Question: Disappearing history from history panel
1
gravatar for david.a.morais
23 months ago by
Canada
david.a.morais110 wrote:

Hi,

We are having problems on our local Galaxy where histories disappears randomly for some users.

When the user tries to switch from one working history to a "broken history" the interface throws a message like " an error was encountered while loading content ..."

There is a detail link that point to a Json (below). The History can be seen from the "saved history" panel but does not show when we click on the top right button.

The history data is on the disk and on the DB.

We are using Galaxy version 15.07 17143:d1f51ff3c495

Is there a way to reset the history metadata (even manually), or any other solution, so it goes back to the history panel?

Thanks

{
  "message": "An error was encountered while loading the contents",
  "agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:49.0) Gecko/20100101 Firefox/49.0",
  "url": "http://galaxy-teaching.genap.ca/galaxy/galaxy/api/histories/cabd158f851f98e8/contents",
  "data": "",
  "options": {},
  "xhr": {
    "readyState": 4,
    "responseText": "{\"err_msg\": \"Uncaught exception in exposed API method:\", \"err_code\": 0}",
    "responseJSON": {
      "err_msg": "Uncaught exception in exposed API method:",
      "err_code": 0
    },
    "status": 500,
    "statusText": "Internal Server Error",
    "responseHeaders": {
      "Server": "nginx/1.10.0 (Ubuntu)\r",
      "Date": "Wed, 09 Nov 2016 19:53:15 GMT\r",
      "Content-Type": "application/json\r",
      "Transfer-Encoding": "chunked\r",
      "Connection": "keep-alive\r",
      "X-Frame-Options": "SAMEORIGIN\r",
      "Cache-Control": "max-age=0,no-cache,no-store\r"
    }
  },
  "source": "CurrentHistoryPanel(Cours 7+9)",
  "user": {
    "username": "eva-bouchard5",
    "quota_percent": 5,
    "total_disk_usage": 2747166533,
    "nice_total_disk_usage": "2.6 GB",
    "email": "Eva@udes.ca",
    "is_admin": false,
    "tags_used": [],
    "model_class": "User",
    "id": "aa6617f4ab9f58a6"
  },
  "historyId": "current",
  "history": {
    "history": {
      "importable": false,
      "create_time": "2016-11-09T19:26:13",
      "contents_url": "/galaxy/api/histories/cabd158f851f98e8/contents",
      "id": "cabd158f851f98e8",
      "size": 916420888,
      "user_id": "aa6617f4ab9f58a6",
      "username_and_slug": null,
      "annotation": null,
      "state_details": {
        "paused": 0,
        "ok": 4,
        "failed_metadata": 0,
        "upload": 0,
        "discarded": 0,
        "running": 0,
        "setting_metadata": 0,
        "error": 0,
        "new": 0,
        "queued": 0,
        "empty": 0
      },
      "state": "ok",
      "empty": false,
      "update_time": "2016-11-09T19:36:32",
      "tags": [],
      "deleted": false,
      "genome_build": "?",
      "nice_size": "874.0 MB",
      "slug": null,
      "name": "TP3",
      "url": "/galaxy/api/histories/cabd158f851f98e8",
      "state_ids": {
        "paused": [],
        "ok": [
          "7bb96fe6e38aed75",
          "df3697112f5e5ef1",
          "4415120a6b2c9398",
          "b60072c81e61f344",
          "0ca721d089da3c9c"
        ],
        "failed_metadata": [],
        "upload": [],
        "discarded": [],
        "running": [],
        "setting_metadata": [],
        "error": [],
        "new": [],
        "queued": [],
        "empty": []
      },
      "published": false,
      "model_class": "History",
      "purged": false
    }
  }
}
gui admin metadata local history • 827 views
ADD COMMENTlink written 23 months ago by david.a.morais110

Hello, I have asked the core admin team about this for review. Quick questions below. Please reply as a comment to help track down the issue.

  1. The upper history refresh icon (double circle) has been clicked on and the history will still not load, correct?

  2. This non-loading behavior is triggered from the history menu (gear icon) "Saved Histories" option to switch the active history? Only? Does switching to another history than back again display some histories and not others? Can this be reproduced when loading from the "View All Histories" function? (book icon far right top of history panel, next to gear icon)?

  3. What size histories are involved? Do you see a trend toward larger histories having this issue? Or does it seem to happen randomly - small and large histories?

  4. If possible, would you list any advanced config options that have been made to the local? See here. In particular, what database did you decide to upgrade to?

  5. Note any other modifications and if the local makes use of custom tools, output datatypes, and the like - and if histories making use of these tools or containing the output seem to be related?

  6. Is the local new and the problem is new? Or existing and the problem new? Or either (specify) and the issue has been encountered by users from the start?

  7. Related to 5 above - was the local upgraded recently? Did the issues start around that time?

Our admin/dev team may have more questions, but this should help them and community to understand the factors involved.

Thanks so much and sorry for the problems! Jen, Galaxy team

ADD REPLYlink written 23 months ago by Jennifer Hillman Jackson25k

HI Jennifer,

Thanks for you quick reply to this post. Here are the answers.

1- Yes, the refresh button has be clicked to no avail.

2- The behavior is triggered after the user logs in. In this case the history panel is completely empty. If a user has other functioning history he can switch to that history but not back to a non-loading one. All histories are listed on the “saved history” panel, but the broken do not show on the “View all History” panel.

https://s5.postimg.org/ic9hw0a07/Empty_history.jpg

https://s5.postimg.org/vvqc1pnzb/saved_history.jpg

https://s5.postimg.org/ufetjkl2f/View_all_history.jpg

3- It’s pretty random. Some users had few MBs and experience this problem, other few GBs, likewise, some user had large and small dataset and never had any problem.

4- We are using Mysql (since we don’t have a large user base < 50) for users and sqlite for tools; Uwsgi (with 8 threads); 3 job handlers; nginx; torque-pbs and Mauí; jobs are dynamically sent destination.py).

5- We have custom tools but no crash happened while using those tools, no custom datatype either.

6- No, the local is not new, we have being using 15.07 for while, since we still use mercurial and our last attempt to move to git did not work very well. The problem is not new either, but does not appear often. We had a similar problem last time we had a workshop on this Galaxy.

7- No, like as said we are still using 15.07.

I hope that my answer helps to pinpoint the cause of this problem.

Thanks again

Cheers

ADD REPLYlink modified 23 months ago • written 23 months ago by david.a.morais110

Thanks for all of the clarification. Our team is reviewing and will get back to you shortly. Jen

ADD REPLYlink written 23 months ago by Jennifer Hillman Jackson25k

This behavior could also be due to some caching issue on the browser. Especially old ones or IE. Closing the browser or cleaning the cache might help as well.

ADD REPLYlink written 23 months ago by Bjoern Gruening5.1k

Unfortunately it is not Bjoern, I have tested in multiple browsers and after a complete shutdown of the computer. Also, tried from different computers to no avail.

ADD REPLYlink written 23 months ago by david.a.morais110
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