[galaxy-dev] How to add images/pictures into Galaxy Published Pages?
Hi, I am trying to create a page in Galaxy and want to add some pictures/ screenshots. So how could I do this? I clicked the image button but it needs a URL not the path from my local computer. 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/
Re: [galaxy-dev] How to add images/pictures into Galaxy Published Pages?
Hi Huayan, in your page-editor you have a picture symbol. As you mentioned you need to specify a path to an image. For my pages I created a history where I store all my pictures. Afterwards I copy the full URL of that picture to the page. So use galaxy to store you image collection :) Hope that helps, Bjoern Hi, I am trying to create a page in Galaxy and want to add some pictures/ screenshots. So how could I do this? I clicked the image button but it needs a URL not the path from my local computer. 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/ ___ 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] Serving Galaxy behind apache mod_security
On 11/03/13 23:20, Vipin TS wrote: On my new server machine I have configured apache server along with mod_security. Now I would like to place my Galaxy installation behind apache and is there any detailed explanation to describes the steps. I am following the galaxy wiki pagehttp://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy# and it is failing to invoke the page. Please share if you have an experience on the same. I have avoided experience with Galaxy and mod_proxy (and once again wonder why mod_wsgi wouldn't be a better and less complicated way of running Galaxy, but that's another issue), but I do have experience with mod_proxy and other solutions that need their own Web server, and I notice that the Wiki page doesn't contain any mention of SELinux. If you have everything set up appropriately, you may need to find out whether SELinux is enabled, because this may demand a small amount of additional configuration work. Paul ___ 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] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset
1 2: Very interesting then. I'll do some more digging as to why a query
would succeed (with the wrong record) with those ids.
3: Good!
4.1: That first line is just the beginning of the diff/patch file and not
something you have to enter. It records the command used to generate the
diff file. That revision was the revision I was updated to when generating
the patch and, since I was using a development version more recently
updated than your machine, your hg can't find it. There's no need to run
that line, tho (see 4.2).
4.2: If you want to import a patch in the future, I've had good luck with 'hg
import --no-commit mypatchfile.patch'. This will make the changes in the
patch file without committing them ('--no-commit'). If you want to remove
the changes later (and assuming you haven't made any other changes you want
to keep in that file) you can use 'hg revert thefilethatwaschanged.py'
and that will return the file to the previous state. Keep in mind, of
course, that patches (like any changes) may make updating, and/or merging
your instance later more difficult.
A question I forgot to ask: what database backend are you using
(postgresql, mysql, etc.)?
Carl
On Mon, Mar 11, 2013 at 12:34 PM, Jean-Francois Payotte
jean-francois.payo...@dnalandmarks.ca wrote:
Dear Dannon, John and Carl,
Thank you for your answers and for taking the time to help me solve this
issue.
Here are my answers to your questions:
1. I don't think our number of HDAs is large enough to cause an
overflow. From what I can see, the HDAs number in our two faulty galaxy
instances are:
galaxy_prod : 263,163 HDAs
galaxy_dev : 14,119 HDAs
2. Here is a list of hashed IDs for HDAs where I'm seeing this
behaviour:
(None of them are of 16-digit integers)
3. I've also tried applying John's patch on our development Galaxy
instance and so far, *it seems to do the trick*.
I've run my test tool (wich output a message to stderr) about 50
times, and the bug report always displayed the correct dataset. Yay!!
4. I would have two question though before applying the patch to our
production Galaxy instance:
1. If I run the below hg diff -r f25f3fee4da7
lib/galaxy/webapps/galaxy/controllers/dataset.py command, I receive the
following error:
*abort: unknown revision 'f25f3fee4da7'!*
Is this a normal behaviour? Are we missing something important?
2. Also, out of curiosity, is there a particular way to apply a
patch (like the one you sent me), or if I simply have to manually edit
the
file? (That's what I did.)
Thanks again for your help! This is greatly appreciated!
*Jean-Francois*
From:Carl Eberhard carlfeberh...@gmail.com
To:John Chilton chil...@msi.umn.edu
Cc:Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca,
galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Date:08/03/2013 06:07 PM
Subject:Re: [galaxy-dev] Strange issue where the dataset reported
in the bug report doesn't correspond to the current dataset
--
Hello,
We explored this for quite a while this afternoon and believe John is
correct about the location as well as the design decision.
It may be that the hashes generated in some instances will correctly parse
as 16 digit integers and, since an integer lookup is tried first (and you
may either have an extraordinary large number of HDAs or there is some
integer roll over/overflow - at a guess), the incorrect dataset is being
returned without attempting to decode the hash into the proper dataset.
This may also explain why it is consistent but intermittent.
I would be curious to see the hashed ids of the HDAs where you're seeing
this behavior. Can you provide some?
If the hash produces fully integer strings as we're (tentatively)
guessing, the if not str( id ).isdigit() may still branch improperly
unfortunately.
In any event and to John's last point, from what we can tell,
dataset.errors is only called from the new history panel and only encoded
ids are used there - so the backwards compatibility may not be needed at
this point.*
I will thoroughly check that that controller method isn't called elsewhere
with a raw id, but, in the meantime: Jean-Francois, can you apply the patch
below (and attached) to your more updated installation and (when
convenient) see if that helps?
*PS. if user's are still using the older history panel - please, do not
apply this patch as it relies on the older, raw ids for this function.
diff -r f25f3fee4da7 lib/galaxy/webapps/galaxy/controllers/dataset.py
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py Fri Mar 08 16:01:25
2013 -0500
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py Fri Mar 08 17:41:46
2013 -0500
@@ -171,14 +171,17 @@
@web.expose
def errors( self, trans, id ):
+hda = None
try:
-
Re: [galaxy-dev] Error Report contains STDERR from different job
Hey,I applied the patch and it does not help, instead I received a server error since hda was none. If it helps at all I am using mysql as my backend.-Eric-Carl Eberhard carlfeberh...@gmail.com wrote: -To: Jean-Francois Payotte jean-francois.payo...@dnalandmarks.caFrom: Carl Eberhard carlfeberh...@gmail.comDate: 03/08/2013 05:10PMCc: eric.e...@phac-aspc.gc.ca, "galaxy-...@bx.psu.edu" galaxy-...@bx.psu.eduSubject: Re: [galaxy-dev] Error Report contains STDERR from different jobHello,Does applying the patch from "[galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset" help? If not, we can diagnose further. Thanks,CarlOn Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca wrote: Dear Eric, I'm glad to know that I am not the only one having this bug. (Even though I would prefer if neither of us would have it). ;) I've already written twice to the galaxy mailing-list, but I didn't receive any answers so far. Let's hope someone will be able to help us solve this issue. You can see my mail thread here: http://dev.list.galaxyproject.org/Strange-issue-where-the-dataset-reported-in-the-bug-report-doesn-t-correspond-to-the-current-dataset-td4658707.html Best regards, Jean-Francois From: Eric Enns eric.e...@phac-aspc.gc.ca To: galaxy-...@bx.psu.edu Date: 08/03/2013 03:14 PM Subject: [galaxy-dev] Error Report contains STDERR from different job Sent by: galaxy-dev-boun...@lists.bx.psu.edu Hey, When clicking the "View or report this error button" the error message shown occasionally is from a different job. If you go into the info for the job you can select stderr and see the correct error. If the user submits the error to admins they receive the wrong error message and a link to the wrong history. -Eric ___ 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/ ___ 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] Error Report contains STDERR from different job
Hey,My bad I didn't see the patch and thought you had wanted me to revert to the Sept 12 release for that function. I now applied the patch, and am seeing the correct error when clicking the bug button. If I encounter any issue I will post back.-Eric-Carl Eberhard carlfeberh...@gmail.com wrote: -To: Eric Enns eric.e...@phac-aspc.gc.caFrom: Carl Eberhard carlfeberh...@gmail.comDate: 03/12/2013 10:15AMCc: "galaxy-...@bx.psu.edu" galaxy-...@bx.psu.edu, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.caSubject: Re: [galaxy-dev] Error Report contains STDERR from different jobThanks, EricSince the HDA is None, the if statement should be sending you the trans.show_error_message.Just to make sure we're on the same page, could you please attach or post the errors method from the dataset controller in your installation. It can be found at lib/galaxy/webapps/galaxy/controllers/dataset.py? CarlOn Tue, Mar 12, 2013 at 10:59 AM, Eric Enns eric.e...@phac-aspc.gc.ca wrote: The following is the stack trace I got when I applied the patch and clicked the bug icon. "GET /dataset/errors?id=c39bc73d0eae67dd HTTP/1.0" 500 - "http://galaxy/history"Error - type 'exceptions.AttributeError': 'NoneType' object has no attribute 'hid' URL: http://galaxy/dataset/errors?id=c39bc73d0eae67ddFile '/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 '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response)File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response)File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response )File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 in handle_request body = method( trans, **kwargs )File '/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 175 in errors return trans.fill_template( "dataset/errors.mako", hda=hda )File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 848 in fill_template return self.fill_template_mako( filename, **kwargs )File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 859 in fill_template_mako return template.render( **data )File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data)File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data))File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec _template(inherit, lclcontext, args=args, kwargs=kwargs)File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable _(context, *args, **kwargs)File '/galaxy-dist/database/compiled_templates/dataset/errors.mako.py', line 27 in render_body __M_writer(unicode(hda.hid))AttributeError: 'NoneType' object has no attribute 'hid'-Carl Eberhard carlfeberh...@gmail.com wrote: - To: Eric Enns eric.e...@phac-aspc.gc.caFrom: Carl Eberhard carlfeberh...@gmail.com Date: 03/12/2013 09:47AMCc: "galaxy-...@bx.psu.edu" galaxy-...@bx.psu.edu, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca Subject: Re: [galaxy-dev] Error Report contains STDERR from different jobCan you post the stack trace from the error, please?Thanks for the info,Carl On Tue, Mar 12, 2013 at 10:37 AM, Eric Enns eric.e...@phac-aspc.gc.ca wrote: Hey,I applied the patch and it does not help, instead I received a server error since hda was none. If it helps at all I am using mysql as my backend.-Eric-Carl Eberhard carlfeberh...@gmail.com wrote: - To: Jean-Francois Payotte jean-francois.payo...@dnalandmarks.caFrom: Carl Eberhard carlfeberh...@gmail.com Date: 03/08/2013 05:10PMCc: eric.e...@phac-aspc.gc.ca, "galaxy-...@bx.psu.edu" galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error Report contains STDERR from different jobHello,Does applying the patch from "[galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset" help? If not, we can diagnose further. Thanks,CarlOn Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca wrote: Dear Eric, I'm glad to know that I am not the only one having this bug. (Even though I would prefer if neither of us would have it). ;) I've already written twice to the galaxy mailing-list, but I didn't receive any answers so far. Let's hope someone will be able to help us solve this issue. You can see my mail thread here: http://dev.list.galaxyproject.org/Strange-issue-where-the-dataset-reported-in-the-bug-report-doesn-t-correspond-to-the-current-dataset-td4658707.html Best regards, Jean-Francois From: Eric Enns eric.e...@phac-aspc.gc.ca To: galaxy-...@bx.psu.edu Date:
Re: [galaxy-dev] Error Report contains STDERR from different job
Glad to hear it's working, Carl On Tue, Mar 12, 2013 at 11:47 AM, Eric Enns eric.e...@phac-aspc.gc.cawrote: Hey, My bad I didn't see the patch and thought you had wanted me to revert to the Sept 12 release for that function. I now applied the patch, and am seeing the correct error when clicking the bug button. If I encounter any issue I will post back. -Eric -Carl Eberhard carlfeberh...@gmail.com wrote: - To: Eric Enns eric.e...@phac-aspc.gc.ca From: Carl Eberhard carlfeberh...@gmail.com Date: 03/12/2013 10:15AM Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca Subject: Re: [galaxy-dev] Error Report contains STDERR from different job Thanks, Eric Since the HDA is None, the if statement should be sending you the trans.show_error_message. Just to make sure we're on the same page, could you please attach or post the errors method from the dataset controller in your installation. It can be found at lib/galaxy/webapps/galaxy/controllers/dataset.py? Carl On Tue, Mar 12, 2013 at 10:59 AM, Eric Enns eric.e...@phac-aspc.gc.cawrote: The following is the stack trace I got when I applied the patch and clicked the bug icon. GET /dataset/errors?id=c39bc73d0eae67dd HTTP/1.0 500 - http://galaxy/history; Error - type 'exceptions.AttributeError': 'NoneType' object has no attribute 'hid' URL: http://galaxy/dataset/errors?id=c39bc73d0eae67dd File '/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 '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 in handle_request body = method( trans, **kwargs ) File '/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 175 in errors return trans.fill_template( dataset/errors.mako, hda=hda ) File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 848 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 859 in fill_template_mako return template.render( **data ) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec _template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable _(context, *args, **kwargs) File '/galaxy-dist/database/compiled_templates/dataset/errors.mako.py', line 27 in render_body __M_writer(unicode(hda.hid)) AttributeError: 'NoneType' object has no attribute 'hid' -Carl Eberhard carlfeberh...@gmail.com wrote: - To: Eric Enns eric.e...@phac-aspc.gc.ca From: Carl Eberhard carlfeberh...@gmail.com Date: 03/12/2013 09:47AM Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca Subject: Re: [galaxy-dev] Error Report contains STDERR from different job Can you post the stack trace from the error, please? Thanks for the info, Carl On Tue, Mar 12, 2013 at 10:37 AM, Eric Enns eric.e...@phac-aspc.gc.cawrote: Hey, I applied the patch and it does not help, instead I received a server error since hda was none. If it helps at all I am using mysql as my backend. -Eric -Carl Eberhard carlfeberh...@gmail.com wrote: - To: Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca From: Carl Eberhard carlfeberh...@gmail.com Date: 03/08/2013 05:10PM Cc: eric.e...@phac-aspc.gc.ca, galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Error Report contains STDERR from different job Hello, Does applying the patch from [galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset help? If not, we can diagnose further. Thanks, Carl On Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca wrote: Dear Eric, I'm glad to know that I am not the only one having this bug. (Even though I would prefer if neither of us would have it). ;) I've already written twice to the galaxy mailing-list, but I didn't receive any answers so far. Let's hope someone will be able to help us solve this issue. You can see
[galaxy-dev] redirection vulnerability via URL injection
Hello dev-members, We are trying to place our public Galaxy instancehttp://galaxy.raetschlab.orgin a more secured manner, Currently I am playing with few test cases about the redirection vulnerabilities. The following link uses a URL variable called “redirect_url” to redirect a user to a given page. While this variable is intended to only direct a user to a trusted page, it fails to validate the provided value and therefore can be used to redirect to any page. http://localhost:8080/datasets/332056/display_at/ucsc_test?redirect_url=http://www.google.comdisplay_url=http://localhost:8080/root This example redirects a user to Google, but it could just as easily be used to direct a user to a page that contains any malware. To resolve the issue, may be validate all user controlled input, including the GET request variables. If the input is intended to redirect a user, it must be validated to ensure it only presents them with a page on the trusted site. any comments or suggestions to work around this. thanks --/Vipin Rätschlab, Computational biology dept. Memorial Sloan-Kettering Cancer Center ___ 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] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset
Hi Carl,
We are using a mysql database backend as well.
Thank you for your help and do not hesitate if I can sen you any other
useful information about our local Galaxy instance.
Thanks,
Jean-Francois
From: Carl Eberhard carlfeberh...@gmail.com
To: Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca
Cc: John Chilton chil...@msi.umn.edu, galaxy-dev@lists.bx.psu.edu
galaxy-dev@lists.bx.psu.edu
Date: 12/03/2013 09:18 AM
Subject:Re: [galaxy-dev] Strange issue where the dataset reported
in the bug report doesn't correspond to the current dataset
1 2: Very interesting then. I'll do some more digging as to why a query
would succeed (with the wrong record) with those ids.
3: Good!
4.1: That first line is just the beginning of the diff/patch file and not
something you have to enter. It records the command used to generate the
diff file. That revision was the revision I was updated to when generating
the patch and, since I was using a development version more recently
updated than your machine, your hg can't find it. There's no need to run
that line, tho (see 4.2).
4.2: If you want to import a patch in the future, I've had good luck with
'hg import --no-commit mypatchfile.patch'. This will make the changes in
the patch file without committing them ('--no-commit'). If you want to
remove the changes later (and assuming you haven't made any other changes
you want to keep in that file) you can use 'hg revert
thefilethatwaschanged.py' and that will return the file to the previous
state. Keep in mind, of course, that patches (like any changes) may make
updating, and/or merging your instance later more difficult.
A question I forgot to ask: what database backend are you using
(postgresql, mysql, etc.)?
Carl
On Mon, Mar 11, 2013 at 12:34 PM, Jean-Francois Payotte
jean-francois.payo...@dnalandmarks.ca wrote:
Dear Dannon, John and Carl,
Thank you for your answers and for taking the time to help me solve this
issue.
Here are my answers to your questions:
1. I don't think our number of HDAs is large enough to cause an
overflow. From what I can see, the HDAs number in our two faulty galaxy
instances are:
galaxy_prod : 263,163 HDAs
galaxy_dev : 14,119 HDAs
2. Here is a list of hashed IDs for HDAs where I'm seeing this
behaviour:
(None of them are of 16-digit integers)
3. I've also tried applying John's patch on our development Galaxy
instance and so far, it seems to do the trick.
I've run my test tool (wich output a message to stderr) about 50 times,
and the bug report always displayed the correct dataset. Yay!!
4. I would have two question though before applying the patch to our
production Galaxy instance:
1. If I run the below hg diff -r f25f3fee4da7
lib/galaxy/webapps/galaxy/controllers/dataset.py command, I receive the
following error:
abort: unknown revision 'f25f3fee4da7'!
Is this a normal behaviour? Are we missing something important?
2. Also, out of curiosity, is there a particular way to apply a
patch (like the one you sent me), or if I simply have to manually edit the
file? (That's what I did.)
Thanks again for your help! This is greatly appreciated!
Jean-Francois
From:Carl Eberhard carlfeberh...@gmail.com
To:John Chilton chil...@msi.umn.edu
Cc:Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca,
galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Date:08/03/2013 06:07 PM
Subject:Re: [galaxy-dev] Strange issue where the dataset reported
in the bug report doesn't correspond to the current dataset
Hello,
We explored this for quite a while this afternoon and believe John is
correct about the location as well as the design decision.
It may be that the hashes generated in some instances will correctly parse
as 16 digit integers and, since an integer lookup is tried first (and you
may either have an extraordinary large number of HDAs or there is some
integer roll over/overflow - at a guess), the incorrect dataset is being
returned without attempting to decode the hash into the proper dataset.
This may also explain why it is consistent but intermittent.
I would be curious to see the hashed ids of the HDAs where you're seeing
this behavior. Can you provide some?
If the hash produces fully integer strings as we're (tentatively)
guessing, the if not str( id ).isdigit() may still branch improperly
unfortunately.
In any event and to John's last point, from what we can tell,
dataset.errors is only called from the new history panel and only encoded
ids are used there - so the backwards compatibility may not be needed at
this point.*
I will thoroughly check that that controller method isn't called elsewhere
with a raw id, but, in the meantime: Jean-Francois, can you apply the
patch below (and attached) to your more updated installation and (when
convenient) see if that helps?
*PS. if user's are still using the
[galaxy-dev] Galaxy on Cluster - how to set -a flag with username
In our local galaxy install we want the cluster jobs to be run from the galaxy user but we want to include a -a [account name] to our grid software bills properly. Here's what I currently have in universe.wsgi: default_cluster_job_runner = drmaa://-V -pe batch 8/ What I want is something like this: default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/ Is this possible? Thanks, Greg ___ 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] Serving Galaxy behind apache mod_security
Hello Paul, Due to various security issues, we thought to run our instance (will be public soon) behind apache web server. It seems that the SELinux is disabled on my machine. I have followed the steps and restarted apache, still not able to invoke the Galaxy page through http://servername:8080/ Thanks, --/Vipin Rätschlab, Computational biology dept. Memorial Sloan-Kettering Cancer Center On Tue, Mar 12, 2013 at 8:15 AM, Paul Boddie paul.bod...@biotek.uio.nowrote: On 11/03/13 23:20, Vipin TS wrote: On my new server machine I have configured apache server along with mod_security. Now I would like to place my Galaxy installation behind apache and is there any detailed explanation to describes the steps. I am following the galaxy wiki pagehttp://wiki.**galaxyproject.org/Admin/**Config/Apache%20Proxy#http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy# and it is failing to invoke the page. Please share if you have an experience on the same. I have avoided experience with Galaxy and mod_proxy (and once again wonder why mod_wsgi wouldn't be a better and less complicated way of running Galaxy, but that's another issue), but I do have experience with mod_proxy and other solutions that need their own Web server, and I notice that the Wiki page doesn't contain any mention of SELinux. If you have everything set up appropriately, you may need to find out whether SELinux is enabled, because this may demand a small amount of additional configuration work. Paul ___ 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] example_watch_folder.py : URL did not return JSON data
I'm trying to get the example_watch_folder.py to work with a simple example, but I am running into an error (Caveat, python is not my native language) I call the following script, but get the subsequent error: $ ./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f http://localhost:8080/ /Users/Rob/Documents/galaxy-db/input/ /Users/Rob/Documents/galaxy-db/output/ API Imports 2a56795cad3c7db3 * URL did not return JSON data* The preconditions I have in place are: 1. I copied my api_key: 8c25bc83f6f9e4001dd21eb7b64f063f 2. I created a new history on http://localhost:8080 3. I downloaded the the exons from hg19/chr22 from UCSC 3. On the dataset I performed a Text Manipulation Select first (20 lines) 4. I extracted a workflow from the history and recorded the workflow id (2a56795cad3c7db3). 5. I created directories: - /Users/Rob/Documents/galaxy-db/input/ - /Users/Rob/Documents/galaxy-db/output/ My args may be malformed. Can someone provide me an example of a theirs? Cheers, Rob ___ 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] example_watch_folder.py : URL did not return JSON data
The second argument there should point to the url of Galaxy's API -- in this case http://localhost:8080/api, I'm guessing. -Dannon On Tue, Mar 12, 2013 at 6:11 PM, Rob Leclerc robert.lecl...@gmail.com wrote: I'm trying to get the example_watch_folder.py to work with a simple example, but I am running into an error (Caveat, python is not my native language) I call the following script, but get the subsequent error: $ ./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f http://localhost:8080/ /Users/Rob/Documents/galaxy-db/input/ /Users/Rob/Documents/galaxy-db/output/ API Imports 2a56795cad3c7db3 URL did not return JSON data The preconditions I have in place are: 1. I copied my api_key: 8c25bc83f6f9e4001dd21eb7b64f063f 2. I created a new history on http://localhost:8080 3. I downloaded the the exons from hg19/chr22 from UCSC 3. On the dataset I performed a Text Manipulation Select first (20 lines) 4. I extracted a workflow from the history and recorded the workflow id (2a56795cad3c7db3). 5. I created directories: /Users/Rob/Documents/galaxy-db/input/ /Users/Rob/Documents/galaxy-db/output/ My args may be malformed. Can someone provide me an example of a theirs? Cheers, Rob ___ 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] example_watch_folder.py : URL did not return JSON data
Hi Dannon. Thanks! I had been experimenting with BioBlend and forgot to add
the /api/ on the url.
./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
http://localhost:8080/api/ /Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/ API Imports 2a56795cad3c7db3
However, I am now running into a new error when it tries to create the API
Imports folder
Traceback (most recent call last):
File ./example_watch_folder.py, line 87, in module
main(api_key, api_url, in_folder, out_folder, data_library, workflow )
File ./example_watch_folder.py, line 30, in main
library_id = library[0]['id']
KeyError: 0
(This is coming from the section that creates 'API Imports' library if it
doesn't already exist)
24: for library in libs:
25: if library['name'] == data_library:
26: library_id = library['id']
27: if not library_id:
28:lib_create_data = {'name':data_library}
29:library = submit(api_key, api_url + 'libraries',
lib_create_data, return_formatted=False)
30:library_id = library[0]['id']
As I mentioned, I'm not familiar with python, but I can't see where
'library[0]['id']' is set or is in scope, since this seems to be the
item in the iterator above this section.
Cheers,
Rob
Rob Leclerc, PhD
http://www.linkedin.com/in/robleclerc https://twitter.com/#!/robleclerc
P: (US) +1-(917)-873-3037
P: (Shanghai) +86-1-(861)-612-5469
Personal Email: rob.lecl...@aya.yale.edu
On Tue, Mar 12, 2013 at 6:14 PM, Dannon Baker dannon.ba...@gmail.comwrote:
The second argument there should point to the url of Galaxy's API --
in this case http://localhost:8080/api, I'm guessing.
-Dannon
On Tue, Mar 12, 2013 at 6:11 PM, Rob Leclerc robert.lecl...@gmail.com
wrote:
I'm trying to get the example_watch_folder.py to work with a simple
example,
but I am running into an error (Caveat, python is not my native language)
I call the following script, but get the subsequent error:
$ ./example_watch_folder.py 8c25bc83f6f9e4001dd21eb7b64f063f
http://localhost:8080/ /Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/ API Imports 2a56795cad3c7db3
URL did not return JSON data
The preconditions I have in place are:
1. I copied my api_key: 8c25bc83f6f9e4001dd21eb7b64f063f
2. I created a new history on http://localhost:8080
3. I downloaded the the exons from hg19/chr22 from UCSC
3. On the dataset I performed a Text Manipulation Select first (20
lines)
4. I extracted a workflow from the history and recorded the workflow id
(2a56795cad3c7db3).
5. I created directories:
/Users/Rob/Documents/galaxy-db/input/
/Users/Rob/Documents/galaxy-db/output/
My args may be malformed. Can someone provide me an example of a theirs?
Cheers,
Rob
___
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and other Galaxy lists, please use the interface at:
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___
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] How to add images/pictures into Galaxy Published Pages?
Thanks Bjoern! I figured it out too. I put the pictures in the static/images/Pages folder, then use them in the page. The main idea is to find a place with valid URL to store the pictures first. :-) Best, Huayan On Tue, Mar 12, 2013 at 5:41 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Huayan, in your page-editor you have a picture symbol. As you mentioned you need to specify a path to an image. For my pages I created a history where I store all my pictures. Afterwards I copy the full URL of that picture to the page. So use galaxy to store you image collection :) Hope that helps, Bjoern Hi, I am trying to create a page in Galaxy and want to add some pictures/ screenshots. So how could I do this? I clicked the image button but it needs a URL not the path from my local computer. 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/ ___ 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/
