Question: Do i need to make history accessible for download "Export history to File"?
1
gravatar for massa.kassa.sc3na
13 days ago by
massa.kassa.sc3na10 wrote:

Hi,

I'm rather new to galaxy and I'm confused with documentation.

I'm attempting to download whole history using the History>Export History to File.

The generated link does not work, and while the message says

You will need to make this history 'accessible' in order to import this to another galaxy sever.

It doesn't says anything about direct download from browser.

The documentation https://galaxyproject.org/support/download-data/ does not states any special step in order to download the history file.

The question is: Do I need to "share and publish" the history in order to backup my analysis?

Best regards Marek

download history galaxy • 83 views
ADD COMMENTlink modified 12 days ago by Jennifer Hillman Jackson25k • written 13 days ago by massa.kassa.sc3na10
0
gravatar for Jennifer Hillman Jackson
12 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Click on the archive link a second time, it will show the status of the archive creation. If the message starts with "Exporting History 'test history archive'. " that means the archive is still being created. You can leave a window open and click on the link periodically to refresh the status, or wait a bit and go back to "History menu > Export History to File" to see if it is ready. The larger the history, the large the archive, and the more time it takes to create.

Once ready to download, click on the link to start up an automatic download. This begins with a pop-up where the local destination name/location can be modified. Click on save and the file download will proceed.

The link will not start an automatic download until the archive creation is completed. And the history does not need to be made accessible for download -- it is only needed when importing into another Galaxy server using the link URL using "History menu > Import from File". We include that warning on all archive messages since it is a commonly missed step and clicking on the link (instead of copying it) starts up the download.

If the functionality is not working for you, please share more details. Where are you using Galaxy? Public? What is the URL?

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 12 days ago • written 12 days ago by Jennifer Hillman Jackson25k

Hello,

thanks for the response.

I've clicked the link multiple times (few seconds to about an hour between clicks). I have fairly small history which I've chosen to try the feature (1.4 Gb). The second click appears to trigger some action but no popup is shown (adblock off). The click triggers the small blue window with link to reload, but nothing happens.

After some inspection it seems that the link points to complete html-document (with all tags) which can be loaded in separate browser window and contains session token, my user id etc.

Server: usegalaxy.org

Browsers tried: firefox and chrome.

OS: ubuntu 14.04

The generated link:

admin redacted for data privacy

Best regards

Marek

ADD REPLYlink modified 11 days ago by Jennifer Hillman Jackson25k • written 11 days ago by massa.kassa.sc3na10

It looks like the archive is still being generated. Perhaps you started the export over again?

When the message in Galaxy starts with this, that means the archive is not ready yet to download.

Exporting History 'history_name'.

Adblock should not be a factor for the download dialogue pop-up.

ADD REPLYlink written 11 days ago by Jennifer Hillman Jackson25k

I also just started an archive generation/download test with a small history to make sure more is not going on. Feedback/result once completed.

ADD REPLYlink written 11 days ago by Jennifer Hillman Jackson25k

Update: I think I found the problem. If the history is "made accessible" (share link) then all functions work as expected.

This shouldn't be required for just downloading the archive, or going back to it under "Export History to File" (these remain on the server for 30 hours). I'm discussing with the team and will likely file a bug report.

So, for now, also generate the share link to get around the problems. Do this before or right after starting the archive export. Once the archive is completed (and the history share link created), clicking on the export link will refresh status until ready. Or, you can go back to it later (within 30 hrs) under "Export History to File".

Thanks for following up on this! Jen

ADD REPLYlink written 11 days ago by Jennifer Hillman Jackson25k
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