Re: [galaxy-dev] Fwd: 'UsesFormDefinitions' is not defined
Hi Scott and Hans-Rudolf, thank you both for your efforts. The fix works perfectly. Alex 2012/10/18 Hans-Rudolf Hotz > Hi Scott > > Thank you very much for your quick reply! > > after fixing (ie replacing "galaxy.web.controllers.**library_common" with > "galaxy.webapps.galaxy.**controllers.library_common") in the following > four files: > > ~/templates/library/common/**library_dataset_search_**results.mako >ldda_info.mako >browse_library_opt.mako >browse_library.mako > > > it works! - both on the fresh install and the upgraded server > > > @Alex: I hope this solves your problem as well. > > > > Regards Hans-Rudolf > > > Than > > > On 10/18/2012 06:12 PM, Scott McManus wrote: > >> >> This was fixed in galaxy-central last week and should be part of >> galaxy-dist. What happened is that controllers were migrated and a >> couple of modules were left out. See changeset 210c39f4bf7f or later, >> which I believe was fixed on October 4th. >> >> In particular, the problem you're seeing had to do with the >> templates/library/common/**library_common.mako pointing to >> galaxy.web.controllers.**library_common instead of >> galaxy.webapps.galaxy.**controllers.library_common. >> A few other files had also been affected. >> >> -Scott >> >> - Original Message - >> >>> Hi Alex >>> >>> I am in the same situation, updating our galaxy servers to the "Oct >>> 5th" >>> release (changeset: 7824:b5bda7a5c345), and I have encountered the >>> same >>> problem. I guess, there are actually two problems: >>> >>> >>> First problem - this happens with a fresh install: >>> ==** >>> >>> I can't create a library at all, I get the following error message: >>> >>> Error attempting to display contents of library (foo): No >>> module named controllers.library_common. >>> >>> >>> >>> There have been a few commits on "library_common.py" over the last >>> few >>> days, which might solve this problem.? >>> >>> >>> >>> Second problem - this happens after upgrading an existing >>> installation >>> ==**==** >>> == >>> >>> Like the situation you reported earlier this morning, I get: >>> >>> >>> Error attempting to display contents of library (haruhotz): >>> name 'UsesFormDefinitions' is not defined. >>> >>> >>> I manage to track down the problem to the fact that >>> >>> in the old version, we've had >>> >>> ~/lib/galaxy/web/controllers/ >>> >>> >>> which apparently has been replaced by >>> >>> ~/lib/galaxy/webapps/galaxy/**controllers/ >>> >>> >>> if I remove ~/lib/galaxy/web/controllers/ >>> >>> >>> I get a new error: >>> >>> Error attempting to display contents of library (haruhotz): No >>> module named library_common. >>> >>> >>> which is very similar to the error you get with a fresh install >>> >>> >>> Obviously, old stuff (ie ~/lib/galaxy/web/controllers/) is still used >>> after the upgrade. >>> >>> >>> Sorry, no solution yet, but maybe it helps the developers to track >>> down >>> the problem and help us getting the servers running again. >>> >>> >>> >>> Regards Hans-Rudolf >>> >>> >>> On 10/18/2012 10:48 AM, Alexander Graf wrote: >>> >>>> Hi, >>>> yesterday I updated Galaxy to the latest revision and now it is not >>>> possible to access any Data Libraries or to create a new one. >>>> Galaxy shows me a read box with following error message: >>>> >>>> *Error attempting to display contents of library >>>> (100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not >>>> defined.* >>>> >>>> The log file message is: >>>> >>>> /"GET >>>> /galaxy/library_common/browse_**library?sort=name&webapp=** >>>> galaxy&f-descripti
[galaxy-dev] Fwd: 'UsesFormDefinitions' is not defined
Hi, yesterday I updated Galaxy to the latest revision and now it is not possible to access any Data Libraries or to create a new one. Galaxy shows me a read box with following error message: *Error attempting to display contents of library (100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not defined.* The log file message is: *"GET /galaxy/library_common/browse_library?sort=name&webapp=galaxy&f-description=All&f-name=All&page=1&cntrller=library&show_item_checkboxes=false&async=false&operation=browse&id=9d04ee723dc2cac7 HTTP/1.1" 302 - " http://x.x.x.x/galaxy/library/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%100326_HWUSI-EAS632R_0002%29%3A+name+__sq__UsesFormDefinitions__sq__+is+not+defined."; "Mozilla/5.0 (X11; Linux x86_64) * Any ideas how to solve this problem or were to start troubleshooting? Thank you in advance Alex ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Error viewing BAM files in IGV
Hello,
I have recently updated our Galaxy dist and I'm running into problems
viewing BAM files in IGV (v2.0.22), saying: Invalid GZIP header.
I have configured the Apache as explained in the Wiki using this *http.conf*
:
ServerName 127.0.0.1
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*)
/opt/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*)
/opt/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /opt/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /opt/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /opt/galaxy/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P]
http://localhost:8081>
Order deny,allow
Allow from all
# Define the authentication method
XSendFile on
XSendFilePath /
# Compress all uncompressed content.http.conf
SetOutputFilter DEFLATE
SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
ExpiresActive On
ExpiresDefault "access plus 6 hours"
By having this parts changed in *universe_wsgi.ini*:
[server:main]
use = egg:Paste#http
port = 8081
host = 0.0.0.0
use_threadpool = True
[filter:gzip]
use = egg:Paste#gzip
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy
[app:main]
paste.app_factory = galaxy.web.buildapp:app_factory
filter-with = proxy-prefix
cookie_path = /galaxy
apache_xsendfile = True
upstream_gzip = False
The resulting *Galaxy error log* is:
-
galaxy.web.framework DEBUG 2011-12-09 12:32:08,825 Error: this request
returned None from get_history(): http://10.153.182.203/galaxy/root
10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "GET
/galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam.bai&dataset_id=9b0f702d0207cd78
HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM
Java/1.6.0_22"
10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD
/galaxy/display_application/9b0f702d0207cd78/igv_bam/local_default/c9a3f3a19e75965d/data/galaxy_9b0f702d0207cd78.bam
HTTP/1.1" 302 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM
Java/1.6.0_22"
galaxy.web.framework DEBUG 2011-12-09 12:32:08,915 Error: this request
returned None from get_history(): http://10.153.182.203/galaxy/root
10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD
/galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam&dataset_id=9b0f702d0207cd78
HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM
Java/1.6.0_22"
Exception happened during processing of request from ('127.0.0.1', 52683)
Traceback (most recent call last):
File "/opt/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line
1053, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__
self.finish()
File "/usr/lib/python2.6/SocketServer.py", line 661, in finish
self.wfile.flush()
File "/usr/lib/python2.6/socket.py", line 297, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
---
Thanks in advance for your help
Alex
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in your mail client. To manage your subscriptions to this
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[galaxy-dev] Error viewing BAM files in IGV
Hello,
I have recently updated our Galaxy dist and I'm running into problems
viewing BAM files in IGV (v2.0.22), saying: Invalid GZIP header.
I have configured the Apache as explained in the Wiki using this *http.conf*
:
ServerName 127.0.0.1
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*)
/opt/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*)
/opt/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /opt/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /opt/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /opt/galaxy/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P]
http://localhost:8081>
Order deny,allow
Allow from all
# Define the authentication method
XSendFile on
XSendFilePath /
# Compress all uncompressed content.http.conf
SetOutputFilter DEFLATE
SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
ExpiresActive On
ExpiresDefault "access plus 6 hours"
By having this parts changed in *universe_wsgi.ini*:
[server:main]
use = egg:Paste#http
port = 8081
host = 0.0.0.0
use_threadpool = True
[filter:gzip]
use = egg:Paste#gzip
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy
[app:main]
paste.app_factory = galaxy.web.buildapp:app_factory
filter-with = proxy-prefix
cookie_path = /galaxy
apache_xsendfile = True
upstream_gzip = False
The resulting *Galaxy error log* is:
-
galaxy.web.framework DEBUG 2011-12-09 12:32:08,825 Error: this request
returned None from get_history(): http://10.153.182.203/galaxy/root
10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "GET
/galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam.bai&dataset_id=9b0f702d0207cd78
HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM
Java/1.6.0_22"
10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD
/galaxy/display_application/9b0f702d0207cd78/igv_bam/local_default/c9a3f3a19e75965d/data/galaxy_9b0f702d0207cd78.bam
HTTP/1.1" 302 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM
Java/1.6.0_22"
galaxy.web.framework DEBUG 2011-12-09 12:32:08,915 Error: this request
returned None from get_history(): http://10.153.182.203/galaxy/root
10.163.241.110 - - [09/Dec/2011:12:32:08 +0200] "HEAD
/galaxy/root?app_action=data&user_id=c9a3f3a19e75965d&app_name=igv_bam&link_name=local_default&action_param=galaxy_9b0f702d0207cd78.bam&dataset_id=9b0f702d0207cd78
HTTP/1.1" 200 - "-" "IGV Version 2.0.22 (1360)11/29/2011 02:24 PM
Java/1.6.0_22"
Exception happened during processing of request from ('127.0.0.1', 52683)
Traceback (most recent call last):
File "/opt/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line
1053, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__
self.finish()
File "/usr/lib/python2.6/SocketServer.py", line 661, in finish
self.wfile.flush()
File "/usr/lib/python2.6/socket.py", line 297, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
---
Thanks in advance for your help
Alex
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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[galaxy-dev] Display BAM with IGV
Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance Alex INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bamNULL content-length at org.broad.igv.util.SeekableHTTPStream.(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75) at org.broad.igv.sam.AlignmentDataManager.(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bamNULL content-length ___ Alexander Graf Laboratory of Functional Genome Analysis Gene Center, University of Munich (LMU) Feodor-Lynen-Strasse 25; 81377 Munich; Germany email: g...@lmb.uni-muenchen.de Internet: www.lafuga.de/genomics.htm ___ ___ 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/
