Upload File: how to see all registered formats ?
Hi again, Emboss_datatypes is installad via tool shed. The 'View datatypes registry' in the Adminstration page, shows all registered data types, including the emboss ones, like e.g. genbank. However, the 'Upload File' tool does not show genbank in the 'File Format' dropdown. How can one configure the upload1 tool so that all registered formats are listed ? I don't understand the from_parameter hocus-pocus in this line (upload.xml): <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]"> The workaround which is used up to now is upload genbank sequences as txt format and change the format later via the history. But that is a 2-step operation, guess there should be a way taking only 1 step ? Regards, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
Hi Marc, please have a look at the datatypes_conf.xml file in your galaxy directory. There should be something like that: <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/> Try to add 'display_in_upload="true"' to the genbank datatype. The 'good' solution would be to define a datatype genbank, with a sniff function, so that galaxy can guess the filetype when you are uploading it. Please find attached my first attempt for that. Im working on some datatypes and converteres, but its not ready yet :( Cheers, Bjoern
Hi again,
Emboss_datatypes is installad via tool shed. The ‘View datatypes registry’ in the Adminstration page, shows all registered data types, including the emboss ones, like e.g. genbank.
However, the ‘Upload File’ tool does not show genbank in the ‘File Format’ dropdown. How can one configure the upload1 tool so that all registered formats are listed ?
I don’t understand the from_parameter hocus-pocus in this line (upload.xml):
<options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]">
The workaround which is used up to now is upload genbank sequences as txt format and change the format later via the history. But that is a 2-step operation, guess there should be a way taking only 1 step ?
Regards,
Marc
________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________ ___________________________________________________________ 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:
-- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/
Hi Björn, I think the issue is that the genbank datatype is coming in via the tool shed and is not taken into account by the upload tool. The genbank datatype is defined in shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml I have added the display_in_upload attribute in the latter file for the genbank datatype, restarted Galaxy but the type did not appear in the selection. Should the genbank datatype be added to the main galaxy datatypes_conf.xml ? Or is it better to explicitly add the emboss' datatypes_conf.xml to the universe_wsgi.ini (but this will break the tool shed update system, right) ? Thanks, Marc -----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Friday, August 03, 2012 4:14 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload File: how to see all registered formats ? Hi Marc, please have a look at the datatypes_conf.xml file in your galaxy directory. There should be something like that: <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/> Try to add 'display_in_upload="true"' to the genbank datatype. The 'good' solution would be to define a datatype genbank, with a sniff function, so that galaxy can guess the filetype when you are uploading it. Please find attached my first attempt for that. Im working on some datatypes and converteres, but its not ready yet :( Cheers, Bjoern
Hi again,
Emboss_datatypes is installad via tool shed. The ‘View datatypes registry’ in the Adminstration page, shows all registered data types, including the emboss ones, like e.g. genbank.
However, the ‘Upload File’ tool does not show genbank in the ‘File Format’ dropdown. How can one configure the upload1 tool so that all registered formats are listed ?
I don’t understand the from_parameter hocus-pocus in this line (upload.xml):
<options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]">
The workaround which is used up to now is upload genbank sequences as txt format and change the format later via the history. But that is a 2-step operation, guess there should be a way taking only 1 step ?
Regards,
Marc
________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________ ___________________________________________________________ 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:
-- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
Hi Marc, You'll need to add the display_in_upload attribute to your local version of the datatypes_conf.xml file installed with your emboss_datatypes repository from the tool shed. This may result in a merge at some point if the contents of the datatypes_conf.xml file changes in the emboss_datatypes repository in the main tool shed and you pull the updates to your local repository. Greg Von Kuster On Aug 3, 2012, at 10:51 AM, Marc Logghe wrote:
Hi Björn, I think the issue is that the genbank datatype is coming in via the tool shed and is not taken into account by the upload tool. The genbank datatype is defined in shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml
I have added the display_in_upload attribute in the latter file for the genbank datatype, restarted Galaxy but the type did not appear in the selection. Should the genbank datatype be added to the main galaxy datatypes_conf.xml ? Or is it better to explicitly add the emboss' datatypes_conf.xml to the universe_wsgi.ini (but this will break the tool shed update system, right) ?
Thanks, Marc
-----Original Message----- From: Björn Grüning [mailto:bjoern.gruening@pharmazie.uni-freiburg.de] Sent: Friday, August 03, 2012 4:14 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload File: how to see all registered formats ?
Hi Marc,
please have a look at the datatypes_conf.xml file in your galaxy directory.
There should be something like that: <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/>
Try to add 'display_in_upload="true"' to the genbank datatype.
The 'good' solution would be to define a datatype genbank, with a sniff function, so that galaxy can guess the filetype when you are uploading it.
Please find attached my first attempt for that. Im working on some datatypes and converteres, but its not ready yet :(
Cheers, Bjoern
Hi again,
Emboss_datatypes is installad via tool shed. The ‘View datatypes registry’ in the Adminstration page, shows all registered data types, including the emboss ones, like e.g. genbank.
However, the ‘Upload File’ tool does not show genbank in the ‘File Format’ dropdown. How can one configure the upload1 tool so that all registered formats are listed ?
I don’t understand the from_parameter hocus-pocus in this line (upload.xml):
<options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]">
The workaround which is used up to now is upload genbank sequences as txt format and change the format later via the history. But that is a 2-step operation, guess there should be a way taking only 1 step ?
Regards,
Marc
________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________ ___________________________________________________________ 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:
-- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br.
Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
___________________________________________________________ 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:
Hi Greg,
You'll need to add the display_in_upload attribute to your local version of the datatypes_conf.xml file installed with your emboss_datatypes repository from the tool shed.
I'am afraid this does not work. At least not in my hands. Like I indicated before, it seems like the upload tool does not take the tool shed emboss_datatypes into account, with or without the display_in_upload attribute set. It seems to work only if you transfer the entire data type definition line to the main galaxy datatypes_conf.xml That is the workaround I currently use. Marc
This may result in a merge at some point if the contents of the datatypes_conf.xml file changes in the emboss_datatypes repository in the main tool shed and you pull the updates to your local repository.
Greg Von Kuster
Hi Björn, I think the issue is that the genbank datatype is coming in via the tool shed and is not taken into account by the upload tool. The genbank datatype is defined in shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml
I have added the display_in_upload attribute in the latter file for the genbank datatype, restarted Galaxy but the type did not appear in the selection. Should the genbank datatype be added to the main galaxy datatypes_conf.xml ? Or is it better to explicitly add the emboss' datatypes_conf.xml to the universe_wsgi.ini (but this will break the tool shed update system, right) ?
Thanks, Marc
________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
Hello Marc, This issue has been resolve din change set 7491:a7a0a5962648, which will be included in the next Galaxy release. It is also currently available in the Galaxy central repository in case you track that repository. The datatypes registry will load any changes you've made to the datatypes_conf.xml file installed with the emboss_datatypes tool shed repository (or any other repository that includes this file). SO display_in_upload will now function correctly for the installed proprietary datatypes. Thanks for reporting this issue, and sorry for the inconvenience. Greg Von Kuster On Aug 3, 2012, at 4:53 PM, Marc Logghe wrote:
Hi Greg,
You'll need to add the display_in_upload attribute to your local version of the datatypes_conf.xml file installed with your emboss_datatypes repository from the tool shed.
I'am afraid this does not work. At least not in my hands. Like I indicated before, it seems like the upload tool does not take the tool shed emboss_datatypes into account, with or without the display_in_upload attribute set.
It seems to work only if you transfer the entire data type definition line to the main galaxy datatypes_conf.xml That is the workaround I currently use.
Marc
This may result in a merge at some point if the contents of the datatypes_conf.xml file changes in the emboss_datatypes repository in the main tool shed and you pull the updates to your local repository.
Greg Von Kuster
Hi Björn, I think the issue is that the genbank datatype is coming in via the tool shed and is not taken into account by the upload tool. The genbank datatype is defined in shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml
I have added the display_in_upload attribute in the latter file for the genbank datatype, restarted Galaxy but the type did not appear in the selection. Should the genbank datatype be added to the main galaxy datatypes_conf.xml ? Or is it better to explicitly add the emboss' datatypes_conf.xml to the universe_wsgi.ini (but this will break the tool shed update system, right) ?
Thanks, Marc
________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
Hi Greg, That is great, I`ll give it a try. Thank a lot, Marc ________________________________________ From: Greg Von Kuster [greg@bx.psu.edu] Sent: Tuesday, August 14, 2012 10:38 PM To: Marc Logghe Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload File: how to see all registered formats ? Hello Marc, This issue has been resolve din change set 7491:a7a0a5962648, which will be included in the next Galaxy release. It is also currently available in the Galaxy central repository in case you track that repository. The datatypes registry will load any changes you've made to the datatypes_conf.xml file installed with the emboss_datatypes tool shed repository (or any other repository that includes this file). SO display_in_upload will now function correctly for the installed proprietary datatypes. Thanks for reporting this issue, and sorry for the inconvenience. Greg Von Kuster On Aug 3, 2012, at 4:53 PM, Marc Logghe wrote:
Hi Greg,
You'll need to add the display_in_upload attribute to your local version of the datatypes_conf.xml file installed with your emboss_datatypes repository from the tool shed.
I'am afraid this does not work. At least not in my hands. Like I indicated before, it seems like the upload tool does not take the tool shed emboss_datatypes into account, with or without the display_in_upload attribute set.
It seems to work only if you transfer the entire data type definition line to the main galaxy datatypes_conf.xml That is the workaround I currently use.
Marc
This may result in a merge at some point if the contents of the datatypes_conf.xml file changes in the emboss_datatypes repository in the main tool shed and you pull the updates to your local repository.
Greg Von Kuster
Hi Björn, I think the issue is that the genbank datatype is coming in via the tool shed and is not taken into account by the upload tool. The genbank datatype is defined in shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml
I have added the display_in_upload attribute in the latter file for the genbank datatype, restarted Galaxy but the type did not appear in the selection. Should the genbank datatype be added to the main galaxy datatypes_conf.xml ? Or is it better to explicitly add the emboss' datatypes_conf.xml to the universe_wsgi.ini (but this will break the tool shed update system, right) ?
Thanks, Marc
________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
participants (3)
-
Björn Grüning -
Greg Von Kuster -
Marc Logghe