Unable to get data from UCSC

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Unable to get data from UCSC

Anna Terry
Hi,

I am having lots of problems with the get data tools installed on our local galaxy server, I'll start with just one.

With the UCSC Main one, I am unable to send data back to galaxy, when I click "Send query to Galaxy" nothing happens, the button is unresponsive.

This is in contrast to when I try the same query from the main galaxy server, on the same browser and the content in correctly transferred back to galaxy.

I have no idea how to start debugging this, there is nothing in paster.log
Does anyone have any ideas?

TIA,
Anna

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Re: Unable to get data from UCSC

Hans-Rudolf Hotz
Hi Anna

I am just guessing, but it might be worth checking the proxy settings of
your local galaxy server.


Regards, Hans-Rudolf


On 01/13/2015 05:39 PM, Anna Terry wrote:

> Hi,
>
> I am having lots of problems with the get data tools installed on our
> local galaxy server, I'll start with just one.
>
> With the UCSC Main one, I am unable to send data back to galaxy, when I
> click "Send query to Galaxy" nothing happens, the button is unresponsive.
>
> This is in contrast to when I try the same query from the main galaxy
> server, on the same browser and the content in correctly transferred
> back to galaxy.
>
> I have no idea how to start debugging this, there is nothing in paster.log
> Does anyone have any ideas?
>
> TIA,
> Anna
>
>
> ___________________________________________________________
> 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:
>    https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
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Re: Unable to get data from UCSC

Anna Terry
Thanks Hans-Rudolf, will do

On 15 January 2015 at 08:24, Hans-Rudolf Hotz <[hidden email]> wrote:
Hi Anna

I am just guessing, but it might be worth checking the proxy settings of your local galaxy server.


Regards, Hans-Rudolf



On 01/13/2015 05:39 PM, Anna Terry wrote:
Hi,

I am having lots of problems with the get data tools installed on our
local galaxy server, I'll start with just one.

With the UCSC Main one, I am unable to send data back to galaxy, when I
click "Send query to Galaxy" nothing happens, the button is unresponsive.

This is in contrast to when I try the same query from the main galaxy
server, on the same browser and the content in correctly transferred
back to galaxy.

I have no idea how to start debugging this, there is nothing in paster.log
Does anyone have any ideas?

TIA,
Anna


___________________________________________________________
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:
   https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/



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Re: Unable to get data from UCSC

Anna Terry
In reply to this post by Anna Terry
Update,
Looking at the browser developer tools error logs in firefox I can see the following error:
Blocked loading mixed active content "http://galaxy.hpc.qmul.ac.uk/tool_runner"

similar error in chrome:

(index):1 The page at 'https://galaxy.hpc.qmul.ac.uk/' was loaded over HTTPS, but displayed insecure content from 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be loaded over HTTPS.

genome.ucsc.edu/cgi-bin/hgTables:1 The page at 'https://genome.ucsc.edu/cgi-bin/hgTables' was loaded over HTTPS, but is submitting data to an insecure location at 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be submitted over HTTPS.

(index):1 Mixed Content: The page at 'https://galaxy.hpc.qmul.ac.uk/' was loaded over HTTPS, but requested an insecure form action 'http://galaxy.hpc.qmul.ac.uk/tool_runner'. This request has been blocked; the content must be served over HTTPS.

Is there any way to change settings so that it points back to https?  The server should redirect to https but I guess the browser doesn't know this?

TIA
Anna

On 13 January 2015 at 16:39, Anna Terry <[hidden email]> wrote:
Hi,

I am having lots of problems with the get data tools installed on our local galaxy server, I'll start with just one.

With the UCSC Main one, I am unable to send data back to galaxy, when I click "Send query to Galaxy" nothing happens, the button is unresponsive.

This is in contrast to when I try the same query from the main galaxy server, on the same browser and the content in correctly transferred back to galaxy.

I have no idea how to start debugging this, there is nothing in paster.log
Does anyone have any ideas?

TIA,
Anna


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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Re: Unable to get data from UCSC

John Chilton-4
Hello Anna,

Can you try something for me -


https://bitbucket.org/galaxy/galaxy-central/commits/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb

On Mon, Jan 19, 2015 at 9:12 AM, Anna Terry <[hidden email]> wrote:

> Update,
> Looking at the browser developer tools error logs in firefox I can see the
> following error:
> Blocked loading mixed active content
> "http://galaxy.hpc.qmul.ac.uk/tool_runner"
>
> similar error in chrome:
>
> (index):1 The page at 'https://galaxy.hpc.qmul.ac.uk/' was loaded over
> HTTPS, but displayed insecure content from
> 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be
> loaded over HTTPS.
>
> genome.ucsc.edu/cgi-bin/hgTables:1 The page at
> 'https://genome.ucsc.edu/cgi-bin/hgTables' was loaded over HTTPS, but is
> submitting data to an insecure location at
> 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be
> submitted over HTTPS.
>
> (index):1 Mixed Content: The page at 'https://galaxy.hpc.qmul.ac.uk/' was
> loaded over HTTPS, but requested an insecure form action
> 'http://galaxy.hpc.qmul.ac.uk/tool_runner'. This request has been blocked;
> the content must be served over HTTPS.
>
> Is there any way to change settings so that it points back to https?  The
> server should redirect to https but I guess the browser doesn't know this?
>
> TIA
> Anna
>
> On 13 January 2015 at 16:39, Anna Terry <[hidden email]> wrote:
>>
>> Hi,
>>
>> I am having lots of problems with the get data tools installed on our
>> local galaxy server, I'll start with just one.
>>
>> With the UCSC Main one, I am unable to send data back to galaxy, when I
>> click "Send query to Galaxy" nothing happens, the button is unresponsive.
>>
>> This is in contrast to when I try the same query from the main galaxy
>> server, on the same browser and the content in correctly transferred back to
>> galaxy.
>>
>> I have no idea how to start debugging this, there is nothing in paster.log
>> Does anyone have any ideas?
>>
>> TIA,
>> Anna
>
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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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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Re: Unable to get data from UCSC

John Chilton-4
Ugh - hit send too soon accidentally.

I was trying to say - that I believe this was recently changed to
allow Galaxy served over HTTPS to access the UCSC in the linked
changeset. I was wondering if you could try to just undo that change
and see if things work for you again.

https://bitbucket.org/galaxy/galaxy-central/commits/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb

If that does work - it might work to set that XML block to something like

<inputs action="//genome.ucsc.edu/cgi-bin/hgTables"
check_values="false" method="get">

which may correctly tell the web browser to infer HTTP or HTTPS and
that would be a change I would be happy to make in -central to fix
this problem.

Sorry again for all the e-mails.

-John

P.S. I would definitely serve Galaxy over HTTPS if at all possible -
so that might be something you just want to do now to side this
problem.


On Mon, Jan 19, 2015 at 8:36 PM, John Chilton <[hidden email]> wrote:

> Hello Anna,
>
> Can you try something for me -
>
>
> https://bitbucket.org/galaxy/galaxy-central/commits/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb
>
> On Mon, Jan 19, 2015 at 9:12 AM, Anna Terry <[hidden email]> wrote:
>> Update,
>> Looking at the browser developer tools error logs in firefox I can see the
>> following error:
>> Blocked loading mixed active content
>> "http://galaxy.hpc.qmul.ac.uk/tool_runner"
>>
>> similar error in chrome:
>>
>> (index):1 The page at 'https://galaxy.hpc.qmul.ac.uk/' was loaded over
>> HTTPS, but displayed insecure content from
>> 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be
>> loaded over HTTPS.
>>
>> genome.ucsc.edu/cgi-bin/hgTables:1 The page at
>> 'https://genome.ucsc.edu/cgi-bin/hgTables' was loaded over HTTPS, but is
>> submitting data to an insecure location at
>> 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be
>> submitted over HTTPS.
>>
>> (index):1 Mixed Content: The page at 'https://galaxy.hpc.qmul.ac.uk/' was
>> loaded over HTTPS, but requested an insecure form action
>> 'http://galaxy.hpc.qmul.ac.uk/tool_runner'. This request has been blocked;
>> the content must be served over HTTPS.
>>
>> Is there any way to change settings so that it points back to https?  The
>> server should redirect to https but I guess the browser doesn't know this?
>>
>> TIA
>> Anna
>>
>> On 13 January 2015 at 16:39, Anna Terry <[hidden email]> wrote:
>>>
>>> Hi,
>>>
>>> I am having lots of problems with the get data tools installed on our
>>> local galaxy server, I'll start with just one.
>>>
>>> With the UCSC Main one, I am unable to send data back to galaxy, when I
>>> click "Send query to Galaxy" nothing happens, the button is unresponsive.
>>>
>>> This is in contrast to when I try the same query from the main galaxy
>>> server, on the same browser and the content in correctly transferred back to
>>> galaxy.
>>>
>>> I have no idea how to start debugging this, there is nothing in paster.log
>>> Does anyone have any ideas?
>>>
>>> TIA,
>>> Anna
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Unable to get data from UCSC

Anna Terry
Hi John,

Unfortunately swapping out this line for the one in the previous version does not work, but get this error when trying to use ucsc rather than just when transferring back:
Blocked loading mixed active content "http://genome.ucsc.edu/cgi-bin/hgTables"

Also, we are serving galaxy over https, I'm not sure why it is linking back to http (although it would work because it is would be redirected to https).
Is there anywhere I can change the address it links back to so it is https?

Many thanks
Anna

On 20 January 2015 at 01:41, John Chilton <[hidden email]> wrote:
Ugh - hit send too soon accidentally.

I was trying to say - that I believe this was recently changed to
allow Galaxy served over HTTPS to access the UCSC in the linked
changeset. I was wondering if you could try to just undo that change
and see if things work for you again.

https://bitbucket.org/galaxy/galaxy-central/commits/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb

If that does work - it might work to set that XML block to something like

<inputs action="//genome.ucsc.edu/cgi-bin/hgTables"
check_values="false" method="get">

which may correctly tell the web browser to infer HTTP or HTTPS and
that would be a change I would be happy to make in -central to fix
this problem.

Sorry again for all the e-mails.

-John

P.S. I would definitely serve Galaxy over HTTPS if at all possible -
so that might be something you just want to do now to side this
problem.


On Mon, Jan 19, 2015 at 8:36 PM, John Chilton <[hidden email]> wrote:
> Hello Anna,
>
> Can you try something for me -
>
>
> https://bitbucket.org/galaxy/galaxy-central/commits/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb
>
> On Mon, Jan 19, 2015 at 9:12 AM, Anna Terry <[hidden email]> wrote:
>> Update,
>> Looking at the browser developer tools error logs in firefox I can see the
>> following error:
>> Blocked loading mixed active content
>> "http://galaxy.hpc.qmul.ac.uk/tool_runner"
>>
>> similar error in chrome:
>>
>> (index):1 The page at 'https://galaxy.hpc.qmul.ac.uk/' was loaded over
>> HTTPS, but displayed insecure content from
>> 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be
>> loaded over HTTPS.
>>
>> genome.ucsc.edu/cgi-bin/hgTables:1 The page at
>> 'https://genome.ucsc.edu/cgi-bin/hgTables' was loaded over HTTPS, but is
>> submitting data to an insecure location at
>> 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be
>> submitted over HTTPS.
>>
>> (index):1 Mixed Content: The page at 'https://galaxy.hpc.qmul.ac.uk/' was
>> loaded over HTTPS, but requested an insecure form action
>> 'http://galaxy.hpc.qmul.ac.uk/tool_runner'. This request has been blocked;
>> the content must be served over HTTPS.
>>
>> Is there any way to change settings so that it points back to https?  The
>> server should redirect to https but I guess the browser doesn't know this?
>>
>> TIA
>> Anna
>>
>> On 13 January 2015 at 16:39, Anna Terry <[hidden email]> wrote:
>>>
>>> Hi,
>>>
>>> I am having lots of problems with the get data tools installed on our
>>> local galaxy server, I'll start with just one.
>>>
>>> With the UCSC Main one, I am unable to send data back to galaxy, when I
>>> click "Send query to Galaxy" nothing happens, the button is unresponsive.
>>>
>>> This is in contrast to when I try the same query from the main galaxy
>>> server, on the same browser and the content in correctly transferred back to
>>> galaxy.
>>>
>>> I have no idea how to start debugging this, there is nothing in paster.log
>>> Does anyone have any ideas?
>>>
>>> TIA,
>>> Anna
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: Unable to get data from UCSC

Anna Terry
Hi John,

we just figured out the problem. 
Had to follow the instructions at https://wiki.galaxyproject.org/Admin/Config/ApacheProxy:

SSL

If you place Galaxy behind a proxy address that uses SSL (e.g. https:// URLs), set the following in your Apache config:

Toggle line numbers
<Location "/">
    RequestHeader set X-URL-SCHEME https
</Location>
Many thanks for your help
Anna

On 21 January 2015 at 11:04, Anna Terry <[hidden email]> wrote:
Hi John,

Unfortunately swapping out this line for the one in the previous version does not work, but get this error when trying to use ucsc rather than just when transferring back:
Blocked loading mixed active content "http://genome.ucsc.edu/cgi-bin/hgTables"

Also, we are serving galaxy over https, I'm not sure why it is linking back to http (although it would work because it is would be redirected to https).
Is there anywhere I can change the address it links back to so it is https?

Many thanks
Anna

On 20 January 2015 at 01:41, John Chilton <[hidden email]> wrote:
Ugh - hit send too soon accidentally.

I was trying to say - that I believe this was recently changed to
allow Galaxy served over HTTPS to access the UCSC in the linked
changeset. I was wondering if you could try to just undo that change
and see if things work for you again.

https://bitbucket.org/galaxy/galaxy-central/commits/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb

If that does work - it might work to set that XML block to something like

<inputs action="//genome.ucsc.edu/cgi-bin/hgTables"
check_values="false" method="get">

which may correctly tell the web browser to infer HTTP or HTTPS and
that would be a change I would be happy to make in -central to fix
this problem.

Sorry again for all the e-mails.

-John

P.S. I would definitely serve Galaxy over HTTPS if at all possible -
so that might be something you just want to do now to side this
problem.


On Mon, Jan 19, 2015 at 8:36 PM, John Chilton <[hidden email]> wrote:
> Hello Anna,
>
> Can you try something for me -
>
>
> https://bitbucket.org/galaxy/galaxy-central/commits/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb
>
> On Mon, Jan 19, 2015 at 9:12 AM, Anna Terry <[hidden email]> wrote:
>> Update,
>> Looking at the browser developer tools error logs in firefox I can see the
>> following error:
>> Blocked loading mixed active content
>> "http://galaxy.hpc.qmul.ac.uk/tool_runner"
>>
>> similar error in chrome:
>>
>> (index):1 The page at 'https://galaxy.hpc.qmul.ac.uk/' was loaded over
>> HTTPS, but displayed insecure content from
>> 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be
>> loaded over HTTPS.
>>
>> genome.ucsc.edu/cgi-bin/hgTables:1 The page at
>> 'https://genome.ucsc.edu/cgi-bin/hgTables' was loaded over HTTPS, but is
>> submitting data to an insecure location at
>> 'http://galaxy.hpc.qmul.ac.uk/tool_runner': this content should also be
>> submitted over HTTPS.
>>
>> (index):1 Mixed Content: The page at 'https://galaxy.hpc.qmul.ac.uk/' was
>> loaded over HTTPS, but requested an insecure form action
>> 'http://galaxy.hpc.qmul.ac.uk/tool_runner'. This request has been blocked;
>> the content must be served over HTTPS.
>>
>> Is there any way to change settings so that it points back to https?  The
>> server should redirect to https but I guess the browser doesn't know this?
>>
>> TIA
>> Anna
>>
>> On 13 January 2015 at 16:39, Anna Terry <[hidden email]> wrote:
>>>
>>> Hi,
>>>
>>> I am having lots of problems with the get data tools installed on our
>>> local galaxy server, I'll start with just one.
>>>
>>> With the UCSC Main one, I am unable to send data back to galaxy, when I
>>> click "Send query to Galaxy" nothing happens, the button is unresponsive.
>>>
>>> This is in contrast to when I try the same query from the main galaxy
>>> server, on the same browser and the content in correctly transferred back to
>>> galaxy.
>>>
>>> I have no idea how to start debugging this, there is nothing in paster.log
>>> Does anyone have any ideas?
>>>
>>> TIA,
>>> Anna
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/