Re: [galaxy-dev] In which Encryption form does Galaxy store password?
Its hashed (sha1) and you can not reverse the hash. Storing passwords in a reversible manner is bad practice. http://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/util/hash_util.html You could maybe authenticate your users from the other program with the same method against the hashed passwords. best, ido On Jan 7, 2013, at 12:43 PM, Sachit Adhikari wrote: Hi, In which encryption galaxy store the password? It's really urgent. I want to decode the password and use in the other program. Thanks ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] fastq_combiner
Hello, The tool you are looking for is: galaxy-dist / tools / fastq / fastq_combiner.py galaxy-dist / tools / fastq / fastq_combiner.xml Hopefully this helps. Next time, please be sure to send questions directly to the galaxy-...@bx.psu.edu email address. Your question went to galaxy-dev-ow...@lists.bx.psu.edu originally, which is not the mailing list, but a way to reach the list moderators if there is a technical problem. Take care, Jen Galaxy team On 1/7/13 3:09 AM, wei liu wrote: Dear all, I have used the local galaxy, and I want to find out which script is used to Combine FASTA and QUAL https://main.g2.bx.psu.edu/tool_runner?tool_id=fastq_combiner into FASTQ. I have tried the scripts in galaxy-dist/tools/next_gen_conversion/solid2fastq.py, but it can not merge the several lines which belong to the same sequence. Looking forward for your reply! Best Regards, Wei Liu. -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] (no subject)
Security warning: DO NOT CLICK on the link in this thread. Rehan Saleem - it is likely that your original sending hotmail email account has been compromised. We have removed it from the galaxy-...@bx.psu.edu mailing list to prevent further unmoderated posts until the problem is cleared. Contacting your local system administrator for help is one place to start. Anyone who did click on the link already should do the same, as this is usually how such viruses spread, although much depends on OS and other factors. Good luck! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Stumped by GridOperation
Ted, have you considered if you can do what you need with the 'allowed' method of GridOperation? It let's you define a callable condition that determines if that operation is allowed on a given item. It does not have access to trans but it would be reasonable to add that. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Mon, Jan 7, 2013 at 2:55 AM, Ted Goldstein t...@soe.ucsc.edu wrote: HI Greg, I thought of this. But there is potential bug in it which has security implications. Though it is a low probability event, I have seen this sort of leakage happen in other environments where user data was stuck into globally shared objects. The grid object is shared by all requests. You are storing user specific data in the GridOperation. So if there is an unfortunate context switch in the middle of the setting the ids int the grid operation but before they are used, the user specific data of one user will be visible to the other user. Of course the solution is to make sure the grid is not shared (e.g. it is instantiated or deep-copied) in the function or at least in the request thread that uses it. Thanks, I will do this with on a deepcopy of the Grid to ensure that it doesn't et shared between threads. You might want to chsnge the code in repository.py Best regards, Ted On Jan 6, 2013, at 4:12 PM, Greg Von Kuster wrote: Hi Ted, If I understand what your trying to do, I believe I've implemented grid operations similar to what your attempting in several places in the Galaxy tool shed, so checking the various grid classes and associated methods in /lib/galaxy/webapps/community/controllers will give you some examples. The trick is that you need to define the grid operations outside of the grid class itself, but in the method that calls the grid (but just before the call to display it) so the request parameters will include the selected page ids. For an example of what I'm talking about, see the following method on about line #740 in my ~/lib/galaxy/webapps/community/controllers/repository.py code file. Here is the relevant snippet of code. def browse_valid_repositories( self, trans, **kwd ): ...irrelevant code not displayed... repository_id = None for k, v in kwd.items(): changset_revision_str = 'changeset_revision_' if k.startswith( changset_revision_str ): repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) if repository.tip( trans.app ) != v: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), changeset_revision=v ) ) url_args = dict( action='browse_valid_repositories', operation='preview_tools_in_changeset', repository_id=repository_id ) self.valid_repository_grid.operations = [ grids.GridOperation( Preview and install, url_args=url_args, allow_multiple=False, async_compatible=False ) ] return self.valid_repository_grid( trans, **kwd ) Sorry if I misunderstood your dilemma and this does not help you. Greg Von Kuster On Jan 6, 2013, at 4:52 PM, Ted Goldstein wrote: Hi, Based on a suggestion by James Taylor, I am working on extending the security model so that pages can use the same RBAC permission system used in libraries. In fact, many of my pages have assets (images, etc) which are stored in a library. So this is a natural model. Therefore I want to make a connection between Pages and Libraries. that is visible to the user and extends the security model of page access. The owner of the page essentially grants anyone with access to a library access to the page as well. This part is going well. It is few lines of code in the page access security code. The implementation is to that I created a many-to-many relationship table LibraryPageAssociation, that Connects Page objects to Library Objects. Grid objects provide a convenient interface to selecting multiple of each. In fact, I just extend the regular PageListGrid instantiated by the /page/list action to select the pages by adding a new GridOperation labeled Select Libraries which then brings up new Grid LibrarySelectGrid (similar to the one visualization.py, but simpler) it has one GridOperation labeled Connect Pages to Libraries (allows_multi=True). Here is the problem: I can pass the page ids (enoded) into the mako page that carries the LibrarySelectGrid. But I don't see a way to parametriize Connect Pages to Libraries GridOperation to pass anything out of the page except the Grid Sttate itself. Do I have to extend GridOperation or am I missing something? I have tried a number of things with url_args and
Re: [galaxy-dev] user creation using API
I am pretty confident there is no way to do this via the API currently, though I imagine it wouldn't be terribly complicated to add and the community would appreciate the contribution. If API-based access isn't a strong requirement and you have direct access to the Galaxy server here is a script-template I have used to automatically create users: https://gist.github.com/4475646 The above gist is probably enough to get going, but here is the full context of how I create such a file if that is of interest: https://github.com/jmchilton/cloudbiolinux/blob/deploy/cloudbio/deploy/galaxy.py -John On Mon, Jan 7, 2013 at 3:37 AM, Hagai Cohen haga...@gmail.com wrote: Hi, I would like to auto create users on my local Galaxy instance. I saw that in the create user on the API, I should enable use_remote_user (which as I understand means that I have to use Apache or nginx). Is there another way besides using Apache to create users automatically? Thanks, Hagai ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] backtrace when attempting to view a shared workflow
Hi Brad, Thanks for reporting this issue. I've committed what I hope is a fix for your issue in changeset 8527:eb4dac39eed5 in galaxy-central. Once you are able to apply these changes, would you mind letting us know if this resolves your broken workflows? Thanks for using Galaxy, Dan On Jan 7, 2013, at 9:11 AM, Langhorst, Brad wrote: I've recently updated to the december 20th revision of galaxy and still have a problem with a few workflows. You can find the backtraces below. based on these I'm starting to look in /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py - but any hints would be appreciated. thanks Brad here's a backtrace from an attempt to edit the problem workflow Error - type 'exceptions.TypeError': 'NoneType' object is unsubscriptable URL: http://galaxy.neb.com/workflow/load_workflow?id=4280bfc7d7999071_=1357567007122 File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 73 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 676 in load_workflow module = module_factory.from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 402 in from_workflow_step return self.module_types[type].from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 217 in from_workflow_step module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2130 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', line 94 in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', line 444 in value_from_basic current_case = rval['__current_case__'] = value['__current_case__'] TypeError: 'NoneType' object is unsubscriptable here's one attempting to run it File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 1473 in run step.module = module_factory.from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 402 in from_workflow_step return self.module_types[type].from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 217 in from_workflow_step module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2130 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', line 94 in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', line 444 in value_from_basic current_case = rval['__current_case__'] = value['__current_case__']
Re: [galaxy-dev] Uploading large files to history through API (some random thoughts)
The pull request for this patch is still on the queue. Is anything
happening with this?
Kyle
On Tue, Nov 27, 2012 at 8:56 AM, John Chilton chil...@msi.umn.edu wrote:
I went down something of a rabbit hole last night, I thought that
uploading files through the API using multipart/form-data worked. It
is only at the very end of my adventure that I realized it only works
for libraries uploads. I think it would be great to get that working
to histories as well. I cannot spend much more time on this right now
(I thought I only needed to spend an hour to implement the client side
stuff), but I thought I would post the progress I made here in case
someone wants to take up the fight someday:
The first thing is that when issuing multipart/form-data requests,
inputs are not currently being deserialized from JSON (so for instance
in the tools api code the inputs variable would be the string
containing the json, not the python dictionary).
To bring multipart/form-data requests in line with other content
requests I modified this in ilb/galaxy/web/framework/__init__.py
payload = kwargs.copy()
named_args, _, _, _ = inspect.getargspec(func)
for arg in named_args:
payload.pop(arg, None)
with this:
payload = kwargs.copy()
named_args, _, _, _ = inspect.getargspec(func)
for arg in named_args:
payload.pop(arg, None)
for k, v in payload.iteritems():
if isinstance(v, (str, unicode)):
try:
payload[k] = simplejson.loads(v)
except:
# may not actually be json, just continue
pass
payload =
util.recursively_stringify_dictionary_keys( payload )
One could also imagine doing this replacement in the tools api
controller directly on payload['input'] instead.
After that change, files still weren't being matched up with inputs
properly:
This debug statement I added to upload_common.py, demonstrates that
file_data is None.
galaxy.tools.actions.upload_common INFO 2012-11-27 00:22:17,585
Uploaded datasets is {'NAME': u'galxtest694734465387762969.txt',
'file_data': None, 'space_to_tab': None, 'url_paste': None,
'__index__': 0, 'ftp_files': None}
To address this, the files_*|file_data parameters need to be moved
inside of the inputs dict.
That means in lib/galaxy/webapps/galaxy/api/tools.py, changing this:
inputs = payload[ 'inputs' ]
To this:
inputs = payload[ 'inputs' ]
for k, v in payload.iteritems():
if k.startswith(files_):
inputs[k] = v
Then the debug line becomes this:
galaxy.tools.actions.upload_common INFO 2012-11-27 00:33:15,168
Uploaded datasets is {'NAME': u'galxtest2484272839208214846.txt',
'file_data': FieldStorage('files_0|file_data',
u'galxtest2484272839208214846.txt'), 'space_to_tab': None,
'url_paste': None, '__index__': 0, 'ftp_files': None}
Which matches pretty well with the same line coming from a web browser
request:
galaxy.tools.actions.upload_common INFO 2012-11-27 00:23:57,590
Uploaded datasets is {'NAME': u'', 'file_data':
FieldStorage('files_0|file_data', u'second_step.png'), 'space_to_tab':
None, 'url_paste': u'', '__index__': 0, 'ftp_files': None}
These changes aside I still wasn't it sill didn't work, that is why
this is a rambling e-mail and not a pull request. I got this exception
http://pastebin.com/hhs1pjtP. I guess something to do with the session
handling stuff being different between API calls and normal web calls.
Anyway, I've inspected the actual requests I was generating and I
think they are reasonable, Galaxy just needs to be augmented to accept
them :). If someone does land up taking a look at this, I have
committed my test case to blend4j so it can be used to really quickly
test such a client request (requires git, Java, and maven):
% git checkout g...@github.com:jmchilton/blend4j.git
% cd blend4j
% mvn test -Dtest=ToolsTest
-Dtest.galaxy.instance=http://localhost:8080/
-Dtest.galaxy.key=testapikey
Thanks,
-John
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Transfer Manager
I'm trying to figure out if I can do this all through the API (so I can skip setting up FTP servers and sharing database servers). I can scan one system, and initiate downloads on the destination system (using upload1). So as far as moving files from one machine to another, it should be fine. I could push all the data, with correct names, annotations and tags. But then it becomes a matter of the pushing the metadata onto the object on the destination system. But there are two problems, 1) No way to push tool info and input parameter data, everything would be a product of 'upload1'. 2) No global IDs. If I try to sync a second time, it may be difficult to figure out which elements have been previously pushed. Comparing names could lead to problems... Kyle On Fri, Jan 4, 2013 at 4:54 AM, Rémy Dernat remy...@gmail.com wrote: Hi, A good practise is to create a ftp server http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP and use a tool to send / retrieve informations to this ftp server : http://toolshed.g2.bx.psu.edu/ - Data Source / data_nfs Then export your ftp directory by NFS to your galaxy installations. For databases, it is a little bit complex. If you have a database server, you could share access to a single database, but your installation between your server should be the same, and all working directories must be shared with NFS on all galaxy servers... Regards 2012/12/6 Kyle Ellrott kellr...@soe.ucsc.edu Is there any documentation on the transfer manager? Is this a mechanism that I could use to synchronize data libraries between two different Galaxy installations? Kyle ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Stumped by GridOperation
Hi Greg and James,
This has become a plumbing project. What starts off as fixing a leaky faucet
ends being a $200 bill replacing the entire sink ;-). But I don't see anyway
around it.
Yes, there is a lot of power in the allowed method since it uses a function or
a lambda. There are two problems with this: idea (1) it feels wrong to have a
predicate method called allowed modify the state of the object.
and worse,(2) the Python context that the lambda is capturing is at global
instantiation time. But the data that I need captured and saved in the page
exist only after the user has made a set of choices. Thus it only exists in a
previous call to thePage.list() method.
Another problem.
Since this is a multi operation, the state that needs to be passed cannot go
into the form URL itself of the form. I see that the call to get the URL of
the form in grid_base.mako at line 702 does not take any operation arguments.
Which is correct. Normally the submit button on an HTML form does not modify
the form's URL The usual solution from an HTML perspective is to have hidden
input fields on an HTML form. So the solution would be to extend the Grid
class to generate and use hidden input fields. This would be done on a copy
of the grid object;. So there needs to be a new Grid method.
(my changes in bold)
class Grid
...
def clone_with_pass_through_data(self, data_dict):
# make a copy of myself for use in passing though data
clone = deepcopy(self)
clone.pass_through_data = data_dict
return clone
my example use in Page.list()
# Clone a copy of grid to have the pageids.
grid =
self._libraries_selection_grid.clone_with_pass_through_data({pageids:
pageidsraw});
return trans.fill_template(
page/library_datasets_select_grid.mako, pagetitles=pagetitles, grid=grid,
**kwargs)
pass_through_data has a three line implementation in grid_base.mako
form action=${url()} method=post onsubmit=return false;
input type=hidden name=webapp value=${webapp}/
%for pass_name, pass_value in grid.pass_through_data.items():
input type=hidden name=${pass_name} value=${pass_value}/
%endfor
..
But nothing is simple, form parameters arguments are more complex than they
sem at first.
function go_to_URL() {
// Not async request.
url_args['async'] = false;
// Build argument string.
var arg_str = ;
for (var arg in url_args) {
arg_str = arg_str + arg + = + url_args[arg] + ;
}
// add in hidden fields
$('input[type=hidden]').each(function() {
if (this.name == webapp || this.name == select_all_checkbox)
return
else
arg_str = arg_str + this.name + = + this.value + ;
})
// Go.
window.location = encodeURI( ${h.url_for()}? + arg_str );
}
What do you think of this idea?
Ted
On Jan 7, 2013, at 7:00 AM, James Taylor wrote:
Ted, have you considered if you can do what you need with the 'allowed'
method of GridOperation? It let's you define a callable condition that
determines if that operation is allowed on a given item. It does not have
access to trans but it would be reasonable to add that.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Jan 7, 2013 at 2:55 AM, Ted Goldstein t...@soe.ucsc.edu wrote:
HI Greg,
I thought of this. But there is potential bug in it which has security
implications. Though it is a low probability event, I have seen this sort of
leakage happen in other environments where user data was stuck into globally
shared objects. The grid object is shared by all requests. You are storing
user specific data in the GridOperation. So if there is an unfortunate
context switch in the middle of the setting the ids int the grid operation
but before they are used, the user specific data of one user will be visible
to the other user. Of course the solution is to make sure the grid is not
shared (e.g. it is instantiated or deep-copied) in the function or at least
in the request thread that uses it.
Thanks, I will do this with on a deepcopy of the Grid to ensure that it
doesn't et shared between threads. You might want to chsnge the code in
repository.py
Best regards,
Ted
On Jan 6, 2013, at 4:12 PM, Greg Von Kuster wrote:
Hi Ted,
If I understand what your trying to do, I believe I've implemented grid
operations similar to what your attempting in several places in the Galaxy
tool shed, so checking the various grid classes and associated methods in
/lib/galaxy/webapps/community/controllers will give you some examples.
The trick is that you need to define the grid operations outside of the grid
class itself, but in the method that calls the grid
[galaxy-dev] Galaxy submitting jobs to remote cluster
Hello: I am trying to configure Galaxy to submit jobs to a remote cluster (specifically, an XSEDE resource to which I don't have administrative access). I'm familiar with LWR and have read another response about configuring the Galaxy host as a PBS submit host. What is the best approach to accomplish what I'm after? I have experimented with the cli job runner with the SecureShell and Torque plugins. With some minimal modifications, I can run jobs via this mechanism, but file staging fails. I haven't looked into the details of the staging failure yet. Is this a viable approach? Is the cli job runner supported? (the universe_wsgi.ini file says available job runners include pbs and drmaa) I've found a similar question on the galaxy-dev mailing list, with mention of some relevant recent work: http://dev.list.galaxyproject.org/Remote-Job-Submission-from-Local-Install-td4655144.html What is the status of the work referenced in that post? Thanks, Tom Uram ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] File import recovery
Editing the DB and manually fixing all the errors in the UI doesn't seem like a long term solution. Is there a way to do this through the API? If not, where should I start working to add it in? Kyle On Wed, Jan 2, 2013 at 7:41 AM, Nate Coraor n...@bx.psu.edu wrote: On Dec 31, 2012, at 8:18 PM, Kyle Ellrott wrote: I'm currently adding a large number of files into my Galaxy instance's dataset library. During the import some of the files (a small percentage) failed with: /inside/depot4/galaxy/set_metadata.sh: line 4: 14790 Segmentation fault (core dumped) python ./scripts/set_metadata.py $@ I think it's probably standard cluster shenanigans, and may work just fine if run again. But there doesn't seem to be a way retry. Is there a way to deal with this that is easier than manually deleting and re-uploading the offending files? Hi Kyle, Unfortunately, there's not going to be a way to do this entirely in the UI. Your best shot is to change the state of the datasets in the database from 'error' to 'ok' and then try using the metadata auto-detect button in the UI. --nate Kyle ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Tool tests
Hi, I hope I'm writing to the right area (if not, please point me in the right direction and I'll go on my way). I have a set of tools that our team have built and been using for functional genomics analysis, which I would like to integrate into Galaxy. My first concern is with the tests. Our code is unit tested but one script is tasked with downloading gene sets from Ensembl. We have a local copy of much of the Ensembl DB (5TB worth) and even this is fairly slow to pull from (5-10 mins). Pulling from the publicly available Ensembl site would be horrifically slow. Since it's stated here: http://wiki.galaxyproject.org/Admin/Tools/Writing%20Tests that functional tests are required, I'm looking for suggestions as to how to meet this requirement without taking up an hour of the test runner's time (for one tool). My second question is if a file is produced by a script and given a specific name based on its inputs, how should I (if at all) define the output of this script. My last question is how much functional testing is required?. I have a script here whose job is to produce plots of data. There are about 30 command-line options and many of these have multiple choices available to them. Do I need to provide functional tests for every one of these? I can imagine having to provide 100 PNG files to compare my output again I have searched for answers to the above (made much more tricky thanks to Samsung), I don't wish to waste anyone's time. Many thanks in advance, Cameron ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] variables not defined
These bugs have been fixed in our development repository (galaxy-central) and will be available in the next distribution, which should occur in the coming week. Thanks, J. On Jan 7, 2013, at 6:23 AM, MONJEAUD wrote: Hello all, I am using my own Galaxy instance and I had a problem with page and visualization tabs. For example, when I want to edit attributes of a page, I've got this error traceback : NameError: global name 'VALID_SLUG_RE' is not defined and when I want to remove or share a page or a visualization, I've got this one : NameError: global name 'util' is not defined To fix these errors, I added in the lib/galaxy/webapps/galaxy/controllers/page.py and lib/galaxy/webapps/galaxy/controllers/visualization.py these lines : from galaxy import util import re VALID_SLUG_RE = re.compile( ^[a-z0-9\-]+$ ) So, I want to know if you know these problems or if it's only for my instance of galaxy. Maybe some files (where these variables are defined) are not present in my own galaxy. Cheers, Cyril Monjeaud -- Cyril Monjeaud Equipe Symbiose / Plate-forme GenOuest Bureau D156 IRISA-INRIA, Campus de Beaulieu 35042 Rennes cedex, France Tél: +33 (0) 2 99 84 74 17 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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] anybody seen 403s after a recent upgrade?
galaxy.web.framework WARNING 2013-01-07 22:06:30,044 User logged in as '(null)' externally, but has a cookie as 'langho...@neb.commailto:langho...@neb.com' invalidating session 10.254.254.86 - - [07/Jan/2013:22:06:30 -0400] GET /api/histories/4c8cd68e0b9ed4a7 HTTP/1.1 403 - http://galaxy.neb.com/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:17.0) Gecko/20100101 Firefox/17.0 i did not observe this before today… but maybe I've screwed things up in my hg fiddling today. Did anybody else see this? manual refreshes work, but automatic ones don't Brad -- Brad Langhorst langho...@neb.commailto:langho...@neb.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/
