Adding a download link to the "Download or Export Workflow" page with load balancing
Dear Galaxy developers, I am interested in adding a download link to the “Download or Export Workflow” page of a workflow. I am able to add the link through the files in the templates directory and correctly add the necessary API functions in the lib/webapps/galaxy/controllers/workflow.py file. I wanted to ask for some help in figuring out what I might be missing when I try to download a file when I have load balancing feature activated. The page looks something like this: Download to File Download workflow to file so that it can be saved or imported into another Galaxy server. <https://dev.globusgenomics.org/u/arodri7/w/workflow-1-for-asms-2016-workshop-imported-from-uploaded-file-1/json-download> New Test Download ( test file) URL for Importing to Another Galaxy This workflow must be accessible before it can be imported into another Galaxy. <https://dev.globusgenomics.org/workflow/sharing?id=a728237e0d32bb8c> As you can see I added the “New test Download” link. I have added and tested the function which gets me the information about the workflow I want correctly. For now it’s just a “hello world” string. When I don’t use load balancing I get the contents I want downloaded to the file correctly. However, when I activate load balancing, it only downloads an empty file. I can print the contents of the test download file to the galaxy log, but as I said nothing gets printed on the actual file. Is there some javascript code I also need to add for this functionality that I might be missing such that the download works with load balancing? As I mentioned I do get a proper download when load balancing is not activated. BTW, all other existing download links work properly with both load balancing and no load balancing. Thanks, Alex
Can you elaborate on the load balancing that you've implemented which seems to be causing the problem? This might help figure out what's going on. On Mon, Jul 25, 2016 at 8:56 AM Alex Rodriguez <a.rodriguez1215@gmail.com> wrote:
Dear Galaxy developers, I am interested in adding a download link to the “Download or Export Workflow” page of a workflow. I am able to add the link through the files in the templates directory and correctly add the necessary API functions in the lib/webapps/galaxy/controllers/workflow.py file. I wanted to ask for some help in figuring out what I might be missing when I try to download a file when I have load balancing feature activated. The page looks something like this: Download to FileDownload workflow to file so that it can be saved or imported into another Galaxy server. <https://dev.globusgenomics.org/u/arodri7/w/workflow-1-for-asms-2016-workshop-imported-from-uploaded-file-1/json-download>
New Test Download ( test file) URL for Importing to Another GalaxyThis workflow must be accessible before it can be imported into another Galaxy. <https://dev.globusgenomics.org/workflow/sharing?id=a728237e0d32bb8c>
As you can see I added the “New test Download” link. I have added and tested the function which gets me the information about the workflow I want correctly. For now it’s just a “hello world” string. When I don’t use load balancing I get the contents I want downloaded to the file correctly. However, when I activate load balancing, it only downloads an empty file. I can print the contents of the test download file to the galaxy log, but as I said nothing gets printed on the actual file.
Is there some javascript code I also need to add for this functionality that I might be missing such that the download works with load balancing? As I mentioned I do get a proper download when load balancing is not activated. BTW, all other existing download links work properly with both load balancing and no load balancing.
Thanks,
Alex
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Hi Dannon, Sorry for the delay in getting back to you. Below are the configuration changes we do to get load balancing set. We are installing the following packages on the machine: Install packages: apt-get install build-essential apt-get install python-dev pip install uwsgi ============================= In the galaxy.ini file we are making the following modifications: config galaxy.ini: [uwsgi] processes = 8 stats = 127.0.0.1:9191 socket = 127.0.0.1:8080 pythonpath = lib threads = 4 logto = /var/log/genomics/galaxy.log master = True [app:main] static_enabled = False track_jobs_in_database = True ============================= And for Nginx we make the following modifications: In Nginx config, add: uwsgi_read_timeout 180; location / { uwsgi_pass 127.0.0.1:8080; uwsgi_param UWSGI_SCHEME $scheme; include uwsgi_params; } ============================= Any suggestions will help greatly! Thanks, Alex
On Jul 25, 2016, at 8:35 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Can you elaborate on the load balancing that you've implemented which seems to be causing the problem? This might help figure out what's going on.
On Mon, Jul 25, 2016 at 8:56 AM Alex Rodriguez <a.rodriguez1215@gmail.com <mailto:a.rodriguez1215@gmail.com>> wrote: Dear Galaxy developers, I am interested in adding a download link to the “Download or Export Workflow” page of a workflow. I am able to add the link through the files in the templates directory and correctly add the necessary API functions in the lib/webapps/galaxy/controllers/workflow.py file. I wanted to ask for some help in figuring out what I might be missing when I try to download a file when I have load balancing feature activated. The page looks something like this: Download to File Download workflow to file so that it can be saved or imported into another Galaxy server. <https://dev.globusgenomics.org/u/arodri7/w/workflow-1-for-asms-2016-workshop-imported-from-uploaded-file-1/json-download>
New Test Download ( test file) URL for Importing to Another Galaxy This workflow must be accessible before it can be imported into another Galaxy. <https://dev.globusgenomics.org/workflow/sharing?id=a728237e0d32bb8c>
As you can see I added the “New test Download” link. I have added and tested the function which gets me the information about the workflow I want correctly. For now it’s just a “hello world” string. When I don’t use load balancing I get the contents I want downloaded to the file correctly. However, when I activate load balancing, it only downloads an empty file. I can print the contents of the test download file to the galaxy log, but as I said nothing gets printed on the actual file.
Is there some javascript code I also need to add for this functionality that I might be missing such that the download works with load balancing? As I mentioned I do get a proper download when load balancing is not activated. BTW, all other existing download links work properly with both load balancing and no load balancing.
Thanks,
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: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <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/
Hey, no problem Alex. I wonder if you might be running into a uwsgi bug I fixed a little while back. Can you test your modifications to galaxy using a version that includes https://github.com/galaxyproject/galaxy/pull/2630? On Aug 9, 2016 5:02 PM, "Alex Rodriguez" <a.rodriguez1215@gmail.com> wrote:
Hi Dannon, Sorry for the delay in getting back to you. Below are the configuration changes we do to get load balancing set. We are installing the following packages on the machine:
Install packages: apt-get install build-essential apt-get install python-dev pip install uwsgi
=============================
In the galaxy.ini file we are making the following modifications:
config galaxy.ini: [uwsgi] processes = 8 stats = 127.0.0.1:9191 socket = 127.0.0.1:8080 pythonpath = lib threads = 4 logto = /var/log/genomics/galaxy.log master = True
[app:main] static_enabled = False track_jobs_in_database = True
=============================
And for Nginx we make the following modifications:
In Nginx config, add: uwsgi_read_timeout 180;
location / { uwsgi_pass 127.0.0.1:8080; uwsgi_param UWSGI_SCHEME $scheme; include uwsgi_params; }
=============================
Any suggestions will help greatly!
Thanks,
Alex
On Jul 25, 2016, at 8:35 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Can you elaborate on the load balancing that you've implemented which seems to be causing the problem? This might help figure out what's going on.
On Mon, Jul 25, 2016 at 8:56 AM Alex Rodriguez <a.rodriguez1215@gmail.com> wrote:
Dear Galaxy developers, I am interested in adding a download link to the “Download or Export Workflow” page of a workflow. I am able to add the link through the files in the templates directory and correctly add the necessary API functions in the lib/webapps/galaxy/controllers/workflow.py file. I wanted to ask for some help in figuring out what I might be missing when I try to download a file when I have load balancing feature activated. The page looks something like this: Download to FileDownload workflow to file so that it can be saved or imported into another Galaxy server. <https://dev.globusgenomics.org/u/arodri7/w/workflow-1-for-asms-2016-workshop-imported-from-uploaded-file-1/json-download>
New Test Download ( test file) URL for Importing to Another GalaxyThis workflow must be accessible before it can be imported into another Galaxy. <https://dev.globusgenomics.org/workflow/sharing?id=a728237e0d32bb8c>
As you can see I added the “New test Download” link. I have added and tested the function which gets me the information about the workflow I want correctly. For now it’s just a “hello world” string. When I don’t use load balancing I get the contents I want downloaded to the file correctly. However, when I activate load balancing, it only downloads an empty file. I can print the contents of the test download file to the galaxy log, but as I said nothing gets printed on the actual file.
Is there some javascript code I also need to add for this functionality that I might be missing such that the download works with load balancing? As I mentioned I do get a proper download when load balancing is not activated. BTW, all other existing download links work properly with both load balancing and no load balancing.
Thanks,
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: 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/
Hi Dannon, That update fixed the issue I am having. I am now able to download the test file through the link with and without load balancing. Thanks! Alex
On Aug 10, 2016, at 1:01 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey, no problem Alex. I wonder if you might be running into a uwsgi bug I fixed a little while back. Can you test your modifications to galaxy using a version that includes https://github.com/galaxyproject/galaxy/pull/2630 <https://github.com/galaxyproject/galaxy/pull/2630>?
On Aug 9, 2016 5:02 PM, "Alex Rodriguez" <a.rodriguez1215@gmail.com <mailto:a.rodriguez1215@gmail.com>> wrote: Hi Dannon, Sorry for the delay in getting back to you. Below are the configuration changes we do to get load balancing set. We are installing the following packages on the machine:
Install packages: apt-get install build-essential apt-get install python-dev pip install uwsgi
=============================
In the galaxy.ini file we are making the following modifications:
config galaxy.ini: [uwsgi] processes = 8 stats = 127.0.0.1:9191 <http://127.0.0.1:9191/> socket = 127.0.0.1:8080 <http://127.0.0.1:8080/> pythonpath = lib threads = 4 logto = /var/log/genomics/galaxy.log master = True
[app:main] static_enabled = False track_jobs_in_database = True
=============================
And for Nginx we make the following modifications:
In Nginx config, add: uwsgi_read_timeout 180;
location / { uwsgi_pass 127.0.0.1:8080 <http://127.0.0.1:8080/>; uwsgi_param UWSGI_SCHEME $scheme; include uwsgi_params; }
=============================
Any suggestions will help greatly!
Thanks,
Alex
On Jul 25, 2016, at 8:35 AM, Dannon Baker <dannon.baker@gmail.com <mailto:dannon.baker@gmail.com>> wrote:
Can you elaborate on the load balancing that you've implemented which seems to be causing the problem? This might help figure out what's going on.
On Mon, Jul 25, 2016 at 8:56 AM Alex Rodriguez <a.rodriguez1215@gmail.com <mailto:a.rodriguez1215@gmail.com>> wrote: Dear Galaxy developers, I am interested in adding a download link to the “Download or Export Workflow” page of a workflow. I am able to add the link through the files in the templates directory and correctly add the necessary API functions in the lib/webapps/galaxy/controllers/workflow.py file. I wanted to ask for some help in figuring out what I might be missing when I try to download a file when I have load balancing feature activated. The page looks something like this: Download to File Download workflow to file so that it can be saved or imported into another Galaxy server. <https://dev.globusgenomics.org/u/arodri7/w/workflow-1-for-asms-2016-workshop-imported-from-uploaded-file-1/json-download>
New Test Download ( test file) URL for Importing to Another Galaxy This workflow must be accessible before it can be imported into another Galaxy. <https://dev.globusgenomics.org/workflow/sharing?id=a728237e0d32bb8c>
As you can see I added the “New test Download” link. I have added and tested the function which gets me the information about the workflow I want correctly. For now it’s just a “hello world” string. When I don’t use load balancing I get the contents I want downloaded to the file correctly. However, when I activate load balancing, it only downloads an empty file. I can print the contents of the test download file to the galaxy log, but as I said nothing gets printed on the actual file.
Is there some javascript code I also need to add for this functionality that I might be missing such that the download works with load balancing? As I mentioned I do get a proper download when load balancing is not activated. BTW, all other existing download links work properly with both load balancing and no load balancing.
Thanks,
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: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <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/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <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/
participants (2)
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Alex Rodriguez -
Dannon Baker