi Martin, Actually I want a NGS Toolbox Beta tool panel exactly like the usegalaxy.org. How can I achieve this? I found myself looking for the tools and put them to tool_conf.xml which is very tedious. Is there a better way to do it? Best, Huayan On Thu, Mar 20, 2014 at 11:43 AM, Huayan Gao huayan...@gmail.com wrote: Thanks Martin! One more question, I want to install all the migrated tools from stage 9, that is NGS tools to my local galaxy. I tried but always got some problems. Do you have the instructions on wiki too? Thanks, Huayan On Thu, Mar 20, 2014 at 10:27 AM, Martin Čech mar...@bx.psu.edu wrote: Hello again Huayan, the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :) thank you for using Galaxy! Martin On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.comwrote: Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan ___ 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/
Re: [galaxy-dev] adding E.coli K-12 genome for mapping
Hi, I added your request to the card where we track these: https://trello.com/c/mJWnAuuQ/1511-to-request-reference-genome-comment-on-this-card Martin Galaxy team On Wed, Mar 26, 2014 at 3:17 PM, t...@caltech.edu wrote: Hi Guys, is it possible to add E.coli K12 genome for mapping with Bowtie on Andromeda-NCBI portal? thanks, timur ___ 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/
Re: [galaxy-dev] create local galaxy in mac os
Hi, for installing tools into Galaxy please see the full guide: https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy for adding custom tools please see: https://wiki.galaxyproject.org/Admin/Tools and https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial Martin On Tue, Mar 25, 2014 at 9:51 AM, Chunjiang He camel...@gmail.com wrote: I am adding tools to local galaxy and encountered some problems. when I install samtools from Tool Shed, it stays on installing dependent tools for long time. I am not sure where is the problem. Anyone can help. Or I would like to create XML myself for downloaded packages. How to do that? Thanks, Cam ___ 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com wrote: Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan ___ 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/
Re: [galaxy-dev] Bowtie2 and tophat2 data library set up
Hello again Huayan, the page got renamed and redirect was not in place. I have put it there and the new page has even more info on it! :) thank you for using Galaxy! Martin On Wed, Mar 19, 2014 at 10:18 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Huayan, I don't know why the wiki page disappeared and I will investigate it. In the meantime I have found a cached copy for you: http://webcache.googleusercontent.com/search?q=cache:SWWpt6XsmCkJ:https://wiki.galaxyproject.org/Admin/NGS%2520Local%2520Setup+cd=1hl=enct=clnkgl=us Martin, Galaxy team On Wed, Mar 19, 2014 at 9:44 PM, Huayan Gao huayan...@gmail.com wrote: Hi, I wanted to use bowtie2 and tophat2 locally. I remembered you have instructions about how to set up the library here, but it is not accessible any more. https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Can you direct me to the right page or send me the documents please? Thanks, Huayan ___ 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/
Re: [galaxy-dev] ToolSheds
Hi, Tool Shed was down today morning due to hardware relocation. It is up since cca 3pm (EST) today. For up to date info about Galaxy including the downtimes (both planned unplanned) please follow us on twitter. https://twitter.com/galaxyproject thanks for using Galaxy! Martin On Mon, Mar 17, 2014 at 12:46 PM, César Acevedo cesar.acev...@aomail.uab.cat wrote: Hi everyone, I am just wondering if there is some problems with: http://testtoolshed.g2.bx.psu.edu/ ? Getting operation time out from my galaxy stand-alone admin view when i try to search and browse tools, no response to ping neither. Thanks! CA ___ 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/
Re: [galaxy-dev] 回复： Re: Local Galaxy web layout
Hello Shenwiyn, the position of the menu items is defined by the order of these items in the galaxy.menu.js file. What do you mean by changing the galaxy interface? Martin On Mon, Mar 10, 2014 at 8:27 AM, Weiyan Shen shenw...@gmail.com wrote: Hi Sam, Using static/scripts/galaxy.menu.js,I can add/remove/change labels of my local Galaxy successfully,but I don't know how to change the positions ,as well as the Galaxy interface.So are there any details or guidances for this help?Thank youvery much. Regards, Shenwiyn -- 原始邮件 -- *发件人:* sam guerler;aysam.guer...@gmail.com; *发送时间:* 2014年2月19日(星期三) 晚上11:06 *收件人:* shenw...@gmail.comshenw...@gmail.com; *抄送:* hrhh...@fmi.ch; galaxy-devgalaxy-dev@lists.bx.psu.edu; *主题:* Re: Re: [galaxy-dev] Local Galaxy web layout Hi Shenwiyn, Can you specify what is not working? Did you find the file? Thanks, Sam On Wed, Feb 19, 2014 at 1:42 AM, shenw...@gmail.com shenw...@gmail.comwrote: Hi Sam and Hans-Rudolf， Thank you very much for your help.It seems that the static/scripts/galaxy.menu.js fail to work in my local Galaxy.As a result,would you please show me some more details about this? Regards, Shenwiyn *From:* sam guerler aysam.guer...@gmail.com *Date:* 2014-02-18 01:20 *To:* Hans-Rudolf Hotz h...@fmi.ch *CC:* shenw...@gmail.com; galaxy-dev galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Local Galaxy web layout Hi Shenwiyn, This has changed recently. Please take a look at: static/scripts/galaxy.menu.js Using that file, you can add/remove/change labels and their position. It is recommended to run pack_scripts.py after changing the source file. Regards, Sam On Mon, Feb 17, 2014 at 11:33 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Shenwiyn Have a look at: ~/galaxy_dist/database/compiled_templates/base_panels.mako.py Regards, Hans-Rudolf On 02/17/2014 08:04 AM, shenw...@gmail.com wrote: Galaxy developers: I want to change my local Galaxy web layout,for example,delete the top button of Visualization and Cloud or change their positions.Could anyone show me some details about this? Thank you very much. shenw...@gmail.com ___ 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/ ___ 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/
Re: [galaxy-dev] upload error
Awesome. How is the upload behaving? Are you still having issues with it? M. On Sat, Mar 8, 2014 at 12:20 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi John, Thanks for the note. Please see inline. On Fri, Mar 7, 2014 at 7:18 PM, John Chilton jmchil...@gmail.com wrote: Hmm... I am not certain but it sounds like the migration script ripped something out of your Galaxy tool panel that you did not want it to? This is unfortunate - but I don't think it would happen again now that the migration process is complete. Some future update to Galaxy may include additional migrations scripts but now that macs is out it won't ever be migrated again. imagine you can just update your tool_conf.xml file to point to your existing macs wrapper you set up manually and you can either leave the devteam version of macs in place or uninstall it if you prefer your own. Is it not this easy? Yes that's what I thought, but I was worrying that if I remove devteam version of macs from the migrated_tool.conf, I might break something potentially useful for galaxy. Mainly, I try not to manually change things since that would not be maintainable over time. That's why I was asking how to handle this properly. It's great to have your confirmation that it works this way. :-) Thanks, Rui ___ 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/
Re: [galaxy-dev] Galaxy reports
Hello Philip, the page you are talking about should look like this: https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png How does yours look like? Martin On Thu, Mar 6, 2014 at 4:43 PM, Philippe Moncuquet philippe.m...@gmail.comwrote: Hi, We have recently updated our instance, I have noticed a bug display in the report page. In the section 'Jobs per Month', the month column does not contain any month name but number instead. Has anybody experienced the same thing ? Regards, Philip ___ 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/
Re: [galaxy-dev] Galaxy reports
Awesome, I am glad it is working for you. Thank you for using Galaxy! regards Martin On Thu, Mar 6, 2014 at 5:18 PM, steve.mcma...@csiro.au wrote: Hi Philippe, I realised we hadn’t restarted the reports application after the upgrade. I’ve done that it seems to be working fine. Cheers. *Steve McMahon* Solution Architect and Senior System Administrator | Scientific Computing *Information Management and Technology* CSIRO T +61 2 6214 2968 Alt +61 4 0077 9318 steve.mcma...@csiro.au | www.csiro.au 1 Wilf Crane Crescent, Yarralumla ACT 2600 *PLEASE NOTE* The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. *Please consider the environment before printing this email.* *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Martin Cech *Sent:* Friday, 7 March 2014 9:09 AM *To:* Philippe Moncuquet *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Galaxy reports Hello Philip, the page you are talking about should look like this: https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png How does yours look like? Martin On Thu, Mar 6, 2014 at 4:43 PM, Philippe Moncuquet philippe.m...@gmail.com wrote: Hi, We have recently updated our instance, I have noticed a bug display in the report page. In the section 'Jobs per Month', the month column does not contain any month name but number instead. Has anybody experienced the same thing ? Regards, Philip ___ 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/
Re: [galaxy-dev] Galaxy command line API information
Dear Benoît Meilhac, In my plugin, I would have to import the workflow, then run it with inputs listed in the executable command line, and after a successful execution, I would have to retrieve the outputs generated, then delete the created workflow and any files related that exist. The inputs (datasets) on which the workflow will run have to exist within the Galaxy's system - you can't supply the files to the workflow directly. Is it currently possible for me, in a short time, to develop such plugin performing operations previously described using the existing API? If yes, could you please provide me more information on the current API or some help on the different tools I should use? You might consider the following flow. I believe all steps can be performed via API. 1. Import datasets into Galaxy ( using Tool API of the upload tool you have 2 options: either by linking the files - https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFilesor by direct uploading - the choice depends mostly on the size of inputs ) 2. Import workflow( https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.workflows ) 3. Run workflow on the datasets in Galaxy 4. Download results from history( https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories ) 5. Delete histories 6. Delete workflow Let me know how this works for you. thank you for using Galaxy! Martin On Fri, Feb 28, 2014 at 9:10 AM, Benoit Meilhac b.meil...@westminster.ac.uk wrote: Dear Sir or Madam, I am working for the University of Westminster on the ER-Flow project ( http://www.erflow.eu/home). I'm currently investigating a way to use the galaxy workflow engine with a command line interface in order to support it within our project. The idea would be to develop a plugin that could make a link between our repository, where a galaxy workflow can be specified (workflow and inputs stored and output declared), and a galaxy server. We have a specific way our existing plugins work. It would be something like: ./executable -w workflow list of inputs And then, outputs are retrieved and returned (they don't need to be given as command line parameters). I had a quick look at the provided API within the galaxy project and I have some questions. I saw this is possible to import the workflow to the server, then to execute it. In my plugin, I would have to import the workflow, then run it with inputs listed in the executable command line, and after a successful execution, I would have to retrieve the outputs generated, then delete the created workflow and any files related that exist. Is it currently possible for me, in a short time, to develop such plugin performing operations previously described using the existing API? If yes, could you please provide me more information on the current API or some help on the different tools I should use? Many thanks and kind regards, Benoît Meilhac The University of Westminster is a charity and a company limited by guarantee. Registration number: 977818 England. Registered Office: 309 Regent Street, London W1B 2UW. This message and its attachments are private and confidential. If you have received this message in error, please notify the sender and remove it and its attachments from your system. ___ 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/
Re: [galaxy-dev] Where to add Account activation
Hello, Björn has a point on the proper way to upgrade the Galaxy config file. Please do not forget that you have to have your email server set up and have Galaxy connected to it by changing the settings mentioned in the wiki page. Without the server the activation will not be used even if user_activation_on = True. thank you for using Galaxy Martin On Fri, Feb 21, 2014 at 9:03 AM, Björn Grüning bjo...@gruenings.eu wrote: Hi Danielle, are you running the latest Galaxy version? If so you will have a universe_wsgi.ini.sample file included in your Galaxy-Root directory. Please merge the latest changes into your universe_wsgi.ini file. Your user_activation_on options will be included during the merge. You can use meld for a graphical merge. Cheers, Bjoern I was reading the link: https://wiki.galaxyproject.org/Admin/UserAccounts I wonder where should I add the following line of code in the file universe_wsgi.ini user_activation_on = True I tried adding at the end of the code. I also tried to add in the [app: main] However, it is not functioning. Best Regards, Danielle Furtado. ___ 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/ ___ 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/
Re: [galaxy-dev] Galaxy-LIMS and multiple sample
Hello Davide, yes it does. Also these two modifications of Galaxy might be if an interest to you as they enhanced the sample tracking further: http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/ http://bioinformatics.oxfordjournals.org/content/29/9/1233.long Martin On Wed, Feb 19, 2014 at 9:51 AM, Davide Cittaro daweonl...@gmail.comwrote: Dear all, I don't have an instance of galaxy that manages sequencing requests. I would like to, but I would like to know a single thing: Is the interface friendly enough to make me define multiple sample at once in a single request? Thanks d ___ 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/
Re: [galaxy-dev] Error in Galaxy Reports
Hi, this has been resolved in galaxy-central repo (not dist). You can apply the patch manualy, it is less than one-liner. https://bitbucket.org/galaxy/galaxy-central/commits/3691fd3e12ef8160ae993cef5ebd51ddeee95da1 Martin On Fri, Feb 14, 2014 at 1:28 PM, Nikos Sidiropoulos nikos.sid...@gmail.comwrote: Hi Sam, thank you for the quick reply but I can't seem to find the revision, or maybe don't know how to pull it. I tried to check galaxy-dist on BitBucket but couldn't find any updates related to Galaxy Reports. Bests, Nikos 2014-02-13 17:35 GMT+01:00 sam guerler aysam.guer...@gmail.com: Hi Nikos, Thank you so much for your report. This issue should be fixed now. Please update your revision and try again. Thanks, Sam On Thu, Feb 13, 2014 at 7:52 AM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi all, after the February 2014 galaxy update I'm experiencing errors in Galaxy Reports. It only occurs when I'm trying to see which jobs were ran at a specific date (e.g. I can see how many jobs were ran today, but when I click on the number to see which ones it returns the following error): URL: http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13 Module paste.exceptions.errormiddleware:*144* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# body *=* method*(* trans*,* kwargs *)* Module galaxy.webapps.reports.controllers.jobs:*177* in specified_date_handler http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*specified_date_list_grid*(* trans*,* kwd *)* Module galaxy.web.framework.helpers.grids:*296* in __call__ http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# kwargs*=*kwargs *)* Module galaxy.web.framework:*1184* in fill_template http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* self*.*fill_template_mako*(* filename*,* kwargs *)* Module galaxy.web.framework:*1199* in fill_template_mako http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* template*.*render*(* data *)* Module mako.template:*296* in render http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# _kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs *)* Module mako.runtime:*718* in _exec_template http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# callable_*(*context*,* ***args*,* kwargs*)* Module _base_mako:*45* in render_body http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*next*.*body*(**)**)**)* Module _grid_base_mako:*134* in render_body http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# __M_writer*(*unicode*(*self*.*load*(**)**)**)* Module _grid_base_mako:*108* in render_load http://localhost:9001/jobs/specified_date_handler?webapp=reportsspecified_date=2014-02-13# self*.*grid_javascripts*(**)* Module _grid_base_mako:*517* in render_grid_javascripts
Re: [galaxy-dev] Galaxy Reports
Thank you Eric for the wiki page.
I agree that Galaxy Reports are not visible enough and this might help.
Martin, Galaxy Team
On Fri, Jan 17, 2014 at 12:29 PM, Eric Rasche rasche.e...@yandex.ru wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Well! This is the first I've heard of a Galaxy Reports page. Too bad I
already re-invented the wheel because I hadn't ever heard of this tool...
Anyway, since run_reports.sh was only mentioned once anywhere in the
wiki (according to search, in a DevNewsBrief from 2008), I've added a
wiki page for the report tool.
Please add whatever information you all feel I've left out.
https://wiki.galaxyproject.org/Admin/Usage%20Reports
Cheers,
Eric Rasche
On 01/17/2014 10:38 AM, Liisa Koski wrote:
Hello,
First..I love the Galaxy Reports tool...thanks so much for this.
I did however come across an error when trying to few the Registered
Users per month link. It would be really nice to have this working :)
Thanks in advance,
Liisa
URL: http://domain:9001/users/registered_users_per_month
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month
Module paste.exceptions.errormiddleware:*144* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
app_iter*=*
self*.*application*(*environ*,* sr_checker*)*
Module paste.debug.prints:*106* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
environ*,*
self*.*app*)*
Module paste.wsgilib:*543* in intercept_output_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
app_iter*=*
application*(*environ*,* replacement_start_response*)*
Module paste.lint:*170* in lint_app_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
iterator*=*
application*(*environ*,* start_response_wrapper*)*
Module paste.recursive:*84* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
*return*self*.*application*(*environ*,*
start_response*)*
Module paste.httpexceptions:*633* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
*return*self*.*application*(*environ*,*
start_response*)*
Module galaxy.web.framework.base:*132* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
*return*self*.*handle_request*(*
environ*,* start_response*)*
Module galaxy.web.framework.base:*190* in handle_request_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
body*=*
method*(* trans*,* kwargs*)*
Module galaxy.webapps.reports.controllers.users:*29* in
registered_users_per_month_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
*for*row*in*q*.*execute*():*
Module sqlalchemy.sql.expression:*2841* in execute
Module sqlalchemy.engine.base:*2453* in _execute_clauseelement
Module sqlalchemy.engine.base:*1584* in _execute_clauseelement
Module sqlalchemy.engine.base:*1698* in _execute_context
Module sqlalchemy.engine.base:*1691* in _execute_context
Module sqlalchemy.engine.default:*331* in do_execute
Module MySQLdb.cursors:*173* in execute
Module MySQLdb.connections:*36* in defaulterrorhandler*
OperationalError: (OperationalError) (1305, 'FUNCTION
galaxy_production.date_trunc does not exist') 'SELECT date_trunc(%s,
date(galaxy_user.create_time)) AS date, count(galaxy_user.id) AS
num_users \nFROM galaxy_user GROUP BY date_trunc(%s,
date(galaxy_user.create_time)) ORDER BY date DESC' ('month', 'month')*
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in your mail client. To manage
Re: [galaxy-dev] Share history (or change history ownership) through the Galaxy API?
Hi Daniel, I am sorry but Galaxy API doesn't support sharing of histories yet. For further notice these two parts of the API documentation are the most relevant for the histories API: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.history_contents Martin, Galaxy Team On Wed, Jan 15, 2014 at 1:36 PM, Daniel Sobral dsob...@igc.gulbenkian.ptwrote: Hello, Is it possible to share a history with a user (by user name) or change ownership through the Galaxy API? I didn't see any example doing this. Thanks. Cheers, Daniel -- Daniel Sobral, Bioinformatics Unit Instituto Gulbenkian de Ciência ___ 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/
Re: [galaxy-dev] Share history (or change history ownership) through the Galaxy API?
Daniel: You can create a history item through API by importing dataset from library (that would be this method: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#galaxy.webapps.galaxy.api.history_contents.HistoryContentsController.create ). For uploading bigger files I would recommend using the FTP ( https://wiki.galaxyproject.org/FTPUpload) Martin On Wed, Jan 15, 2014 at 2:18 PM, Daniel Sobral dsob...@igc.gulbenkian.ptwrote: Thanks Martin, I saw that you can upload a file directly to a history using the API through the upload tool, but then it has limitations in terms of file size, no? Would it be useable with large files? Thanks, Daniel On 01/15/2014 07:05 PM, Martin Čech wrote: Hi Daniel, I am sorry but Galaxy API doesn't support sharing of histories yet. For further notice these two parts of the API documentation are the most relevant for the histories API: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.history_contents Martin, Galaxy Team On Wed, Jan 15, 2014 at 1:36 PM, Daniel Sobral dsob...@igc.gulbenkian.ptwrote: Hello, Is it possible to share a history with a user (by user name) or change ownership through the Galaxy API? I didn't see any example doing this. Thanks. Cheers, Daniel -- Daniel Sobral, Bioinformatics Unit Instituto Gulbenkian de Ciência ___ 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/ -- Daniel Sobral, Bioinformatics Unit Instituto Gulbenkian de Ciência ___ 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/
Re: [galaxy-dev] I still can't use API to create a user!
Hi,
I have tested user creation on local instance running galaxy-central and it
is running fine for me. Please se attached request and response
(printscreen from postman chrome extension):
https://www.dropbox.com/s/g7iiluq1tqc426p/Screenshot%202014-01-14%2014.22.45.png
Martin, Galaxy Team
On Tue, Jan 14, 2014 at 4:32 AM, xlwang xlwang_0...@163.com wrote:
When I use API to create a user, I get an error! And this time I use the
galaxy instance from galaxy-central.
The command is:
#curl -d '{username:test,password:test,email:1...@123.com}'
http://myip:8080/api/users?key=my_key
I get some information:
And the web server give me some error information:
galaxy.web.framework ERROR 2014-01-14 17:18:42,257 Uncaught exception in
exposed API method:
Traceback (most recent call last):
File /galaxy-central/lib/galaxy/web/framework/__init__.py, line 197,
in decorator
rval = func( self, trans, *args, **kwargs)
File /galaxy-central/lib/galaxy/webapps/galaxy/api/users.py, line 97,
in create
username = payload[ 'username' ]
KeyError: 'username'
10.10.10.1 - - [14/Jan/2014:17:18:42 +0800] POST
/api/users?key=e2424e1d238292b5dfe4e3fdcc411dd1 HTTP/1.1 500 - -
curl/7.15.5 (x86_64-redhat-linux-gnu) libcurl/7.15.5 OpenSSL/0.9.8b
zlib/1.2.3 libidn/0.6.5
I don't know why it happened. Please help me to fix this error. Thank you!
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截图2.png___
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Re: [galaxy-dev] Create user error
Hi Nikos, did you update your galaxy version recently? Did you use galaxy form definitions at any time? Martin On Tue, Jan 14, 2014 at 8:30 AM, Nikos Sidiropoulos nikos.sid...@gmail.comwrote: I found the error in the logs: Error - type 'exceptions.AttributeError': 'NoneType' object has no attribute 'id' URL: http://galaxy.bric.dk/user/manage_user_info?cntrller=user File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py', line 926 in manage_user_info status=status ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1002 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1017 in fill_template_mako return template.render( **data ) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/steno-internal/projects/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/steno-internal/projects/galaxy/galaxy-dist/database/compiled_templates/ base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/steno-internal/projects/galaxy/galaxy-dist/database/compiled_templates/webapps/galaxy/user/ manage_info.mako.py', line 93 in render_body __M_writer(unicode(trans.security.encode_id( user_type_form_definition.id ))) AttributeError: 'NoneType' object has no attribute 'id' 2014/1/14 Nikos Sidiropoulos nikos.sid...@gmail.com Hi all, Although users were able to create accounts till recently, now the following error pops up whenever someone is trying to register as a new user after filling the fields and clicking submit. Select the user's type and information Is anyone familiar with this error? Bests, Nikos ___ 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/
Re: [galaxy-dev] Can REMOTE_USER be changed to another header variable?
Prakash: not unless your default pull is* galaxy-central* repository. M. On Fri, Jan 3, 2014 at 11:49 AM, Velayutham, Prakash (Prakash) prakash.velayut...@cchmc.org wrote: Hi Nate, If I do a hg clone of my default pull, this should already be there? Thanks, Prakash On Jan 3, 2014, at 11:45 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Prakash, This was not previously possible, but I have added a config option for it: https://bitbucket.org/galaxy/galaxy-central/commits/e92e13e9c103cc1f36dff65e1523479bf5cb17ed If you're running the stable branch, you can apply the changes from this commit manually. --nate On Thu, Jan 2, 2014 at 11:09 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Prakash, I am going to move this over to the galaxy-...@bx.psu.edu mailing list where it will have greater visibility within our development community. Best, Jen Galaxy team https://wiki.galaxyproject.org/MailingLists#The_lists On 1/2/14 7:27 AM, Velayutham, Prakash (Prakash) wrote: Hi, We have a SSO environment provided by Oracle Fusion products and for some reason, they don't like to send over HTTP_REMOTE_USER as a header variable to downstream servers. I have seen it before with other web sites I have integrated with Oracle Access Manager. Is there a way Galaxy can accept another HEADER variable than REMOTE_USER for its external authentication? As an extension: - With just enabling HTTP_REMOTE_USER as a header variable from an external authenticator, Galaxy works without any issues. I tried this with a default Apache/mod_ldap/mod_authnz_ldap setup. - However, when I mix the Oracle gateways into the mix, things break down. - I made OAM send HTTP_AUTH_USER over to Galaxy. - I changed all instances of REMOTE_USER to AUTH_USER in the installed location of Galaxy in my server. - Authentication works fine, but I get issues with HISTORY part of Galaxy (below), when I access a workflow or basically any part of Galaxy that depends on HISTORY Error Traceback: View as: Interactivehttps://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# | Texthttps://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# | XMLhttps://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# (full)https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# ⇝ AttributeError: 'NoneType' object has no attribute 'user' URL: http://xxx.xxx.xxx/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False Module weberror.evalexception.middleware:*364* in respond Mail Attachment.jpeg https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# viewhttps://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# app_iter *=* self*.*application*(*environ*,* detect_start_response*)* Module paste.recursive:*84* in __call__ Mail Attachment.jpeg https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# viewhttps://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.middleware.remoteuser:*91* in __call__ Mail Attachment.jpeg https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# viewhttps://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# *return* self*.*app*(* environ*,* start_response *)* Module paste.httpexceptions:*633* in __call__ Mail Attachment.jpeg https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# viewhttps://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ Mail Attachment.jpeg https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# viewhttps://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# https://galaxy.research.cchmc.org/dataset/list?sort=-update_timef-name=Allf-tags=Allf-deleted=False# *return*
Re: [galaxy-dev] how to create users through Galaxy API?
Hello, to create a user through API you send a POST request to /api/users More information about User API here: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.users Martin On Fri, Dec 27, 2013 at 5:11 AM, xlwang xlwang_0...@163.com wrote: hello, I want to create users through Galaxy API.For example, I can get users information through url like this(use postman): http://localhost:8080/api/users?key=my_key But how to create a user? ___ 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/
Re: [galaxy-dev] How to use Galaxy API?
Hello, by API controller I meant the Python module that takes control over the endpoints of API thus providing logic. You don't need to 'use them' - you can create API requests by many different means by specifying URL (sometimes +params+payload). Look at the extension link I have sent you, that will help you call the API from the browser. M. On Wed, Dec 18, 2013 at 3:15 AM, xlwang xlwang_0...@163.com wrote: Hi, thank you very much for such a quick relpy. Now, I can connect to galaxy via API. In addition, please tell me what is API controller?How to use those modules and where are they in galaxy? At 2013-12-18 12:13:58,Martin Čech mar...@bx.psu.edu wrote: Hi, the best start for using the API, that you found already, is the documentation that, with a nice introduction, is nicely available here: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html Regarding libraries your main controllers of interest are: *libraries*, *library_contents*, *folders, **folder_contents* - *please beware that folders API is considered work-in-progress and will probably be deprecated in future releases.* If you want to test how the API behaves you can use something like Postman extension ( https://chrome.google.com/webstore/detail/postman-rest-client/fdmmgilgnpjigdojojpjoooidkmcomcm?hl=en) for chrome or other browser that allows you to nicely simulate API calls. As of your error make sure that your local Galaxy, that you are trying to connect to via API, runs on the 4096 port that you specified for the script (by default local Galaxy runs at port 8080 - see universe_wsgi.ini for config changes). Thank you for using Galaxy and let us know how it goes! Martin, Galaxy Team On Tue, Dec 17, 2013 at 9:26 PM, xlwang xlwang_0...@163.com wrote: Hello, I want to know how to use Galaxy API(the path is /galaxy-dist/scripts/api). I follow the README but get errors. For instance, I have generated my_key and use this script: ./display.py my_key http://localhost:4096/api/libraries I get an error: urlopen error [Errno 111] Connection refused I do not know how it happened. Please tell me how to fix it. Thank you! In addition, my main purpose is to manage the data library in another system. Should I use the api such as library_create_library.py, library_upload_from_import_dir.py and so on? ___ 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/
Re: [galaxy-dev] How to use Galaxy API?
Hi, the best start for using the API, that you found already, is the documentation that, with a nice introduction, is nicely available here: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html Regarding libraries your main controllers of interest are: *libraries*, *library_contents*, *folders, **folder_contents* - *please beware that folders API is considered work-in-progress and will probably be deprecated in future releases.* If you want to test how the API behaves you can use something like Postman extension ( https://chrome.google.com/webstore/detail/postman-rest-client/fdmmgilgnpjigdojojpjoooidkmcomcm?hl=en) for chrome or other browser that allows you to nicely simulate API calls. As of your error make sure that your local Galaxy, that you are trying to connect to via API, runs on the 4096 port that you specified for the script (by default local Galaxy runs at port 8080 - see universe_wsgi.ini for config changes). Thank you for using Galaxy and let us know how it goes! Martin, Galaxy Team On Tue, Dec 17, 2013 at 9:26 PM, xlwang xlwang_0...@163.com wrote: Hello, I want to know how to use Galaxy API(the path is /galaxy-dist/scripts/api). I follow the README but get errors. For instance, I have generated my_key and use this script: ./display.py my_key http://localhost:4096/api/libraries I get an error: urlopen error [Errno 111] Connection refused I do not know how it happened. Please tell me how to fix it. Thank you! In addition, my main purpose is to manage the data library in another system. Should I use the api such as library_create_library.py, library_upload_from_import_dir.py and so on? ___ 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/
Re: [galaxy-dev] Library permission page broken
Hi Sam, you can reproduce this easily by going to Admin/Manage Data Libraries and try to edit permissions for any of the existing library. M. On Wed, Nov 27, 2013 at 3:27 PM, sam guerler aysam.guer...@gmail.comwrote: Hello David, Could you provide more details on how to reproduce this i.e. which buttons to click to get there? Thanks, Sam On Wed, Nov 27, 2013 at 11:11 AM, David Hoover hoove...@helix.nih.govwrote: After the latest update, the Manage library permissions page is broken. The Roles not associated boxes are pushed to the left of the frame, and the double arrow buttons are misplaced down the page. This occurs under Safari (5.1.10) and Chrome (31.0.1650.57) on a Mac running OS X 10.6.8. Firefox (25.0.1), however, seems ok. ___ 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/ ___ 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/
Re: [galaxy-dev] Security vulnerability in Galaxy filtering tools
John just made it to the Wiki: http://wiki.galaxyproject.org/Develop/SecurityToolTips Feel free to add/edit/delete. M. On Thu, Nov 7, 2013 at 12:27 PM, John Chilton chil...@msi.umn.edu wrote: Hello Ido, The project has had a lot of contributors over the years, it is probably not safe to assume they have all been experts and frequently experts know of little tricks or shortcuts that can result in a lot of trouble (this case in point) - a less sophisticated developer probably would not have even known about the Python functionality that resulted in this trouble. I suspect the mere fact that you are concerned about writing secure tools means you would do a better job than many professional software developers whom you may term as experts. Furthermore, you are absolutely right there should be some documentation or something somewhere to aid in writing secure tools - the rest of this e-mail contains a couple quick notes hopefully it can be translated to the wiki at some point and grown over time. If your tool is not taking in text inputs - its all numbers and select parameters, etc it is very likely secure. These sorts of vulnerabilities would usually come into play when users are allowed to pass free text and the tool or wrapper use this text in such a way that it can be broken out of the intended context (these are broadly characterized as code injection attacks). 95% of how these text parameters are going to be used is likely passing them as a command-line argument to another program. For this reason Galaxy preprocesses the text and sanitizes it so it cannot contain characters that would result in the text easily result in code injections. So for this reason - you are still probably fine unless you are circumventing this text preprocessing. For instance, Galaxy will translate quotations marks to '__dq__', this tool explicitly retranslates those back to quotations marks ( https://bitbucket.org/galaxy/galaxy-central/src/f2f1cce4678cf1eb188d9611b05f00706afc8897/tools/stats/filtering.py?at=default#cl-176 ). There is a reason to do this in this case but you will not need for most bioinformatics applications. If your tools are doing this it is time to start getting extra careful. If you are really interested in this topic or when it is time to get extra careful, I would recommend picking up the book The Web Application Hacker's Handbook - it is pretty good. Most of it would not be relevant for tool developers, but chapter 1, chapter 2, and all of chapter 9 could be very relevant and would probably leave one with a solid grasp of what to look for in many different contexts - not just the ones the book discusses explicitly. Hopefully over time the IUC will provide guidance about this sort of thing (informing you if there are potential security vulnerabilities in your tools). Also feel free to post example tool configurations to this list you might be concerned about and I am sure someone would be happy to look it over and tell you if there are any red flags. -John On Tue, Nov 5, 2013 at 12:30 PM, Ido Tamir ta...@imp.ac.at wrote: On Nov 5, 2013, at 6:28 PM, Nate Coraor n...@bx.psu.edu wrote: Hi Ido, Thanks for the feedback. Replies below. On Nov 5, 2013, at 9:54 AM, Ido Tamir wrote: This seems to happen often e.g. http://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix I'm not sure I'd agree that it's often - we've had 4 or 5 vulnerabilities over the life of the project. 2 allowed arbitrary code execution, the others were less severe. But these were written by experts, not by people like me, that don't know what the galaxy framework really does/does not do with the input, so I guess I make many more mistakes. a) are there general guidelines in the wiki on how to avoid these problems when creating tools? The guidelines for writing a Galaxy tool are no different from best practices for writing secure code. In specific for this vulnerability, execution of user input should be handled with extreme care, and this tool had some gaps in its input validation and sanitization. For what it's worth, the filter tool (on which the other vulnerable tools were based) is one of the few tools surviving from the very early days of Galaxy, and would not be implemented the same way if written today. I think it would be nice to have a small outline on the wiki of what galaxy does with the input data and how it could affect a tool. What sanitisation is there by default so I don't have to worry about it, but what could happen I if I don't care to check/remove sanitise ' | or ..., maybe with examples. b) is there a way to check automatically if all input fields are correctly escaped in a tool? I am not sure how Galaxy could do this. Galaxy sanitizes the command line so that input fields passed to a tool as command line arguments cannot be crafted to exploit the
Re: [galaxy-dev] latest galaxy-central version
Hi Robert, We are currently working on improving data libraries including the speed enhancements. In the meantime one of our users also reported that he is using for the dataset folders multiple libraries - each having less folder-depth which for him improves performance significantly. Maybe it will be of use to you. --Martin On Tue, Nov 5, 2013 at 5:19 PM, Robert Baertsch robert.baert...@gmail.comwrote: Carl, Thanks for building a great tool. Can you fix the library performance problem? Steps to reproduce: 1. http://su2c-dev.ucsc.edu/library 2. open library TCGA Pancan. It takes more than 20 seconds! -Robert On Nov 5, 2013, at 1:29 PM, Carl Eberhard carlfeberh...@gmail.com wrote: Thanks for the thorough report, Robert. I've added some sanity checking to the panel in default:11240:c271cdb443c6 My only guess as to why the panel javascript is trying to load at all in the library section is a link to the controller/datasets methods (unhide, delete, etc.) that still assume histories are in their own frames. Still investigating. On Tue, Nov 5, 2013 at 12:06 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: Carl, Just to make sure I just deleted my tree and did a fresh checkout and tried a third time. It happened all three times. I'm using a postgres database and this time I started with a fresh config files and just changed the setting below. I didn't see the javascript error in Chrome, perhaps it is some strangeness in Firebug. I've seen strange errors before in Firebug. Attached are two screen grab of the lastest try before and after browser refresh. changeset: 11227:151b7d3b2f1b branch: stable tag: tip parent: 11219:5c789ab4144a user:Carl Eberhard carlfeberh...@gmail.com date:Tue Nov 05 11:33:06 2013 -0500 summary: History panel: fix naming bug in purge async error handling -Robert 29c29 port = 8585 --- #port = 8080 34c34 host = 0.0.0.0 --- #host = 127.0.0.1 96d95 database_connection = postgresql://localhost/medbookgalaxycentral3 542c541 allow_library_path_paste = True --- #allow_library_path_paste = False 599c598 admin_users = baert...@soe.ucsc.edu --- #admin_users = None Screen Shot 2013-11-05 at 8.35.09 AM.png Screen Shot 2013-11-05 at 8.37.04 AM.png On Nov 5, 2013, at 8:21 AM, Carl Eberhard carlfeberh...@gmail.com wrote: Hello, Robert I'm having difficulty reproducing this with a fresh install of galaxy_central:default:11226:c67b9518c1e0. Is this an intermittent error or does it happen reliably each time with the steps above? Is it still the same javascript error you mentioned above? I'll investigate further. On Mon, Nov 4, 2013 at 7:29 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: I updated to the stable release and reproduced the issue. Step to reproduce 1. go to admin 2. Manage data librarieshttp://su2c-dev.ucsc.edu:8383/library_admin/browse_libraries 3. add dataset 4. select Upload files from filesystem paths 5. paste full path to any bam file. 6. leave defaults: auto-detect and copy files into galaxy 7. select role to restrict access 8. click upload to start Screen shows strange formatting and Job is running for Bam file. python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpJoasJl /data/galaxy-central/database/tmp/tmpzZO8t1 8877:/data/galaxy-central/database/job_working_directory/004/4548/dataset_8877_files:/data/galaxy-central/database/files/008/dataset_8877.dat If I do a firefox refresh and go back to the library, the formatting is normal. I'm assuming the fix is to just render the page before waiting for the job to complete. -Robert On Nov 4, 2013, at 12:45 PM, Martin Čech mar...@bx.psu.edu wrote: Hello, I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation. --Marten On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: It keeps doing posts, and I'm not seeing any new errors. POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in) Galaxy.currUser is undefined on Line 631 in history-panel.js When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things. -Robert On Nov 4, 2013, at 11:14 AM, James Taylor ja...@jamestaylor.org wrote: Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired. Are there any javascript errors? Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might
Re: [galaxy-dev] latest galaxy-central version
Hello, I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation. --Marten On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: It keeps doing posts, and I'm not seeing any new errors. POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in) Galaxy.currUser is undefined on Line 631 in history-panel.js When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things. -Robert On Nov 4, 2013, at 11:14 AM, James Taylor ja...@jamestaylor.org wrote: Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired. Are there any javascript errors? Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console. -- James Taylor, Associate Professor, Biology/CS, Emory University On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update. I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server. During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted Do you finish rendering the screen after the copy operation is complete? -Robert Screen Shot 2013-11-04 at 10.53.02 AM.png ___ 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/
Re: [galaxy-dev] User activations
Hello Jordi, user activation feature and other features described at the page you mentioned are implemented and part of the development galaxy-central ( https://bitbucket.org/galaxy/galaxy-central) repository. However they are not yet part of the official release repository (galaxy-dist - https://bitbucket.org/galaxy/galaxy-dist) but the next release which includes these features is going out soon so stay tuned! I am sorry about the confusion that I caused by publishing the documentation before the actual official release without a notice to which version it applies to. Thank you for using Galaxy and please let us know what do you think about the new features! regards Marten p.s. the official test page at https://test.galaxyproject.org/ is running all of these features, you can test some of them there On Thu, Oct 31, 2013 at 6:08 PM, jo...@biociphers.org wrote: Hi all, Recently I have updated our test galaxy server in order to check some new features like user email activation using emails. I saw that in the admin page http://wiki.galaxyproject.org/Admin/UserAccounts . But I download the last version and the conf values that are supose to be in the universe_wsgi.ini are not present ( at least in the sample file). Do you know if this is a future feature or there is anything I need to do for testing it? thanks everyone for your help Jordi ___ 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/
Re: [galaxy-dev] browse directories on galaxy server
Hello David, please see whether Data Libraries ( http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries) with the file import ( http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles) and especially the *Upload files from filesystem paths* feature do solve your problem. It enables you to work with the datasets while keeping them untouched on the file system. thank you for using Galaxy! regards Martin On Thu, Oct 31, 2013 at 3:05 PM, David Hoover hoove...@helix.nih.govwrote: Is there any desire to create a way in galaxy to browse local directories on the galaxy server itself? Not the client machine running the web browwser, but the machine on which galaxy is running. I've created a tool that allows a user to upload a single file from their own personal directory on the galaxy server into galaxy directly, without going through Apache. However, this is very limiting. It would be very helpful to be able to browse directories that are deemed accessible to the galaxy user, and before I begin trying to develop anything I'd like to know if there is any support for such a feature. David Hoover Helix Systems Staff National Institutes of Health ___ 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/
Re: [galaxy-dev] Local Galaxy Install - Debug Report FROM address as Admin and not User?
Hi Adam, you are right about the behaviour, this is what Galaxy does. However it sends the email to the user too, so Reply all will reach the user's email address. This is how the feature was meant to be used. Martin On Tue, Oct 1, 2013 at 12:59 PM, Adam Brenner aebre...@uci.edu wrote: Howdy, On our local Galaxy install, everytime a user submits a bug report, it does email all the admins -- as defined in universe_wsgi.ini -- but the FROM address is not of the user, but rather the first email address from the admin list. Is this normal? May we have it changed so the FROM address is that of the user? Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.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/ 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/
Re: [galaxy-dev] Local Galaxy Install - Debug Report FROM address as Admin and not User?
Adam, it is function *report_error* in /lib/galaxy/webapps/galaxy/controllers/dataset.py you need to set this line * frm = to_address * to * frm = email* and you should be all set. Martin On Tue, Oct 1, 2013 at 2:12 PM, Adam Brenner aebre...@uci.edu wrote: Martin, Thanks for the response. Yes, I do notice the reply-to address does include the user, but wouldn't it be better if the FROM address was from the actual user reporting the error? When checking my email, for example, I do not want to see emails that are FROM me, to MYSELF when its really from our users. Do you know which of the python files contain the code that relates to this? Or point me in the right direction so I can change this? Thanks! -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Tue, Oct 1, 2013 at 10:52 AM, Martin Čech mar...@bx.psu.edu wrote: Hi Adam, you are right about the behaviour, this is what Galaxy does. However it sends the email to the user too, so Reply all will reach the user's email address. This is how the feature was meant to be used. Martin On Tue, Oct 1, 2013 at 12:59 PM, Adam Brenner aebre...@uci.edu wrote: Howdy, On our local Galaxy install, everytime a user submits a bug report, it does email all the admins -- as defined in universe_wsgi.ini -- but the FROM address is not of the user, but rather the first email address from the admin list. Is this normal? May we have it changed so the FROM address is that of the user? Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.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/ 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/
Re: [galaxy-dev] pbkdf2 encryption - disabling does not work
Jan,
It works for me with the newest galaxy-central version. I registered new
user without a problem having the pbkdf2 turned off.
What version are you using now?
Martin
On Thu, Sep 26, 2013 at 4:02 AM, Jan Hapala j...@hapala.cz wrote:
Ahoj Martine,
thanks for your response. That was a pretty stupid mistake, hard to notice
even though I program in Python.
However, this has not solved my problem, I get the same error. (I have
also made sure that it is in the right section.)
Jan
2013/9/25 Martin Čech emulato...@gmail.com
Ahoj Honzo,
Python is case-sensitive. Use 'use_pbkdf2 = False' and make sure you put
it under the '[app:main]' section in the config file.
Enjoy Galaxy!
best
Martin Cech
On Wed, Sep 25, 2013 at 9:15 AM, Jan Hapala j...@hapala.cz wrote:
Hi,
I need to run Galaxy with ProFTPd, therefore I need to disable the
PBKDF2 encryption of the passwords (as stated here
http://dev.list.galaxyproject.org/disable-PBKDF2-revert-to-SHA1-td4661274.html
).
However, when I do add this line:
use_pbkdf2 = false
to the universe_wsgi.ini, restart Galaxy, submit the form for the
password change (or register as a new user) I get an error _hashlib.HASH
object has no attribute __getitem__.
I got the same result with a version as of Jul 2 and the most recent tag
(10411:c42567f43aa7, Aug 19).
I would be much grateful for your suggestions!
Regards,
Jan
URL:
http://127.0.0.1:8080/user/edit_info?cntrller=useruser_id=f2db41e1fa331b3e
File
'.../eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in
__call__
return self.application(environ, start_response)
File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line
633 in __call__
return self.application(environ, start_response)
File '.../lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '.../lib/galaxy/web/framework/base.py', line 190 in handle_request
body = method( trans, **kwargs )
File '.../lib/galaxy/webapps/galaxy/controllers/user.py', line 842 in
edit_info
trans.sa_session.flush()
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py',
line 114 in do
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py',
line 1718 in flush
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py',
line 1789 in _flush
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py',
line 331 in execute
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py',
line 475 in execute
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py',
line 59 in save_obj
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py',
line 485 in _emit_update_statements
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
line 1449 in execute
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
line 1584 in _execute_clauseelement
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
line 1651 in _execute_context
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
line 1647 in _execute_context
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py',
line 475 in _init_compiled
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py',
line 626 in process
File '.../lib/galaxy/model/custom_types.py', line 125 in
process_bind_param
value = value[0:self.impl.length]
StatementError: '_hashlib.HASH' object has no attribute '__getitem__'
(original cause: TypeError: '_hashlib.HASH' object has no attribute
'__getitem__') 'UPDATE galaxy_user SET update_time=%(update_time)s,
password=%(password)s WHERE galaxy_user.id = %(galaxy_user_id)s'
[{u'galaxy_user_id': 1, 'password': sha1 HASH object @ 0x7338bc0}]
___
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
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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/
Re: [galaxy-dev] pbkdf2 encryption - disabling does not work
Ahoj Honzo,
Python is case-sensitive. Use 'use_pbkdf2 = False' and make sure you put it
under the '[app:main]' section in the config file.
Enjoy Galaxy!
best
Martin Cech
On Wed, Sep 25, 2013 at 9:15 AM, Jan Hapala j...@hapala.cz wrote:
Hi,
I need to run Galaxy with ProFTPd, therefore I need to disable the PBKDF2
encryption of the passwords (as stated here
http://dev.list.galaxyproject.org/disable-PBKDF2-revert-to-SHA1-td4661274.html
).
However, when I do add this line:
use_pbkdf2 = false
to the universe_wsgi.ini, restart Galaxy, submit the form for the password
change (or register as a new user) I get an error _hashlib.HASH object has
no attribute __getitem__.
I got the same result with a version as of Jul 2 and the most recent tag
(10411:c42567f43aa7, Aug 19).
I would be much grateful for your suggestions!
Regards,
Jan
URL:
http://127.0.0.1:8080/user/edit_info?cntrller=useruser_id=f2db41e1fa331b3e
File
'.../eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
app_iter = self.application(environ, detect_start_response)
File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in
__call__
return self.application(environ, start_response)
File '.../eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633
in __call__
return self.application(environ, start_response)
File '.../lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '.../lib/galaxy/web/framework/base.py', line 190 in handle_request
body = method( trans, **kwargs )
File '.../lib/galaxy/webapps/galaxy/controllers/user.py', line 842 in
edit_info
trans.sa_session.flush()
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py',
line 114 in do
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py',
line 1718 in flush
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py',
line 1789 in _flush
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py',
line 331 in execute
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py',
line 475 in execute
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py',
line 59 in save_obj
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py',
line 485 in _emit_update_statements
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
line 1449 in execute
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
line 1584 in _execute_clauseelement
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
line 1651 in _execute_context
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py',
line 1647 in _execute_context
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py',
line 475 in _init_compiled
File
'.../eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py',
line 626 in process
File '.../lib/galaxy/model/custom_types.py', line 125 in process_bind_param
value = value[0:self.impl.length]
StatementError: '_hashlib.HASH' object has no attribute '__getitem__'
(original cause: TypeError: '_hashlib.HASH' object has no attribute
'__getitem__') 'UPDATE galaxy_user SET update_time=%(update_time)s,
password=%(password)s WHERE galaxy_user.id = %(galaxy_user_id)s'
[{u'galaxy_user_id': 1, 'password': sha1 HASH object @ 0x7338bc0}]
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